Article
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publication date
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author
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author name string
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published in
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Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.
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2008-05-18
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Jürg Bähler Ian Goodhead Valerie Wood
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Brian T Wilhelm Samuel Marguerat Stephen Watt Falk Schubert Christopher J Penkett Jane Rogers Jürg Bähler
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Nature
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The transcriptional landscape of the yeast genome defined by RNA sequencing
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2008-06-06
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Mark Bender Gerstein
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Ugrappa Nagalakshmi Zhong Wang Karl Waern Chong Shou Debasish Raha Michael Snyder
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Science
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A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome
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2008-07-03
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Stefan Haas
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Marc Sultan Marcel H Schulz Hugues Richard Alon Magen Andreas Klingenhoff Matthias Scherf Martin Seifert Tatjana Borodina Aleksey Soldatov Dmitri Parkhomchuk Dominic Schmidt Sean O'Keeffe Martin Vingron Hans Lehrach Marie-Laure Yaspo
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Science
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RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays
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2008-09
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Yoav Gilad John C Marioni
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Christopher E Mason Shrikant M Mane Matthew Stephens
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Genome Research
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Transcript length bias in RNA-seq data confounds systems biology
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2009
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Alicia Oshlack Matthew Wakefield
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Biology Direct
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RNA-Seq: a revolutionary tool for transcriptomics
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2009-01
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Mark Bender Gerstein
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Zhong Wang Michael Snyder
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Nature Reviews Genetics
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Estimating accuracy of RNA-Seq and microarrays with proteomics
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2009-04-16
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Wei Chen
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Xing Fu Ning Fu Song Guo Zheng Yan Ying Xu Hao Hu Corinna Menzel Yixue Li Rong Zeng Philipp Khaitovich
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BMC Genomics
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TopHat: discovering splice junctions with RNA-Seq
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2009-05-01
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Steven Salzberg Lior Pachter
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Cole Trapnell
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Bioinformatics
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A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi.
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2009-07-17
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Julian Parkhill Paul P. Gardner Jyoti Choudhary Nicholas Thomson
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Timothy T Perkins Robert A Kingsley Maria C Fookes Keith D James Lu Yu Samuel A Assefa Miao He Nicholas J Croucher Derek J Pickard Duncan J Maskell Gordon Dougan
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PLOS Genetics
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A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos.
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2009-09-01
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Simon J van Heeringen Gert Jan C Veenstra
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Robert C Akkers Ulrike G Jacobi Eva M Janssen-Megens Kees-Jan Françoijs Hendrik G Stunnenberg
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Developmental Cell
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Identifiability of isoform deconvolution from junction arrays and RNA-Seq.
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2009-09-16
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Hui Jiang
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David Hiller Weihong Xu Wing Hung Wong
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Bioinformatics
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Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.
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2009-10-16
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Chad Nusbaum
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Joshua Z Levin Michael F Berger Xian Adiconis Peter Rogov Alexandre Melnikov Timothy Fennell Levi A Garraway Andreas Gnirke
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Genome Biology
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Transcript quantification with RNA-Seq data.
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2009-10-19
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Gunnar Rätsch
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Regina Bohnert Jonas Behr
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BMC Bioinformatics
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DEGseq: an R package for identifying differentially expressed genes from RNA-seq data.
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2009-10-24
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Likun Wang Xi Wang
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Zhixing Feng Xiaowo Wang Xuegong Zhang
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Bioinformatics
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RNA-seq: from technology to biology.
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2009-10-27 2010-02-01
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Jürg Bähler
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Samuel Marguerat Jürg Bähler
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Cellular and Molecular Life Sciences
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GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.
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2009-11-12
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M Boutros
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Moritz Gilsdorf Thomas Horn Zeynep Arziman Oliver Pelz Evgeny Kiner
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Nucleic Acids Research
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Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome.
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2009-11-18
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Cynthia Sharma Jörg Vogel Richard Reinhardt
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Marco Albrecht Thomas Rudel
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Nucleic Acids Research
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H-DBAS: human-transcriptome database for alternative splicing: update 2010
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2009-12-07
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Takashi Gojobori Tadashi Imanishi
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Jun-ichi Takeda Yutaka Suzuki Ryuichi Sakate Yoshiharu Sato Sumio Sugano
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Nucleic Acids Research
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An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data
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2009-12-11
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Daniel Ramsköld Rickard Sandberg
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Eric T Wang Christopher B Burge
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PLOS Computational Biology
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Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs.
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2009-12-30
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Kathryn J Boor Martin Wiedmann Uri Keich
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Haley F Oliver Renato H Orsi Lalit Ponnala Wei Wang Qi Sun Samuel W Cartinhour Melanie J Filiatrault
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BMC Genomics
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Differential expression analysis for sequence count data
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2010
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Simon Anders Wolfgang Huber
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Genome Biology
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Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements
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2010
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Sandro Banfi Elia Stupka Vincenzo Alessandro Gennarino Remo Sanges
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Danilo Licastro Francesca Petrera
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BMC Genomics
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From RNA-seq reads to differential expression results
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2010 2010-12-22
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Alicia Oshlack Mark D. Robinson
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Matthew D Young
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Genome Biology
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A scaling normalization method for differential expression analysis of RNA-seq data
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2010
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Alicia Oshlack Mark D. Robinson
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Genome Biology
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Global and unbiased detection of splice junctions from RNA-seq data
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2010
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Ulf Gyllensten Adam Ameur
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Anna Wetterbom Lars Feuk
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Genome Biology
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Genome-wide analysis of allelic expression imbalance in human primary cells by high-throughput transcriptome resequencing.
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2010-01-01
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Vincent Plagnol Graham Heap Charles Mein David A van Heel Richard Dobson Lude Franke
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Jennie H M Yang Kate Downes Barry C Healy Karen A Hunt Nicholas Bockett Patrick C Dubois Thomas J Albert Matthew J Rodesch David G Clayton John A Todd
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Human Molecular Genetics
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Next-generation sequencing
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2010-01-01
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Jonathan Arnold
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Momiao Xiong Zhongming Zhao Fuli Yu
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Journal of Biomedicine and Biotechnology
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Defining transcribed regions using RNA-seq.
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2010-01-21
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Jürg Bähler
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Brian T Wilhelm Samuel Marguerat Ian Goodhead Jürg Bähler
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Nature Protocols
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Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life
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2010-01-26
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Mark Johnston Antonis Rokas
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Chris Todd Hittinger John T Tossberg
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Proceedings of the National Academy of Sciences of the United States of America
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Characterization of transcriptional complexity during berry development in Vitis vinifera using RNA-Seq.
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2010-01-29
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Luciano Xumerle Giovanni Malerba Diana Bellin
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Sara Zenoni Alberto Ferrarini Enrico Giacomelli Marianna Fasoli Mario Pezzotti Massimo Delledonne
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Plant Physiology
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New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq.
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2010-02-04
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Thomas D Otto Arnab Pain Chris Newbold Matthew Berriman Ulrike Böhme
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Daniel Wilinski Sammy Assefa Thomas M Keane Louis R Sarry Jacob Lemieux Bart Barrell Manuel Llinás
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Molecular Microbiology
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Gene ontology analysis for RNA-seq: accounting for selection bias.
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2010-02-04
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Alicia Oshlack Matthew Wakefield Gordon K Smyth
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Matthew D Young
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Genome Biology
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Close association of RNA polymerase II and many transcription factors with Pol III genes
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2010-02-05
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Mark Bender Gerstein
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Debasish Raha Zhong Wang Zarmik Moqtaderi Linfeng Wu Guoneng Zhong Kevin Struhl Michael Snyder
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Proceedings of the National Academy of Sciences of the United States of America
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Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.
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2010-02-11
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Marie-Laure Yaspo Stefan Haas Hans Lehrach Martin Vingron
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Hugues Richard Marcel H Schulz Marc Sultan Asja Nürnberger Sabine Schrinner Daniela Balzereit Emilie Dagand Axel Rasche Marie-Laure Yaspo
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Nucleic Acids Research
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RNA-Seq analysis to capture the transcriptome landscape of a single cell.
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2010-02-25
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Azim Surani
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Fuchou Tang Catalin Barbacioru Ellen Nordman Bin Li Nanlan Xu Vladimir I Bashkirov Kaiqin Lao
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Nature Protocols
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The primary transcriptome of the major human pathogen Helicobacter pylori
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2010-03-11
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Peter F. Stadler Jörg Vogel Kristin Reiche Fabien Darfeuille Cynthia Sharma Jörg Hackermüller Richard Reinhardt
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Steve Hoffmann Jérémy Reignier Sven Findeiss Alexandra Sittka Sandrine Chabas
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Nature
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Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.
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2010-03-19
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Qiye Li Guojie Zhang Jun Wang Karsten Kristiansen Huanming Yang Jian Wang Xiuqing Zhang
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Guangwu Guo Xueda Hu Yong Zhang Ruiqiang Li Ruhong Zhuang Zhike Lu Zengquan He Xiaodong Fang Li Chen Wei Tian Yong Tao Songgang Li
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Genome Research
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In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines
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2010-03-25
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Daniel Klevebring
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Magnus Bjursell Olof Emanuelsson Joakim Lundeberg
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PLOS ONE
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Integrative analysis of the melanoma transcriptome
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2010-04
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Eric Lander Chad Nusbaum Carrie Sougnez Andreas Gnirke Gad Getz Kristian Cibulskis Wendy Winckler Reinhard Dummer Liuda Ziaugra Jordi Barretina Matthew Meyerson Stacey Gabriel
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Michael F Berger Joshua Z Levin Krishna Vijayendran Andrey Sivachenko Xian Adiconis Jared Maguire Laura A Johnson James Robinson Roel G Verhaak Robert C Onofrio Elisabeth Laine David E Fisher David B Jaffe Levi A Garraway
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Genome Research
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mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
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2010-04-01
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Stéphane Audic Chantal Abergel Jean-Michel Claverie Julie Poulain Pascal Hingamp
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Matthieu Legendre Olivier Poirot Virginie Seltzer Deborah Byrne Audrey Lartigue Magali Lescot Alain Bernadac
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Genome Research
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Detection of splice junctions from paired-end RNA-seq data by SpliceMap.
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2010-04-05
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Hui Jiang
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Kin Fai Au Lan Lin Yi Xing Wing Hung Wong
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Nucleic Acids Research
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Genome-wide analysis of mRNA abundance in two life-cycle stages of Trypanosoma brucei and identification of splicing and polyadenylation sites
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2010-04-12
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Tim Nicolai Siegel
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Doeke R Hekstra Xuning Wang Scott Dewell George A M Cross
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Nucleic Acids Research
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Supersplat--spliced RNA-seq alignment.
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2010-04-21
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Weng-Keen Wong
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Douglas W Bryant Rongkun Shen Henry D Priest Todd C Mockler
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Bioinformatics
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Bacillus anthracis genome organization in light of whole transcriptome sequencing
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2010-04-29
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Karla D Passalacqua
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Jeffrey Martin Wenhan Zhu Nicholas Bergman Mark Borodovsky
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BMC Bioinformatics
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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
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2010-05
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Steven Salzberg Lior Pachter
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Cole Trapnell Brian A Williams Geo Pertea Ali Mortazavi Gordon Kwan Marijke J van Baren Barbara J Wold
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Nature Biotechnology
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Tracing the derivation of embryonic stem cells from the inner cell mass by single-cell RNA-Seq analysis.
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2010-05-01
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Azim Surani
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Fuchou Tang Catalin Barbacioru Siqin Bao Caroline Lee Ellen Nordman Xiaohui Wang Kaiqin Lao
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Cell Stem Cell
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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
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2010-05-02
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J Z Levin Magdalena J Koziol John L. Rinn
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Mitchell Guttman Manuel Garber Julie Donaghey James Robinson Xian Adiconis Lin Fan Andreas Gnirke Chad Nusbaum Eric S Lander Aviv Regev
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Nature Biotechnology
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A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling
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2010-05-05
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James R. Bradford Crispin J. Miller
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Yvonne Hey Tim Yates Yaoyong Li Stuart D Pepper
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BMC Genomics
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Modeling non-uniformity in short-read rates in RNA-Seq data
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2010-05-11
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Jun Li
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Hui Jiang Wing Hung Wong
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Genome Biology
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Screening the human exome: a comparison of whole genome and whole transcriptome sequencing.
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2010-05-28
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Elizabeth T Cirulli
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Abanish Singh Kevin V Shianna Dongliang Ge Jason P Smith Jessica M Maia Erin L Heinzen James J Goedert David B Goldstein Center for HIV/AIDS Vaccine Immunology (CHAVI)
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Genome Biology
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rQuant.web: a tool for RNA-Seq-based transcript quantitation
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2010-06-15
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Gunnar Rätsch
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Regina Bohnert
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Nucleic Acids Research
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Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.
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2010-06-17
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Andrea Sboner Joel Rozowsky Mark Bender Gerstein Valerie Reinke
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Ashish Agarwal David Koppstein Lukas Habegger Ladeana W Hillier Rajkumar Sasidharan Robert H Waterston
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BMC Genomics
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A probabilistic framework for aligning paired-end RNA-seq data
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2010-06-23
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Derek Y Chiang
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Yin Hu Kai Wang Xiaping He Jan F Prins Jinze Liu
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Bioinformatics
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Uncovering the complexity of transcriptomes with RNA-Seq.
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2010-06-27
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Valerio Costa Claudia Angelini Italia DeFeis
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Alfredo Ciccodicola
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Journal of Biomedicine and Biotechnology
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Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq
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2010-06-28
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Dale Hedges Erik K Flemington
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Guorong Xu Claire Fewell Christopher Taylor Nan Deng Dale Hedges Xia Wang Kun Zhang Michelle Lacey Haitao Zhang Qinyan Yin Jennifer Cameron Zhen Lin Dongxiao Zhu
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RNA
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RNA-seq analysis of sulfur-deprived Chlamydomonas cells reveals aspects of acclimation critical for cell survival.
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2010-06-29
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David Casero Sabeeha Merchant Matteo Pellegrini
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David González-Ballester Shawn Cokus Arthur R Grossman
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The Plant Cell
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Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq.
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2010-07-01
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PLOS Computational Biology
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Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice.
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2010-07-01
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Timofey Skvortsov
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Acta naturae
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Next-generation sequencing techniques for eukaryotic microorganisms: sequencing-based solutions to biological problems.
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2010-07-02
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Minou Nowrousian
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Eukaryotic Cell
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Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.
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2010-07-13
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Genome Research
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An integrative approach to genomic introgression mapping.
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2010-07-23
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David L. Hyten
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Plant Physiology
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Transcriptome sequencing, microarray, and proteomic analyses reveal cellular and metabolic impact of hepatitis C virus infection in vitro.
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2010-08-01
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Paul Klenerman
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Stephen D Woodhouse Ramamurthy Narayan Sally Latham Sheena Lee Robin Antrobus Bevin Gangadharan Shujun Luo Gary P Schroth Nicole Zitzmann
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Hepatology
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RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome
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2010-08-05
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Michelle Graham Gary J Muehlbauer
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Andrew J Severin Jenna L Woody Yung-Tsi Bolon Bindu Joseph Brian W Diers Andrew D Farmer Rex T Nelson David Grant James E Specht Steven B Cannon Gregory D May Carroll P Vance Randy C Shoemaker
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BMC Plant Biology
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Recent advances in RNA sequence analysis
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2010-08-19
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Steven Salzberg
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F1000 biology reports
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Transcribed dark matter: meaning or myth?
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2010-08-25
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Chris Ponting
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T Grant Belgard
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Human Molecular Genetics
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MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.
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2010-08-27
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Charles M. Perou Piotr A Mieczkowski Derek Y Chiang
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Nucleic Acids Research
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Comparison between NuGEN's WT-Ovation Pico and one-direct amplification systems.
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2010-09-01
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Lauren McIntyre
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Journal of Biomolecular Techniques
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Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.
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2010-09-01
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Gavin Sherlock Sadie L Marjani
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Genome Research
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2010-09-16
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Current Opinion in Microbiology
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Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
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2010-09-19
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Christoph Bock Peggy Farnham David Haussler Junchen Gu Mattia Pelizzola Ryan Lister Alexander Meissner
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Nature Biotechnology
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Statistical Issues in the Analysis of ChIP-Seq and RNA-Seq Data.
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2010-09-27
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Zhaohui Steve Qin
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Debashis Ghosh
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Genes
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Studying bacterial transcriptomes using RNA-seq.
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2010-09-29 2010-10-01
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Nicholas Thomson
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Nicholas J Croucher
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Current Opinion in Microbiology
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Single molecule sequencing with a HeliScope genetic analysis system
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2010-10-01
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John F Thompson
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Kathleen E Steinmann
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Current protocols in molecular biology
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De novo assembly and analysis of RNA-seq data.
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2010-10-10
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Shaun Jackman Malachi Griffith Timothee Cezard Steven Jones Pamela A. Hoodless Inanc Birol
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Gordon Robertson Jacqueline Schein Readman Chiu Richard Corbett Matthew Field Karen Mungall Sam Lee Hisanaga Mark Okada Jenny Q Qian Anthony Raymond Nina Thiessen Yaron S Butterfield Richard Newsome Simon K Chan Rong She Richard Varhol Baljit Kamoh Anna-Liisa Prabhu Angela Tam YongJun Zhao Richard A Moore Martin Hirst Marco A Marra
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Nature Methods
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Quantitative and qualitative RNA-Seq-based evaluation of Epstein-Barr virus transcription in type I latency Burkitt's lymphoma cells.
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2010-10-13
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Erik K Flemington
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Zhen Lin Guorong Xu Nan Deng Christopher Taylor Dongxiao Zhu
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Journal of Virology
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Analysis of next-generation genomic data in cancer: accomplishments and challenges
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2010-10-15
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Elaine Mardis
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Li Ding Michael C Wendl Daniel C Koboldt
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Human Molecular Genetics
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The RNA-Seq approach to studying the expression of mosquito mitochondrial genes.
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2010-10-19
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Gareth J Lycett
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M Neira-Oviedo A Tsyganov-Bodounov V Kokoza A S Raikhel J Krzywinski
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Insect Molecular Biology
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RNA-seq analysis of 2 closely related leukemia clones that differ in their self-renewal capacity.
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2010-10-27
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Geneviève Boucher
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Brian T Wilhelm Mathieu Briau Pamela Austin Amélie Faubert Pierre Chagnon Kristin Hope Simon Girard Nadine Mayotte Josette-Renee Landry Josée Hébert Guy Sauvageau
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Blood
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Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing.
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2010-10-29
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Andrea Sboner Stéphane Terry Francesca Demichelis Mark Rubin Mark Bender Gerstein
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Genome Research
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SNP discovery in the bovine milk transcriptome using RNA-Seq technology
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2010-11-06
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Alma Islas-Trejo
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Angela Cánovas Gonzalo Rincon Saumya Wickramasinghe Juan F Medrano
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Mammalian Genome
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Analysis and design of RNA sequencing experiments for identifying isoform regulation
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2010-11-07
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Edoardo M Airoldi
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Nature Methods
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Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads
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2010-11-24
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Gavin Sherlock Matthew Blow
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Jeffrey Martin Vincent M Bruno Zhide Fang Xiandong Meng Tao Zhang Michael Snyder Zhong Wang
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BMC Genomics
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Scaffolding a Caenorhabditis nematode genome with RNA-seq
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2010-12
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Erich M Schwarz Paul W. Sternberg
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Ali Mortazavi Brian Williams Lorian Schaeffer Igor Antoshechkin Barbara J Wold
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Genome Research
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RNA-Seq Read Alignments with PALMapper
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2010-12
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Gunnar Rätsch
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Géraldine Jean André Kahles Vipin T. Sreedharan Fabio De Bona
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Defining the transcriptome and proteome in three functionally different human cell lines.
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2010-12-01
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Cajsa Algenäs Daniel Klevebring Linn Fagerberg Ivan Matic Mathias Uhlén
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Emma Lundberg Tamar Geiger Juergen Cox Cajsa Algenäs Joakim Lundeberg Matthias Mann
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Molecular Systems Biology
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A high-resolution comparative map of porcine chromosome 4 (SSC4).
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2010-12-01
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Lawrence B. Schook Craig W. Beattie
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J-G Ma T-C Chang H Yasue A D Farmer J A Crow K Eyer H Hiraiwa T Shimogiri S N Meyers J E Beever E F Retzel W-S Liu
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Animal Genetics
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Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.
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2010-12-01
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Xi Wang
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Zhengpeng Wu Xuegong Zhang
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Journal of Bioinformatics and Computational Biology
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De novo transcriptome sequencing in Anopheles funestus using Illumina RNA-seq technology
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2010-12-02
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Jacob E. Crawford
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Wamdaogo M Guelbeogo Antoine Sanou Alphonse Traoré Kenneth D Vernick N'Fale Sagnon Brian P Lazzaro
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PLOS ONE
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Analysis of transcript and protein overlap in a human osteosarcoma cell line.
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2010-12-02
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Mathias Uhlén Daniel Klevebring Linn Fagerberg
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Emma Lundberg Olof Emanuelsson Joakim Lundeberg
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BMC Genomics
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RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.
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2010-12-05
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Andrea Sboner Joel Rozowsky Mark Bender Gerstein
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Lukas Habegger Tara A Gianoulis Ashish Agarwal Michael Snyder
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Bioinformatics
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The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment.
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2010-12-14
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Alexey I Nesvizhskii
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Kang Ning
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BMC Bioinformatics
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A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology
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2010-12-14
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Aziz A. Aboobaker
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Martin J Blythe Damian Kao Sunir Malla Joanna Rowsell Ray Wilson Deborah Evans Jamie Jowett Amy Hall Virginie Lemay Sabrina Lam
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PLOS ONE
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H2A.Z demarcates intergenic regions of the plasmodium falciparum epigenome that are dynamically marked by H3K9ac and H3K4me3
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2010-12-16
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Richard Bartfai Arne H Smits Moritz Treeck
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Wieteke A M Hoeijmakers Adriana M Salcedo-Amaya Eva Janssen-Megens Anita Kaan Tim-Wolf Gilberger Kees-Jan Françoijs Hendrik G Stunnenberg
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PLOS Pathogens
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Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq
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2010-12-17
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Wen Huang
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Hasan Khatib
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BMC Genomics
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Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.
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2010-12-17
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Xi Wang
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Zhengpeng Wu Xuegong Zhang
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Bioinformatics
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Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based capture yields a refined and extended description of the C. elegans transcriptome
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2010-12-22
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Ayelet T. Lamm
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Michael R Stadler Huibin Zhang Jonathan I Gent Andrew Z Fire
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Genome Research
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Polycomb preferentially targets stalled promoters of coding and noncoding transcripts
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2010-12-22
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Moritz Gerstung
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Daniel Enderle Christian Beisel Michael B Stadler Prashanth Athri Renato Paro
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Genome Research
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miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1.
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2010-12-31
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Johan Flygare Harvey Lodish
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Lingbo Zhang Piu Wong Bing Lim
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Genes & Development
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Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples
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2011
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Celina Sanchez Rivers Zora Modrusan Brock A Peters
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Serban Nacu Wenlin Yuan Zhengyan Kan Deepali Bhatt Jeremy Stinson Kenneth Jung Somasekar Seshagiri Thomas D Wu
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BMC Medical Genomics
|
Thousands of Novel Transcripts Identified in Mouse Cerebrum, Testis, and ES Cells Based on ribo-minus RNA Sequencing
|
2011
|
Songnian Hu
|
Wanfei Liu Yuhui Zhao Peng Cui Qiang Lin Feng Ding Chengqi Xin Xinyu Tan Shuhui Song Jun Yu
|
Frontiers in Genetics
|
RNA-seq analyses of blood-induced changes in gene expression in the mosquito vector species, Aedes aegypti
|
2011
|
Mariangela Bonnizoni Osvaldo Marinotti
|
W Augustine Dunn Corey L Campbell Ken E Olson Michelle T Dimon Anthony A James
|
BMC Genomics
|
Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans
|
2011
|
Matthew Berriman Karen Mungall Gary Saunders Anna V Protasio Martin Hunt Roz Laing Michael Andrew Quail
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Steven Laing Frank Jackson Robin Beech John S Gilleard
|
PLOS ONE
|
The post-apoptotic fate of RNAs identified through high-throughput sequencing of human hair
|
2011
|
Benjamin Yu
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Gloria K Lefkowitz Anandaroop Mukhopadhyay Christopher Cowing-Zitron
|
PLOS ONE
|
A low-cost library construction protocol and data analysis pipeline for Illumina-based strand-specific multiplex RNA-seq
|
2011
|
Thomas Brutnell
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Lin Wang Yaqing Si Lauren K Dedow Ying Shao Peng Liu
|
PLOS ONE
|
ENCODE whole-genome data in the UCSC genome browser (2011 update)
|
2011-01
|
David Haussler Venkat S Malladi Angie S. Hinrichs Donna Karolchik Hiram Clawson Ann S Zweig
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Brian J Raney Melissa S Cline Kate R Rosenbloom Timothy R Dreszer Katrina Learned Galt P Barber Laurence R Meyer Cricket A Sloan Krishna M Roskin Bernard B Suh Vanessa Kirkup Pauline A Fujita Brooke Rhead Kayla E Smith Andy Pohl Robert M Kuhn W James Kent
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Nucleic Acids Research
|
Insights into global mechanisms and disease by gene expression profiling.
|
2011-01-01
|
Hubert Hackl Johannes Rainer Ana Dopazo
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Fátima Sánchez-Cabo Zlatko Trajanoski
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Methods in Molecular Biology
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Identifying mRNA editing deaminase targets by RNA-Seq.
|
2011-01-01
|
Nina Papavasiliou
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Brad R Rosenberg Scott Dewell F Nina Papavasiliou
|
Methods in Molecular Biology
|
The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq
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2011-01-12
|
Jeff H. Chang
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Yanming Di Daniel W Schafer Jason S Cumbie
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Statistical Applications in Genetics and Molecular Biology
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A pipeline for RNA-seq data processing and quality assessment
|
2011-01-13
|
Alvis Brazma Angela Goncalves
|
Andrew Tikhonov Misha Kapushesky
|
Bioinformatics
|
RNA-Seq analysis of splicing in Plasmodium falciparum uncovers new splice junctions, alternative splicing and splicing of antisense transcripts
|
2011-01-17
|
Katherine Lontok
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Michelle T Dimon Joseph L DeRisi
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Nucleic Acids Research
|
Length bias correction for RNA-seq data in gene set analyses
|
2011-01-19
|
Xiangqin Cui
|
Liyan Gao Zhide Fang Kui Zhang Degui Zhi
|
Bioinformatics
|
Identification of fusion genes in breast cancer by paired-end RNA-sequencing.
|
2011-01-19
|
Olli-Pekka Kallioniemi Anne-Lise Børresen-Dale Sara Kangaspeska Vesa Hongisto Kristine Kleivi
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Henrik Edgren Astrid Murumagi Sara Kangaspeska Daniel Nicorici Vesa Hongisto Inga H Rye Sandra Nyberg Maija Wolf
|
Genome Biology
|
Understanding the pathogenesis of Alzheimer's disease: will RNA-Seq realize the promise of transcriptomics?
|
2011-01-19
|
Greg T. Sutherland Jillian J. Kril
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Michal Janitz
|
Journal of Neurochemistry
|
Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array
|
2011-01-21
|
Shikai Liu Eric Peatman Huseyin Kucuktas Ludmilla Kaltenboeck Shaolin Wang Zhanjiang Liu
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Zunchun Zhou Jianguo Lu Fanyue Sun Hong Liu Yanliang Jiang
|
BMC Genomics
|
Augmented annotation of the Schizosaccharomyces pombe genome reveals additional genes required for growth and viability.
|
2011-01-26
|
Agnes Grallert Valerie Wood Iain M. Hagan Crispin J. Miller
|
Danny A Bitton Paul J Scutt Tim Yates Duncan L Smith
|
Genetics
|
In vitro culture and characterization of putative porcine embryonic germ cells derived from domestic breeds and Yucatan mini pig embryos at Days 20-24 of gestation.
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2011-01-31
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Hendrik Marks Yu Gao Poul Hyttel
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Stoyan G Petkov Tino Klein Rodrigo S Garcia Henk Stunnenberg
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Stem Cell Research
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Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs
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2011-02
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Nina Papavasiliou
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Brad R Rosenberg Claire E Hamilton Michael M Mwangi Scott Dewell F Nina Papavasiliou
|
Nature Structural & Molecular Biology
|
General lack of global dosage compensation in ZZ/ZW systems? Broadening the perspective with RNA-seq
|
2011-02-01
|
Jochen Wolf Jarosław Bryk
|
Jochen Bw Wolf
|
BMC Genomics
|
The next generation: using new sequencing technologies to analyse gene regulation.
|
2011-02-01
|
Olivia Alder Pamela A. Hoodless
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Rebecca Cullum
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Respirology
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Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.
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2011-02-08
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Michael Eisen S E Lott
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Jacqueline E Villalta Gary P Schroth Shujun Luo Leath A Tonkin
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PLOS Biology
|
Identification and optimization of small molecules that restore E-cadherin expression and reduce invasion in colorectal carcinoma cells.
|
2011-02-09
|
Robert Daniel Beauchamp Craig W Lindsley
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Sydney L Stoops A Scott Pearson Connie Weaver Alex G Waterson Emily Days Chris Farmer Suzanne Brady C David Weaver
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ACS Chemical Biology
|
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads.
|
2011-02-10
|
Ernest Turro Angela Goncalves Lachlan Coin Sylvia Richardson Alexandra M. Lewin
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Shu-Yi Su
|
Genome Biology
|
Isoform-level microRNA-155 target prediction using RNA-seq
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2011-02-11
|
Erik K Flemington
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Nan Deng Adriane Puetter Kun Zhang Kristen Johnson Zhiyu Zhao Christopher Taylor Dongxiao Zhu
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Nucleic Acids Research
|
Characterization of the contradictory chromatin signatures at the 3' exons of zinc finger genes.
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2011-02-15
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Peggy Farnham
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Kimberly R Blahnik Lei Dou Lorigail Echipare Sushma Iyengar Henriette O'Geen Erica Sanchez Yongjun Zhao Marco A Marra Martin Hirst Joseph F Costello Ian Korf
|
PLOS ONE
|
Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs.
|
2011-02-16
|
Vineet Bafna Olivier Harismendy
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Marcus Kinsella Masakazu Nakano Kelly A Frazer
|
Bioinformatics
|
Targeted disruption of py235ebp-1: invasion of erythrocytes by Plasmodium yoelii using an alternative Py235 erythrocyte binding protein.
|
2011-02-17
|
Thomas D Otto Arnab Pain Anthony A Holder Rita Tewari
|
Solabomi A Ogun Steven A Howell Ellen Knuepfer Deirdre A Cunningham Zhengyao Xu
|
PLOS Pathogens
|
RNA-seq reveals cooperative metabolic interactions between two termite-gut spirochete species in co-culture
|
2011-02-17
|
Avigdor Eldar
|
Adam Z Rosenthal Eric G Matson Jared R Leadbetter
|
The ISME Journal
|
ACT: aggregation and correlation toolbox for analyses of genome tracks.
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2011-02-23
|
Joel Rozowsky Kevin Y Yip Lucas Lochovsky
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Justin Jee Robert Bjornson Guoneng Zhong Zhengdong Zhang Yutao Fu Jie Wang Zhiping Weng Mark Gerstein
|
Bioinformatics
|
Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System.
|
2011-03-01
|
Traver Hart
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Steven R Head H Kiyomi Komori John Shimashita Lana Schaffer Daniel R Salomon Phillip T Ordoukhanian
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BioTechniques
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Accurate estimation of expression levels of homologous genes in RNA-seq experiments.
|
2011-03-01
|
Bogdan Pasaniuc Noah Zaitlen
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Eran Halperin
|
Journal of Computational Biology
|
The carbonic anhydrase isoforms of Chlamydomonas reinhardtii: intracellular location, expression, and physiological roles.
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2011-03-02
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Bratati Mukherjee
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James V Moroney Yunbing Ma Wesley D Frey Katelyn A Fusilier Trang T Pham Tiffany A Simms Robert J DiMario Jing Yang
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Photosynthesis Research
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Improving RNA-Seq expression estimates by correcting for fragment bias.
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2011-03-16
|
Lior Pachter John L. Rinn
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Adam Roberts Cole Trapnell Julie Donaghey
|
Genome Biology
|
MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers
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2011-03-17
|
Louis M Staudt Ujunwa C Okoye Pedro Farinha Anke van den Berg Steven Jones
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Christian Steidl Sohrab P Shah Bruce W Woolcock Lixin Rui Masahiro Kawahara Nathalie A Johnson Yongjun Zhao Adele Telenius Susana Ben Neriah Andrew McPherson Barbara Meissner Arjan Diepstra Mark Sun Gillian Leung Joseph M Connors David G Huntsman Kerry J Savage Lisa M Rimsza Douglas E Horsman Ulrich Steidl Marco A Marra Randy D Gascoyne
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Nature
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A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii.
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2011-03-21
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Sabeeha Merchant Matteo Pellegrini David Casero
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Janette Kropat Anne Hong-Hermesdorf Petr Ent Madeli Castruita Davin Malasarn
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The Plant Journal
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ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments.
|
2011-03-22
|
Graziano Pesole Ernesto Picardi
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Mattia D'Antonio Danilo Carrabino Tiziana Castrignanò
|
Bioinformatics
|
Composite transcriptome assembly of RNA-seq data in a sheep model for delayed bone healing
|
2011-03-24
|
Peter Robinson Stefan Mundlos
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Marten Jäger Claus-Eric Ott Johannes Grünhagen Jochen Hecht Hanna Schell Stefan Mundlos Georg N Duda Jasmin Lienau
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BMC Genomics
|
Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays
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2011-03-24
|
Nicole A Walter Jessica Ezzell Hunter Michael A Mooney Shannon K McWeeney
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Daniel Bottomly Priscila Darakjian Sunita Kawane Kari J Buck Robert P Searles Robert Hitzemann
|
PLOS ONE
|
Effects of nickel treatment on H3K4 trimethylation and gene expression.
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2011-03-24
|
Stuart M. Brown Phillip R Smith
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Kam-Meng Tchou-Wong Kathrin Kiok Zuojian Tang Thomas Kluz Adriana Arita Max Costa
|
PLOS ONE
|
Developmental changes in transcriptional profiles.
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2011-03-30
|
Gad Shaulsky
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William F Loomis
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Development, Growth and Differentiation
|
RNA-Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation.
|
2011-04-05
|
Vladimir Benes Gunnar Rätsch
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Tanja Dorothe Rösel Lee-Hsueh Hung Jan Medenbach Katrin Donde Stefan Starke Albrecht Bindereif
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The EMBO Journal
|
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma.
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2011-04-08
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Stylianos Antonarakis Christian Iseli Carlo Rivolta Ioannis Xenarios Jacques S. Beckmann Armand Valsesia
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Donata Rimoldi Danielle Martinet Mark Ibberson Paola Benaglio Manfredo Quadroni Patrice Waridel Muriel Gaillard Mireille Pidoux Blandine Rapin Andrew J G Simpson C Victor Jongeneel Brian J Stevenson
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PLOS ONE
|
Genome-wide analysis of the 5' and 3' ends of vaccinia virus early mRNAs delineates regulatory sequences of annotated and anomalous transcripts.
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2011-04-13
|
Bernard Moss
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Zhilong Yang Daniel P Bruno Craig A Martens Stephen F Porcella
|
Journal of Virology
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A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation.
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2011-04-15
|
Jeremy Davis-Turak Yu Zhou
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Kristi Fox-Walsh Hairi Li Xiang-Dong Fu
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Genomics
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Design and validation issues in RNA-seq experiments.
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2011-04-15
|
Xiangqin Cui
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Zhide Fang
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Briefings in Bioinformatics
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Systems biology approach in Chlamydomonas reveals connections between copper nutrition and multiple metabolic steps.
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2011-04-15
|
David Casero Sabeeha Merchant Matteo Pellegrini Astrid Vieler Christoph Benning
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Madeli Castruita Steven J Karpowicz Janette Kropat Scott I Hsieh Weihong Yan Shawn Cokus Joseph A Loo
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The Plant Cell
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Estimation of alternative splicing isoform frequencies from RNA-Seq data
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2011-04-19
|
Ion I. Mandoiu Alexander Zelikovsky
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Marius Nicolae Serghei Mangul
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Algorithms for Molecular Biology
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Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.
|
2011-04-20
|
Luciana D'Apice Aldo Donizetti Monica Rienzo Paola Salvatore Stefania Crispi Valerio Costa Piergiuseppe De Berardinis Teresa Infante Claudia Angelini Marco Picardi Berardo Sarubbi Raffaele Calabrò Claudio Napoli Amelia Casamassimi
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Margherita Mutarelli Linda Sommese Maria Assunta Gallo Marianna Aprile Roberta Esposito Luigi Leone Alfredo Ciccodicola
|
PLOS ONE
|
BM-map: Bayesian mapping of multireads for next-generation sequencing data.
|
2011-04-22
|
Yuan Yuan Han Liang
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Yuan Ji Yanxun Xu Qiong Zhang Kam-Wah Tsui Clift Norris Shoudan Liang
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Biometrics
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Contribution of Hfq to photooxidative stress resistance and global regulation in Rhodobacter sphaeroides.
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2011-04-27
|
Cynthia Sharma Jörg Vogel Gabriele Klug
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Bork A Berghoff Jens Glaeser Monica Zobawa Friedrich Lottspeich
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Molecular Microbiology
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FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq.
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2011-05-05
|
Jeremy Chien Jian Ma
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Yang Li David I Smith
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Bioinformatics
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Protocol dependence of sequencing-based gene expression measurements
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2011-05-06
|
John F Thompson
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Tal Raz Philipp Kapranov Doron Lipson Stan Letovsky Patrice M Milos
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PLOS ONE
|
Detecting copy number status and uncovering subclonal markers in heterogeneous tumor biopsies.
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2011-05-11
|
Antonella Bacchiocchi
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Fabio Parisi Stephan Ariyan Deepak Narayan Kathleen Hoyt Elaine Cheng Fang Xu Peining Li Ruth Halaban Yuval Kluger
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BMC Genomics
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The sensitivity of massively parallel sequencing for detecting candidate infectious agents associated with human tissue
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2011-05-13
|
Curtis A. Suttle Julia A Gustavsen Jan M Friedman Robert A Holt
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Richard A Moore René L Warren J Douglas Freeman Caroline Chénard Yongjun Zhao
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PLOS ONE
|
NSMAP: a method for spliced isoforms identification and quantification from RNA-Seq.
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2011-05-16
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Zheng Xia
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Jianguo Wen Chung-Che Chang Xiaobo Zhou
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BMC Bioinformatics
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FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution.
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2011-05-18
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Wolfgang Hoeck
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Huanying Ge Kejun Liu Todd Juan Fang Fang Matthew Newman
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Bioinformatics
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deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data.
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2011-05-19
|
Malachi Griffith Gavin Ha
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Andrew McPherson Fereydoun Hormozdiari Abdalnasser Zayed Ryan Giuliany Mark G F Sun Alireza Heravi Moussavi Janine Senz Nataliya Melnyk Marina Pacheco Marco A Marra Martin Hirst Torsten O Nielsen S Cenk Sahinalp David Huntsman Sohrab P Shah
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PLOS Computational Biology
|
Genome-wide RNA-seq analysis of human and mouse platelet transcriptomes.
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2011-05-19
|
A S Weyrich
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Jesse W Rowley Andrew J Oler Neal D Tolley Benjamin N Hunter Elizabeth N Low David A Nix Christian C Yost Guy A Zimmerman
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Blood
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The zebrafish transcriptome during early development.
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2011-05-24
|
Juha Kere Outi Hovatta Liselotte Vesterlund
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Hong Jiao Per Unneberg Outi Hovatta
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BMC Developmental Biology
|
Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding
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2011-05-27
|
Antonis Rokas Laurence J. Zwiebel
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R Jason Pitts David C Rinker Patrick L Jones
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BMC Genomics
|
Pyrosequencing-based expression profiling and identification of differentially regulated genes from Manduca sexta, a lepidopteran model insect.
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2011-05-27
|
Haobo Jiang
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Shuguang Zhang Ramesh T Gunaratna Xiufeng Zhang Fares Najar Yang Wang Bruce Roe
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Insect Biochemistry and Molecular Biology
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Megakaryocytes differentially sort mRNAs for matrix metalloproteinases and their inhibitors into platelets: a mechanism for regulating synthetic events.
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2011-05-31
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Loredana Bury A S Weyrich Paolo Gresele
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Luca Cecchetti Neal D Tolley Noemi Michetti
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Blood
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Characterizing the impact of smoking and lung cancer on the airway transcriptome using RNA-Seq
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2011-06
|
Frank Schembri Jennifer Beane Yuriy O Alekseyev Avrum Spira Marc E Lenburg Shawn Levy
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Jessica Vick Christina Anderlind Adam Gower Joshua Campbell Lingqi Luo Xiao Hui Zhang Ji Xiao Shenglong Wang Pierre P Massion
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Cancer Prevention Research
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RNA-seq: technical variability and sampling.
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2011-06-06
|
Lauren McIntyre
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Kenneth K Lopiano Alison M Morse Victor Amin Ann L Oberg Linda J Young Sergey V Nuzhdin
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BMC Genomics
|
Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics.
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2011-06-07
|
Tracy L Bergemann
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Jason Wilson
|
BMC Bioinformatics
|
RNA sequencing reveals two major classes of gene expression levels in metazoan cells.
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2011-06-07
|
Sarah Teichmann Alexander van Oudenaarden Muxin Gu Varodom Charoensawan Daniel Hebenstreit
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Miaoqing Fang
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Molecular Systems Biology
|
PR-domain-containing Mds1-Evi1 is critical for long-term hematopoietic stem cell function.
|
2011-06-10
|
Subhash Juneja
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Yi Zhang Sandra Stehling-Sun Kimberly Lezon-Geyda Lucie Coillard Gouri Chatterjee Charles A Wuertzer Fernando Camargo Archibald S Perkins
|
Blood
|
Poly (A)+ transcriptome assessment of ERBB2-induced alterations in breast cell lines.
|
2011-06-22
|
Dirce Carraro Emmanuel Dias-Neto Helena Brentani Renata Pasqualini
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Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Eduardo Fernandes Abrantes Adriana Priscila Trapé Bedrich L Eckhardt Diana Noronha Nunes Maria Mitzi Brentani Wadih Arap Ricardo Renzo Brentani
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PLOS ONE
|
Deterministic and stochastic allele specific gene expression in single mouse blastomeres
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2011-06-23
|
Azim Surani
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Fuchou Tang Catalin Barbacioru Ellen Nordman Siqin Bao Caroline Lee Xiaohui Wang Brian B Tuch Edith Heard Kaiqin Lao
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PLOS ONE
|
Transcription factor TEAD4 regulates expression of myogenin and the unfolded protein response genes during C2C12 cell differentiation
|
2011-06-24
|
Gabrielle Mengus Irwin Davidson
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A Benhaddou C Keime T Ye A Morlon I Michel B Jost
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Cell Death & Differentiation
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Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation.
|
2011-06-28
|
Filip Van Nieuwerburgh James W Golden
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Britt L Flaherty Steven R Head
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BMC Genomics
|
Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
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2011-07
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Sten Linnarsson Peter Lönnerberg
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Saiful Islam Una Kjällquist Annalena Moliner Pawel Zajac Jian-Bing Fan
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Genome Research
|
Full-length transcriptome assembly from RNA-Seq data without a reference genome
|
2011-07
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Kerstin Lindblad-Toh Aviv Regev Chad Nusbaum Andreas Gnirke Evan Mauceli Nir Friedman Nicholas Rhind Nir Hacohen Raktima Raychowdhury
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Manfred G Grabherr Brian J Haas Moran Yassour Joshua Z Levin Dawn A Thompson Ido Amit Xian Adiconis Lin Fan Raktima Raychowdhury Qiandong Zeng Zehua Chen Federica di Palma Bruce W Birren
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Nature Biotechnology
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Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling.
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2011-07-01
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Paweł P Łabaj Steven Wiley D Kreil
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Germán G Leparc Bryan E Linggi Lye Meng Markillie
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Bioinformatics
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Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus.
|
2011-07-01
|
Antonis Rokas
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John G Gibbons Anne Beauvais Remi Beau Kriston L McGary Jean-Paul Latgé
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Eukaryotic Cell
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Exploring the Schistosoma mansoni adult male transcriptome using RNA-seq.
|
2011-07-02
|
Ricardo DeMarco Sergio Verjovski-Almeida
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Giulliana Tessarin Almeida Murilo Sena Amaral Felipe Cesar Ferrarezi Beckedorff João Paulo Kitajima
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Experimental Parasitology
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An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis.
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2011-07-05
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Iain W Wilson
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Qi Tang Xiaojun Ma Changming Mo Cai Song Huan Zhao Yanfang Yang Wei Fu Deyou Qiu
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BMC Genomics
|
A comparative analysis of DNA methylation across human embryonic stem cell lines.
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2011-07-06
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Matteo Pellegrini
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Pao-Yang Chen Suhua Feng Jong Wha Joanne Joo Steve E Jacobsen
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Genome Biology
|
SOAPsplice: Genome-Wide ab initio Detection of Splice Junctions from RNA-Seq Data
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2011-07-07
|
Tak-Wah Lam
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Songbo Huang Jinbo Zhang Ruiqiang Li Wenqian Zhang Zengquan He Zhiyu Peng Siu-Ming Yiu
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Frontiers in Genetics
|
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.
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2011-07-12
|
David Casero Matteo Pellegrini Sabeeha Merchant
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David Lopez Shawn J Cokus
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BMC Bioinformatics
|
De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome.
|
2011-07-19
|
Ya-Ting Chao
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Chun-lin Su Yao-Chien Alex Chang Wan-Chieh Chen Chun-Yi Chen Ann-Ying Lee Kee Tuan Hwa Ming-Che Shih
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Plant and Cell Physiology
|
Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM).
|
2011-07-19
|
Angel Pizarro Gregory R Grant Eric A Pierce
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Michael H Farkas Nicholas F Lahens Jonathan Schug Brian P Brunk Christian J Stoeckert John B Hogenesch
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Bioinformatics
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RseqFlow: workflows for RNA-Seq data analysis.
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2011-07-27
|
Ewa Deelman
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Ying Wang Gaurang Mehta Rajiv Mayani Jingxi Lu Tade Souaiaia Yangho Chen Andrew Clark Hee Jae Yoon Lin Wan Oleg V Evgrafov James A Knowles Ting Chen
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Bioinformatics
|
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length
|
2011-07-27
|
Jing Woei Li Stephen Kwok-Wing Tsui T F Chan
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Shao-Ke Lou Hao Qin Aldrin Kay-Yuen Yim Leung-Yau Lo Bing Ni Kwong-Sak Leung
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BMC Bioinformatics
|
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data.
|
2011-07-28
|
Tom Maniatis Brad Friedman
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Genome Biology
|
Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure.
|
2011-07-29
|
Mikhail Matz
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E Meyer G V Aglyamova
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Molecular Ecology
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Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression
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2011-07-31
|
John R. Prensner Qi Cao Irfan Asangani Nallasivam Palanisamy
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Matthew K Iyer O Alejandro Balbin Saravana M Dhanasekaran J Chad Brenner Bharathi Laxman Catherine S Grasso Hal D Kominsky Xuhong Cao Xiaojun Jing Xiaoju Wang Javed Siddiqui John T Wei Daniel Robinson Hari K Iyer Christopher A Maher Arul M Chinnaiyan
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Nature Biotechnology
|
RNA-Seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression.
|
2011-08-01
|
Jennifer M Ritchie
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Anjali Mandlik Jonathan Livny William P Robins John J Mekalanos Matthew K Waldor
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Cell Host & Microbe
|
AlleleSeq: analysis of allele-specific expression and binding in a network framework.
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2011-08-02
|
Yong Kong Alexej Abyzov Joel Rozowsky Mark Rubin Mark Bender Gerstein
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Jing Wang Pedro Alves Debasish Raha Arif Harmanci Jing Leng Robert Bjornson Naoki Kitabayashi Nitin Bhardwaj Michael Snyder
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Molecular Systems Biology
|
Synthetic spike-in standards for RNA-seq experiments.
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2011-08-04
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Thomas R. Gingeras
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Lichun Jiang Felix Schlesinger Carrie A Davis Yu Zhang Renhua Li Marc Salit Brian Oliver
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Genome Research
|
Quantitative RNA-seq analysis of the Campylobacter jejuni transcriptome
|
2011-08-04
|
Paul P. Gardner Roy R Chaudhuri Jyoti Choudhary
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Lu Yu Alpa Kanji Timothy T Perkins Duncan J Maskell Andrew J Grant
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Microbiology
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RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes
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2011-08-05
|
Eran Pichersky
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Petra M Bleeker Eleni A Spyropoulou Paul J Diergaarde Hanne Volpin Michiel T J De Both Philipp Zerbe Joerg Bohlmann Vasiliki Falara Yuki Matsuba Eran Pichersky Michel A Haring Robert C Schuurink
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Plant Molecular Biology
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FDM: a graph-based statistical method to detect differential transcription using RNA-seq data.
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2011-08-08
|
Derek Y Chiang
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Darshan Singh Christian F Orellana Yin Hu Corbin D Jones Yufeng Liu Jinze Liu Jan F Prins
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Bioinformatics
|
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts
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2011-08-11
|
Steven Salzberg
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Daehwan Kim
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Genome Biology
|
Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation.
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2011-08-11
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Jason Gertz Katherine E Varley Timothy E Reddy
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Kevin M Bowling Florencia Pauli Stephanie L Parker Katerina S Kucera Huntington F Willard Richard M Myers
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PLOS Genetics
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Genome-Wide Gene Expression Profiling of Nucleus Accumbens Neurons Projecting to Ventral Pallidum Using both Microarray and Transcriptome Sequencing
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2011-08-12
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Robert W. Williams
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Hao Chen Zhimin Liu Suzhen Gong Xingjun Wu William L Taylor Shannon G Matta Burt M Sharp
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Frontiers in Neuroscience
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Local and global factors affecting RNA sequencing analysis.
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2011-08-16
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Graham D Johnson
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Edward Sendler Stephen A Krawetz
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Analytical Biochemistry
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Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma
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2011-08-18
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Martin Hirst Yaron Butterfield Angela Brooks-Wilson Eric Y Zhao Malachi Griffith Andrew Mungall
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Ryan D Morin Maria Mendez-Lago Rodrigo Goya Karen L Mungall Richard D Corbett Nathalie A Johnson Tesa M Severson Readman Chiu Matthew Field Shaun Jackman Martin Krzywinski David W Scott Diane L Trinh Jessica Tamura-Wells Sa Li Marlo R Firme Sanja Rogic Susanna Chan Oleksandr Yakovenko Irmtraud M Meyer Duane Smailus Michelle Moksa Suganthi Chittaranjan Lisa Rimsza John J Spinelli Susana Ben-Neriah Barbara Meissner Bruce Woolcock Merrill Boyle Helen McDonald Angela Tam Yongjun Zhao Allen Delaney Thomas Zeng Kane Tse Inanç Birol Rob Holt Jacqueline Schein Douglas E Horsman Richard Moore Steven J M Jones Joseph M Connors Randy D Gascoyne Marco A Marra
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Nature
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An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype
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2011-08-18
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Michele Balsamo
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Irina M Shapiro Albert W Cheng Nicholas C Flytzanis John S Condeelis Maja H Oktay Christopher B Burge Frank B Gertler
|
PLOS Genetics
|
Transcriptional profiling of psoriasis using RNA-seq reveals previously unidentified differentially expressed genes.
|
2011-08-18
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Ali Jabbari
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Mayte Suárez-Fariñas Scott Dewell James G Krueger
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Journal of Investigative Dermatology
|
The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression
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2011-08-19
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Songnian Hu
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Peng Cui Qiang Lin Lingfang Zhang Feng Ding Chengqi Xin Daoyong Zhang Fanglin Sun Jun Yu
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PLOS ONE
|
Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry.
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2011-08-23
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Daojun Yuan Xianlong Zhang
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Li Xu Longfu Zhu Lili Tu Linlin Liu Li Jin Lu Long
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Journal of Experimental Botany
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Bioaccumulation and effects of CdTe/CdS quantum dots on Chlamydomonas reinhardtii - nanoparticles or the free ions?
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2011-08-25
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Rute F. Domingos Kevin J Wilkinson
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Dana F Simon Charles Hauser
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Environmental Science & Technology
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A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data.
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2011-08-26
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Daniel A Skelly
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Marnie Johansson Jennifer Madeoy Jon Wakefield Joshua M Akey
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Genome Research
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Preservation of the Y transcriptome in a 10-million-year-old plant sex chromosome system.
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2011-09-01
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Deborah Charlesworth
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Roberta Bergero
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Current Biology
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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
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2011-09-02
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Loyal Goff Magdalena J Koziol John L. Rinn
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Moran N Cabili Cole Trapnell Barbara Tazon-Vega Aviv Regev
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Genes & Development
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Wnt gene loss in flatworms.
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2011-09-03
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Nick Riddiford
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Peter D Olson
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Development Genes and Evolution
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SpliceTrap: a method to quantify alternative splicing under single cellular conditions.
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2011-09-06
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W. Richard McCombie Adrian Robert Krainer
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Jie Wu Martin Akerman Shuying Sun Michael Q Zhang
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Bioinformatics
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Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation.
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2011-09-06
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Ross C Hardison James C Mullikin
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Andre M Pilon Subramanian S Ajay Swathi Ashok Kumar Laurie A Steiner Praveen F Cherukuri Stephen Wincovitch Stacie M Anderson NISC Comparative Sequencing Center Patrick G Gallagher Elliott H Margulies David M Bodine
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Blood
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wapRNA: a web-based application for the processing of RNA sequences.
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2011-09-06
|
Songnian Hu
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Wenming Zhao Wanfei Liu Dongmei Tian Bixia Tang Yanqing Wang Caixia Yu Rujiao Li Yunchao Ling Jiayan Wu Shuhui Song
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Bioinformatics
|
RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders.
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2011-09-07
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Deyou Zheng
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Mingyan Lin Erika Pedrosa Abhishek Shah Anastasia Hrabovsky Shahina Maqbool Herbert M Lachman
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PLOS ONE
|
Differential expression in RNA-seq: a matter of depth.
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2011-09-08
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Joaquín Dopazo Ana Conesa Sonia Tarazona Alberto Ferrer
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Fernando García-Alcalde
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Genome Research
|
Proteomic and phosphoproteomic comparison of human ES and iPS cells.
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2011-09-11
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Justin Brumbaugh
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Douglas H Phanstiel Craig D Wenger Shulan Tian Mitchell D Probasco Derek J Bailey Danielle L Swaney Mark A Tervo Jennifer M Bolin Victor Ruotti Ron Stewart James A Thomson Joshua J Coon
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Nature Methods
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Identification of common carp innate immune genes with whole-genome sequencing and RNA-Seq data.
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2011-09-12
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Elia Stupka Christiaan V. Henkel Herman P Spaink
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Yanju Zhang Hans J Jansen Fons J Verbeek
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Journal of integrative bioinformatics
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Integrated genome-wide analysis of transcription factor occupancy, RNA polymerase II binding and steady-state RNA levels identify differentially regulated functional gene classes.
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2011-09-13
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Jurian Schuijers Michal Mokry
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Pantelis Hatzis Nico Lansu Frans-Paul Ruzius Hans Clevers Edwin Cuppen
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Nucleic Acids Research
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Integrative approach involving RNA-Seq, foliar traits and growth measurements revealed genotype-specific plasticity on Eucalyptus subjected to seasonal water shortage.
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2011-09-13
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Christophe Plomion
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Emilie Villar Jean-Marc Gion
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BMC Proceedings
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Pronounced and extensive microtubule defects in a Saccharomyces cerevisiae DIS3 mutant.
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2011-09-15
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Daniel L Kiss
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Sarah B Smith Edward Turk Alan M Tartakoff Erik D Andrulis
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Yeast
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RNA-Seq methods for imperfect samples: development, evaluation and applications
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2011-09-19 2011
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Aviv Regev Chad Nusbaum Gad Getz
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Xian Adiconis Lin Fan David DeLuca Andrey Sivachenko Nathalie Pochet Aaron Berlin Sarah Young Andreas Gnirke Joshua Z Levin
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Genome Biology
|
Differential Expression for RNA Sequencing (RNA-Seq) Data: Mapping, Summarization, Statistical Analysis, and Experimental Design
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2011-09-22
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Davis J McCarthy Alicia Oshlack Gordon K Smyth
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Matthew D. Young Matthew J. Wakefield Mark D. Robinson
|
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Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals.
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2011-09-25
|
Vincent Lynch Gunter P Wagner
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Robert D Leclerc Gemma May
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Nature Genetics
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From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).
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2011-09-28
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Thomas Schmutzer Martin Mascher Uwe Scholz Nils Stein Klaus Mayer Eva Bauer
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Grit Haseneyer Michael Seidel Ruonan Zhou Chris-Carolin Schön Stefan Taudien
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BMC Plant Biology
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Accurate identification of A-to-I RNA editing in human by transcriptome sequencing.
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2011-09-29
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Jae-Hyung Lee Guangdun Peng Xinshu Xiao
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Jae Hoon Bahn Gang Li Christopher Greer
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Genome Research
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Genome-wide transcriptome analysis in murine neural retina using high-throughput RNA sequencing.
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2011-10-01
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Ece D. Gamsiz Eric M. Morrow
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Qing Ouyang Michael Schmidt Shailender Nagpal
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Genomics
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RNA-Seq analysis in MeV.
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2011-10-05
|
John Quackenbush
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Eleanor A Howe Raktim Sinha Daniel Schlauch
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Bioinformatics
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RNA-seq analysis of small RNPs in Trypanosoma brucei reveals a rich repertoire of non-coding RNAs
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2011-10-05
|
Tirza Doniger
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Shulamit Michaeli Sachin Kumar Gupta Omri Wurtzel Mali Romano Damian Visnovezky Rotem Sorek Ron Unger Elisabetta Ullu
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Nucleic Acids Research
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GENE-counter: a computational pipeline for the analysis of RNA-Seq data for gene expression differences.
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2011-10-06
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Jeff H. Chang Jeffrey A Kimbrel James C. Carrington
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Jason S Cumbie Yanming Di Daniel W Schafer Larry J Wilhelm Samuel E Fox Christopher M Sullivan Aron D Curzon Todd C Mockler
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PLOS ONE
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S-MART, a software toolbox to aid RNA-Seq data analysis
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2011-10-06
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Hadi Quesneville
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Matthias Zytnicki
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PLOS ONE
|
Nonrandom gene loss from the Drosophila miranda neo-Y chromosome.
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2011-10-10
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Doris Bachtrog
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Vera B Kaiser Qi Zhou
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Genome Biology and Evolution
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The role of CYP3A4 mRNA transcript with shortened 3'-untranslated region in hepatocyte differentiation, liver development, and response to drug induction.
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2011-10-13
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Gaedigk R Steven N. Hart
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Dan Li J Steven Leeder Xiao-bo Zhong
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Molecular Pharmacology
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RNA-Seq for Plant Pathogenic Bacteria.
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2011-10-13
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Jeffrey A Kimbrel Jeff H. Chang
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Yanming Di Jason S Cumbie
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Genes
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Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens.
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2011-10-18
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Charles D. Johnson Ulisses Braga Neto
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Ying Wang Noushin Ghaffari Hui Wang Rui Chen Huaijun Zhou
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BMC Bioinformatics
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The crystal structure of necrosis- and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity
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2011-10-21
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Paulo José Pereira Lima Teixeira Joan Barau Antonio Costa-filho
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Gustavo Zaparoli Mario Ramos de Oliveira Barsottini Juliana Ferreira de Oliveira Fabio Dyszy Odalys Garcia Andre Luis Berteli Ambrosio Gonçalo Amarante Guimarães Pereira Sandra Martha Gomes Dias
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Biochemistry
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Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster.
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2011-10-23
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Thomas R. Gingeras Jay Shendure David Sturgill
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Xinxian Deng Joseph B Hiatt Di Kim Nguyen Sevinc Ercan LaDeana W Hillier Felix Schlesinger Carrie A Davis Valerie J Reinke Robert H Waterston Brian Oliver Jason D Lieb Christine M Disteche
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Nature Genetics
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Identification of gene fusion transcripts by transcriptome sequencing in BRCA1-mutated breast cancers and cell lines
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2011-10-27
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Anne Vincent-Salomon William D Foulkes Jorge Reis-Filho Rachael Natrajan Alan Ashworth
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Kevin C H Ha Emilie Lalonde Lili Li Luca Cavallone Maryou B Lambros Costas Mitsopoulos Jarle Hakas Iwanka Kozarewa Kerry Fenwick Chris J Lord Mark Basik Jacek Majewski
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BMC Medical Genomics
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RNA-Seq reveals an integrated immune response in nucleated erythrocytes.
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2011-10-27
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Nerea Roher Laia Ribas Joan C Balasch Sebastian Boltana Steven B. Roberts Simon Mackenzie
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Davinia Morera Carmen Doñate Agnes Callol Giles Goetz Frederick W Goetz
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PLOS ONE
|
The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44.
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2011-10-28
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Giovanni Giuliano Kevin L. Childs
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Alicia N Massa Haining Lin Glenn J Bryan C Robin Buell
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PLOS ONE
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RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus
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2011-11-02
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Christophe Plomion Evandro Novaes
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Emilie Villar Christophe Klopp Céline Noirot Matias Kirst Jean-Marc Gion
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BMC Genomics
|
RNA-Seq improves annotation of protein-coding genes in the cucumber genome.
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2011-11-02
|
Zhen Li Sanwen Huang
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Zhonghua Zhang Pengcheng Yan Zhangjun Fei Kui Lin
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BMC Genomics
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deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns.
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2011-11-03
|
Peter F. Stadler Jan Gorodkin David Langenberger Claus T. Ekstrøm Sachin Pundhir
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Steve Hoffmann
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Bioinformatics
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Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.
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2011-11-06
|
Adam Ameur Ulf Gyllensten
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Ammar Zaghlool Jonatan Halvardson Anna Wetterbom Lucia Cavelier Lars Feuk
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Nature Structural & Molecular Biology
|
Exploring the gonad transcriptome of two extreme male pigs with RNA-seq
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2011-11-08
|
Giovanni Bussotti Robert Kofler Cedric Notredame Miguel Perez-Enciso Anna Esteve-Codina
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Nicola Palmieri
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BMC Genomics
|
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq.
|
2011-11-08
|
Ming Hu Zhaohui Steve Qin
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Yu Zhu Jeremy M G Taylor Jun S Liu
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Bioinformatics
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An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs.
|
2011-11-10
|
Andreas Sommer Irena Vlatkovic Hendrik Marks Robert Kralovics
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Ru Huang Markus Jaritz Philipp Guenzl Ido M Tamir Thorsten Klampfl Hendrik G Stunnenberg Denise P Barlow Florian M Pauler
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PLOS ONE
|
Non-laser capture microscopy approach for the microdissection of discrete mouse brain regions for total RNA isolation and downstream next-generation sequencing and gene expression profiling.
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2011-11-13
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Norman Atkins
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Charlie M Miller Joseph R Owens Fred W Turek
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Journal of Visualized Experiments
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ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.
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2011-11-16
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Jeffrey T. Leek Ben Langmead
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Alyssa C Frazee
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BMC Bioinformatics
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Identification of new viral genes and transcript isoforms during Epstein-Barr virus reactivation using RNA-Seq.
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2011-11-16
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Melody Baddoo Dale Hedges Erik K Flemington
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Monica Concha Xia Wang Subing Cao Melody Baddoo Claire Fewell Zhen Lin William Hulme Dale Hedges Jane McBride
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Journal of Virology
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Genetic variation of pre-mRNA alternative splicing in human populations
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2011-11-17
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Zhi-xiang Lu
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Peng Jiang Yi Xing
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Wiley interdisciplinary reviews. RNA
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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
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2011-11-22
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Aviv Regev Eivind Valen Albin Sandelin John L. Rinn
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Andrea Pauli Michael F Lin Manuel Garber Nadine L Vastenhouw Joshua Z Levin Lin Fan Alexander F Schier
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Genome Research
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RNA-Seq and find: entering the RNA deep field.
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2011-11-22
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Lior Pachter
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Adam Roberts
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Genome Medicine
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Estimation of alternative splicing variability in human populations.
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2011-11-23
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Roderic Guigó i Serra Michael Sammeth
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Mar Gonzàlez-Porta Miquel Calvo
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Genome Research
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RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew.
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2011-11-24
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Blake Meyers
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Sridhara G Kunjeti Thomas A Evans Adam G Marsh Nancy F Gregory Saritha Kunjeti Venugopal S Kalavacharla Nicole M Donofrio
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Molecular Plant Pathology
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Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
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2011-11-28
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Robert Tibshirani
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Jun Li
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Statistical Methods in Medical Research
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Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome.
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2011-11-28
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Paola Tosi J Paul Knox Jackie Freeman
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Till K Pellny Alison Lovegrove Christopher G Love Peter R Shewry Rowan A C Mitchell
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Plant Physiology
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Transposase mediated construction of RNA-seq libraries.
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2011-11-29
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Jason Gertz Katherine E Varley
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Nicholas S Davis Bradley J Baas Igor Y Goryshin Ramesh Vaidyanathan Scott Kuersten Richard M Myers
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Genome Research
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Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-Seq.
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2011-11-30
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Jian Luo Mingyao Liu
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Geng Chen Kangping Yin Leming Shi Yuanzhang Fang Ya Qi Peng Li Bing He Tieliu Shi
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PLOS ONE
|
Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120
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2011-11-30
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Agustín Vioque Fabian Haas Wolfgang R Hess Alicia María Muro-Pastor
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Jan Mitschke
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Proceedings of the National Academy of Sciences of the United States of America
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Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.
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2011-12-01
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Jingyi Jessica Li
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Ci-Ren Jiang James B Brown Haiyan Huang Peter J Bickel
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Proceedings of the National Academy of Sciences of the United States of America
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EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.
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2011-12-01
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Jing Qin Junwen Wang
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Lily Yan Wang Panwen Wang Mulin Jun Li Xiaowo Wang Michael Q Zhang
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Epigenetics
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RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).
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2011-12-02
|
Jérôme Salse
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Caroline Pont Florent Murat Carole Confolent Sandrine Balzergue
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Genome Biology
|
X-chromosome hyperactivation in mammals via nonlinear relationships between chromatin states and transcription
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2011-12-04
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Ruslan I Sadreyev
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Eda Yildirim Stefan F Pinter Jeannie T Lee
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Nature Structural & Molecular Biology
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Isoform diversity and its importance for axon regeneration.
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2011-12-13
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John L. Bixby Vance P. Lemmon
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Jessica K Lerch
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Neuropathology
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Protein identification using customized protein sequence databases derived from RNA-Seq data.
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2011-12-14
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David Tabb Daniel C. Liebler
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Xiaojing Wang Robbert J C Slebos Dong Wang Patrick J Halvey Bing Zhang
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Journal of Proteome Research
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Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study.
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2011-12-14
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Qiong-Yi Zhao
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Yi Wang Yi-Meng Kong Da Luo Xuan Li Pei Hao
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BMC Bioinformatics
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GC-content normalization for RNA-Seq data
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2011-12-17
|
Gavin Sherlock Davide Risso
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Katja Schwartz Sandrine Dudoit
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BMC Bioinformatics
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Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast Candida parapsilosis
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2011-12-22
|
Desmond G. Higgins Geraldine Butler Sarah L Maguire Matthew Berriman
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Alessandro Guida Claudia Lindstädt Chen Ding Nicola J Corton
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BMC Genomics
|
Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses.
|
2011-12-22
|
Laurence Florens Swaminathan Venkatesh Michael P. Washburn
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Joshua M Gilmore Mihaela E Sardiu Brent Stutzman Allison Peak Chris W Seidel Jerry L Workman
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Molecular & Cellular Proteomics
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Statistical methods on detecting differentially expressed genes for RNA-seq data.
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2011-12-23
|
Saralees Nadarajah
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Zhongxue Chen Jianzhong Liu Hon Keung Tony Ng Saralees Nadarajah Howard L Kaufman Jack Y Yang Youping Deng
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BMC Systems Biology
|
Modulation of NF-κB-dependent gene transcription using programmable DNA minor groove binders
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2011-12-27
|
Jordan L Meier Peter Dervan
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Jevgenij A Raskatov James W Puckett Fei Yang Parameswaran Ramakrishnan
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Proceedings of the National Academy of Sciences of the United States of America
|
Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer.
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2011-12-28
|
Fangqing Zhao
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Qi Liu Chong Chen Enjian Shen Zhongsheng Sun Jinyu Wu
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Genomics
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Cytoskeleton remodeling and alterations in smooth muscle contractility in the bovine jejunum during nematode infection.
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2011-12-28
|
Steven G Schroeder
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Robert W Li
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Functional and Integrative Genomics
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Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas.
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2011-12-29
|
Steven B. Roberts
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Mackenzie R Gavery
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
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Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms
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2012
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Christina A Cuomo
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Kelly L Robertson Anahita Mostaghim Carissa M Soto Nikolai Lebedev Robert F Bailey Zheng Wang
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PLOS ONE
|
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq
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2012
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John L. Bixby Vance P. Lemmon Dario Motti
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Jessica K Lerch Frank Kuo Richard Morris
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PLOS ONE
|
Genes associated with MUC5AC expression in small airway epithelium of human smokers and non-smokers
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2012
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Jacqueline Salit
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Guoqing Wang Zhibo Xu Rui Wang Mohammed Al-Hijji Yael Strulovici-Barel Ann E Tilley Jason G Mezey Ronald G Crystal
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BMC Medical Genomics
|
The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain
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2012
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Andrea Telatin Stefano Campanaro Giorgio Valle
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Fabio De Pascale Riccardo Schiavon Douglas H Bartlett
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BMC Genomics
|
Computational analysis of noncoding RNAs
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2012
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Manolis Kellis Stefan Washietl Bonnie Berger John L. Rinn
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Sebastian Will David A. Hendrix Loyal A. Goff
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Wiley interdisciplinary reviews. RNA
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Transcriptome analysis reveals strain-specific and conserved stemness genes in Schmidtea mediterranea
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2012
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Brenton R. Graveley
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Alissa M Resch Dasaradhi Palakodeti Yi-Chien Lu Michael Horowitz
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PLOS ONE
|
RNA-seq-based metatranscriptomic and microscopic investigation reveals novel metalloproteases of Neobodo sp. as potential virulence factors for soft tunic syndrome in Halocynthia roretzi
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2012
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Tae Sung Jung
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Ho Bin Jang Young Kyu Kim Carmelo S Del Castillo Seong Won Nho In Seok Cha Seong Bin Park Mi Ae Ha Jun-Ichi Hikima Sung Jong Hong Takashi Aoki
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PLOS ONE
|
GABAergic gene expression in postmortem hippocampus from alcoholics and cocaine addicts; corresponding findings in alcohol-naïve P and NP rats
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2012
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David Goldman
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Mary-Anne Enoch Zhifeng Zhou Mitsuru Kimura Deborah C Mash Qiaoping Yuan
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PLOS ONE
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Tcf7 is an important regulator of the switch of self-renewal and differentiation in a multipotential hematopoietic cell line
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2012
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Mark Bender Gerstein Vincent Schulz
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Jia Qian Wu Montrell Seay Manoj Hariharan David Tuck Jin Lian Jiang Du Minyi Shi Zhijia Ye Michael P Snyder Sherman Weissman
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PLOS Genetics
|
Gene expression profiling of liver cancer stem cells by RNA-sequencing
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2012
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Timothy Wan
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David W Y Ho Zhen Fan Yang Kang Yi Chi Tat Lam Michael N P Ng Wan Ching Yu Joyce Lau Xiaoqi Wang Zhixiang Yan Hang Liu Yong Zhang Sheung Tat Fan
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PLOS ONE
|
Nrac, a novel nutritionally-regulated adipose and cardiac-enriched gene
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2012
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Feng Gao Abdul B Abou-Samra
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Ren Zhang Fayi Yao
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PLOS ONE
|
RNA-seq analysis reveals different dynamics of differentiation of human dermis- and adipose-derived stromal stem cells
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2012
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Sten Linnarsson
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Kersti Jääger Saiful Islam Pawel Zajac Toomas Neuman
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PLOS ONE
|
Stable gene targeting in human cells using single-strand oligonucleotides with modified bases
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2012
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George M. Church
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Xavier Rios Adrian W Briggs Danos Christodoulou Josh M Gorham Jonathan G Seidman
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PLOS ONE
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Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data
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2012
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Jean-Baptiste Veyrieras Daniel J Gaffney
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Jean-Baptiste Veyrieras Joseph K Pickrell Yoav Gilad Matthew Stephens Jonathan K Pritchard
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PLOS ONE
|
Comparing Bowtie and BWA to Align Short Reads from a RNA-Seq Experiment
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2012
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Honghuang Lin
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N. Medina-Medina A. Broka S. Lacey E. S. Klings C. T. Baldwin M. H. Steinberg P. Sebastiani
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Advances in Intelligent and Soft Computing
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DBTSS: DataBase of Transcriptional Start Sites progress report in 2012
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2012-01
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Sumio Sugano
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Riu Yamashita Yutaka Suzuki Kenta Nakai
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Nucleic Acids Research
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Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
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2012-01-01
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Andreas Gnirke Georgia Giannoukos Ashlee Earl Chad Nusbaum Dirk Gevers
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Dawn M Ciulla Katherine Huang Brian J Haas Jacques Izard Joshua Z Levin Jonathan Livny Doyle V Ward Bruce W Birren
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Genome Biology
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How to analyze gene expression using RNA-sequencing data.
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2012-01-01
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Daniel Ramsköld Rickard Sandberg
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Ersen Kavak
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Methods in Molecular Biology
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Detection and quantification of alternative splicing variants using RNA-seq.
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2012-01-01
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Henry D Priest
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Douglas W Bryant Todd C Mockler
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Methods in Molecular Biology
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Retinal transcriptome profiling by directional next-generation sequencing using 100 ng of total RNA.
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2012-01-01
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Anand Swaroop
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Matthew J Brooks Harsha Karur Rajasimha
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Methods in Molecular Biology
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Sex-biased transcriptome evolution in Drosophila.
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2012-01-01
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Doris Bachtrog
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Raquel Assis Qi Zhou
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Genome Biology and Evolution
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Defining the molecular profile of planarian pluripotent stem cells using a combinatorial RNAseq, RNA interference and irradiation approach.
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2012-01-01
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Jordi Solana Aziz A. Aboobaker
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Damian Kao Yuliana Mihaylova Farah Jaber-Hijazi Sunir Malla Ray Wilson
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Genome Biology
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Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology.
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2012-01-01
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Gangqing Hu
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Gang Wei Kairong Cui Keji Zhao
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Methods in Enzymology
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Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells.
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2012-01-01
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Yasuyuki Ohkawa Kazu Kobayakawa Seiji Okada Hideyuki Okano
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Hiromi Kumamaru Hirokazu Saiwai Hisakata Yamada Kensuke Kubota Koichi Akashi Yukihide Iwamoto
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Nature Communications
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Computational analysis of RNA-seq.
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2012-01-01
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Scott A. Givan
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Christopher A Bottoms William G Spollen
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Methods in Molecular Biology
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Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.
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2012-01-03
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Robert K. Bradley
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Jason Merkin Nicole J Lambert Christopher B Burge
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PLOS Biology
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Sequencing and de novo analysis of the Chinese Sika deer antler-tip transcriptome during the ossification stage using Illumina RNA-Seq technology.
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2012-01-03
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Baojin Yao
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Yu Zhao Haishan Zhang Mei Zhang Meichen Liu Hailong Liu Juan Li
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Biotechnology Letters
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PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data.
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2012-01-04
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Zemin Ning Peter A.C. 't Hoen Pieternella E Slagboom
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Yanju Zhang Eric-Wubbo Lameijer Kai Ye
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Bioinformatics
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IQSeq: integrated isoform quantification analysis based on next-generation sequencing.
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2012-01-06
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Andrea Sboner Mark Bender Gerstein
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Jiang Du Jing Leng Lukas Habegger Drew McDermott
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PLOS ONE
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Detection of murine leukemia virus in the Epstein-Barr virus-positive human B-cell line JY, using a computational RNA-Seq-based exogenous agent detection pipeline, PARSES.
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2012-01-11
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Melody Baddoo Erik K Flemington
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Zhen Lin Adriane Puetter Joseph Coco Guorong Xu Michael J Strong Xia Wang Claire Fewell Melody Baddoo Christopher Taylor
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Journal of Virology
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Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.
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2012-01-13
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Andrew C. Allan Xue-ren Yin
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Chao Feng Ming Chen Chang-jie Xu Lin Bai Xian Li Ian B Ferguson Kun-song Chen
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BMC Genomics
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Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy
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2012-01-14
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Peadar Ó Gaora Helen M Roche
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Eoin P Brennan Melissa J Morine David W Walsh Sarah A Roxburgh Maja T Lindenmeyer Derek P Brazil Denise M Sadlier Clemens D Cohen GENIE Consortium Catherine Godson Finian Martin
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Biochimica et Biophysica Acta
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The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression.
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2012-01-17
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Cynthia Sharma
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Vinoy K Ramachandran Neil Shearer Jobin J Jacob Arthur Thompson
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BMC Genomics
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FX: an RNA-Seq analysis tool on the cloud.
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2012-01-17
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Young Seok Ju Thomas Bleazard
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Dongwan Hong Arang Rhie Sung-Soo Park Jongkeun Lee Sujung Kim Saet-Byeol Yu Hyun-Seok Park Hwanseok Rhee Hyonyong Chong Kap-Seok Yang Yeon-Su Lee In-Hoo Kim Jin Soo Lee Jong-Il Kim Jeong-Sun Seo
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Bioinformatics
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MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data.
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2012-01-20
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Zhi-xiang Lu Jian Huang
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Shihao Shen Juw Won Park Kimberly A Dittmar Qing Zhou Russ P Carstens Yi Xing
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Nucleic Acids Research
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Application of RNA-Seq transcriptome analysis: CD151 is an Invasion/Migration target in all stages of epithelial ovarian cancer.
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2012-01-24
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Sergio Marchini Robert Fruscio Maurizio D'Incalci
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Rebecca A Mosig Li Lin Emir Senturk Hardik Shah Fei Huang Peter Schlosshauer Samantha Cohen Ravi Sachidanandam Peter Dottino John A Martignetti
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Journal of Ovarian Research
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A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.
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2012-01-26
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Philip Rosenstiel Ueli Grossniklaus Marc W Schmid
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Anja Schmidt Ulrich C Klostermeier Matthias Barann
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PLOS ONE
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Comparison between Normalised and Unnormalised 454-Sequencing Libraries for Small-Scale RNA-Seq Studies.
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2012-01-26
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Robert Ekblom Jon Slate Terry Burke
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Gavin J Horsburgh Tim Birkhead
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Comparative and Functional Genomics
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Pepitome: evaluating improved spectral library search for identification complementarity and quality assessment.
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2012-01-27
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David Tabb
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Surendra Dasari Matthew C Chambers Misti A Martinez Kristin L Carpenter Amy-Joan L Ham Lorenzo J Vega-Montoto
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Journal of Proteome Research
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Removing technical variability in RNA-seq data using conditional quantile normalization.
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2012-01-27
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Kasper D. Hansen Zhijin Wu
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Rafael A Irizarry
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Biostatistics
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The Transcriptome Analysis and Comparison Explorer--T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms.
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2012-01-27
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Lars Kraemer Philip Rosenstiel
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E E R Philipp D Mountfort M Schilhabel S Schreiber
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Bioinformatics
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A new approach to bias correction in RNA-Seq
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2012-01-28
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Walter L. Ruzzo
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Daniel C Jones Xinxia Peng Michael G Katze
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Bioinformatics
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Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation.
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2012-01-28
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Davis J McCarthy Gordon K Smyth
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Yunshun Chen
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Nucleic Acids Research
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SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.
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2012-01-31
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Asa Ben-Hur
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Mark F Rogers Julie Thomas Anireddy Sn Reddy
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Genome Biology
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Phylogenomic analysis of transcriptome data elucidates co-occurrence of a paleopolyploid event and the origin of bimodal karyotypes in Agavoideae (Asparagaceae).
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2012-02-01
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W. Richard McCombie Norman J Wickett Mark W. Chase
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Michael R McKain Yeting Zhang Saravanaraj Ayyampalayam J Chris Pires Claude W dePamphilis Jim Leebens-Mack
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American Journal of Botany
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Spt4 is selectively required for transcription of extended trinucleotide repeats.
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2012-02-01
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Yijuang Chern
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Chia-Rung Liu Chuang-Rung Chang Tzu-Han Wang Wen-Chieh Hsieh Wen-Chuan Shen Chi-Yuan Chang I-Chieh Chu Ning Deng Stanley N Cohen Tzu-Hao Cheng
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Cell
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The Pseudomonas aeruginosa transcriptome in planktonic cultures and static biofilms using RNA sequencing.
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2012-02-03
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Andreas Dötsch Denitsa Eckweiler Susanne Häussler
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Monika Schniederjans Ariane Zimmermann Vanessa Jensen Maren Scharfe Robert Geffers
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PLOS ONE
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Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing.
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2012-02-07
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Miao Tian
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Jie Xiong Xingyi Lu Zhemin Zhou Yue Chang Dongxia Yuan Zhigang Zhou Lei Wang Chengjie Fu Eduardo Orias Wei Miao
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PLOS ONE
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Genome-wide transcriptional profiling of appressorium development by the rice blast fungus Magnaporthe oryzae.
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2012-02-09
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Nick Talbot
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Darren M Soanes Apratim Chakrabarti Konrad H Paszkiewicz Angus L Dawe
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PLOS Pathogens
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Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation.
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2012-02-09
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Jie Huang Yu Zhou Changwei Shao Yi Zhang
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Rui Xiao Peng Tang Bo Yang Hairi Li Hui Sun Xiang-Dong Fu
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Molecular Cell
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Genome-wide analysis of STAT3 binding in vivo predicts effectors of the anti-inflammatory response in macrophages.
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2012-02-09
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Andrew Paul Hutchins Stéphane Poulain
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Diego Miranda-Saavedra
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Blood
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Specific and sensitive mRNA biomarkers for the identification of skin in 'touch DNA' evidence.
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2012-02-09
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Cordula Haas
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E Hanson R Jucker J Ballantyne
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Forensic Science International: Genetics
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Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome.
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2012-02-12
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Jun Wang Bertrand Chin-Ming Tan Zhiyu Peng
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Yanbing Cheng Lin Kang Zhijian Tian Yuankun Zhu Wenwei Zhang Yu Liang Xueda Hu Xuemei Tan Jing Guo Zirui Dong Yan Liang Li Bao
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Nature Biotechnology
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Uterine gene expression in the live-bearing lizard, Chalcides ocellatus, reveals convergence of squamate reptile and mammalian pregnancy mechanisms
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2012-02-14
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Dan L. Warren Michael B Thompson Gunter P Wagner
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Matthew C Brandley Rebecca L Young
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Genome Biology and Evolution
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RNA-Seq Atlas--a reference database for gene expression profiling in normal tissue by next-generation sequencing.
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2012-02-17
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Jens U Marquardt Ugur Sahin
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Markus Krupp Peter R Galle John Castle Andreas Teufel
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Bioinformatics
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RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus.
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2012-02-17
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Eric Peatman
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Chao Li Yu Zhang Ruijia Wang Jianguo Lu Samiran Nandi Sriprakash Mohanty Jeffery Terhune Zhanjiang Liu
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Fish and Shellfish Immunology
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RNA-seq analysis of the functional compartments within the rat placentation site.
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2012-02-21
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Kartik Shankar
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Ying Zhong Ping Kang Michael L Blackburn Michael J Soares Thomas M Badger Horacio Gomez-Acevedo
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Endocrinology
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RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings.
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2012-02-21
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Jian-Hua Mao Jun Wang Huanming Yang
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Shancheng Ren Zhiyu Peng Yongwei Yu Changjun Yin Xin Gao Zilian Cui Jibin Zhang Kang Yi Weidong Xu Chao Chen Fubo Wang Xinwu Guo Ji Lu Jun Yang Min Wei Zhijian Tian Yinghui Guan Liang Tang Chuanliang Xu Linhui Wang Xu Gao Wei Tian Jian Wang Yinghao Sun
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Cell Research
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Comparative analysis of different label-free mass spectrometry based protein abundance estimates and their correlation with RNA-Seq gene expression data.
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2012-02-29
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Alexey I Nesvizhskii
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Kang Ning Damian Fermin
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Journal of Proteome Research
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RNA-Seq quantification of the human small airway epithelium transcriptome
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2012-02-29
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Juan L Rodriguez-Flores
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Neil R Hackett Marcus W Butler Renat Shaykhiev Jacqueline Salit Larsson Omberg Jason G Mezey Yael Strulovici-Barel Guoqing Wang Lukas Didon Ronald G Crystal
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BMC Genomics
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FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads.
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2012-02-29
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Angelo Valleriani
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Gong Zhang Ivan Fedyunin Sebastian Kirchner Chuanle Xiao Zoya Ignatova
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Nucleic Acids Research
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
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2012-03
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Loyal Goff Steven Salzberg Lior Pachter Harold Pimentel John L. Rinn
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Cole Trapnell Adam Roberts Geo Pertea Daehwan Kim David R Kelley
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Nature Protocols
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Characterization and differential expression analysis of complete coding sequences of Vitis vinifera L. sirtuin genes.
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2012-03-03
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Giacomo Morreale Matteo Busconi Luigi Bavaresco
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M Cucurachi A Zanetti C Fogher
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Plant Physiology and Biochemistry
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A new subtype of bone sarcoma defined by BCOR-CCNB3 gene fusion.
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2012-03-04
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Franck Tirode Olivier Delattre
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Gaëlle Pierron Carlo Lucchesi Stéphanie Reynaud Stelly Ballet Sarah Cohen-Gogo Virginie Perrin Jean-Michel Coindre
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Nature Genetics
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The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines.
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2012-03-08
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Gerton Lunter Izortze Santin Michael Sammeth Miriam Cnop Lorella Marselli Piero Marchetti Fernanda Ortis Mark McCarthy
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Décio L Eizirik Thomas Bouckenooghe Guy Bottu Giorgia Sisino Mariana Igoillo-Esteve Maikel L Colli Jenny Barthson Luc Bouwens Linda Hughes Lorna Gregory
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PLOS Genetics
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HnRNP L and L-like cooperate in multiple-exon regulation of CD45 alternative splicing.
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2012-03-08
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Vladimir Benes Gunnar Rätsch Hans-Martin Jäck
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Marco Preussner Silke Schreiner Lee-Hsueh Hung Martina Porstner Albrecht Bindereif
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Nucleic Acids Research
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Application of the whole-transcriptome shotgun sequencing approach to the study of Philadelphia-positive acute lymphoblastic leukemia.
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2012-03-09
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Annalisa Lonetti Giovanni Malerba Alberto Ferrarini Luciano Xumerle Anna Ferrari Cristina Papayannidis Simona Soverini
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I Iacobucci M Sazzini E Giacomelli D Luiselli A Boattini P Garagnani A Vitale F Pane M Baccarani M Delledonne G Martinelli
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Blood Cancer Journal
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An Interspecies Regulatory Network Inferred from Simultaneous RNA-seq of Candida albicans Invading Innate Immune Cells.
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2012-03-12
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Sascha Brunke Karl Kuchler Reinhard Guthke
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Lanay Tierney Jörg Linde Sebastian Müller Juan Camilo Molina Bernhard Hube Ulrike Schöck
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Frontiers in Microbiology
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A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.
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2012-03-19
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Effie Mutasa-Göttgens Berthold Gottgens
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Anagha Joshi Helen F Holmes Peter Hedden
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BMC Genomics
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Transcriptome landscape of the human placenta
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2012-03-27
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Zhi-xiang Lu Jin-kai Wang
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Jinsil Kim Keyan Zhao Peng Jiang Jeffrey C Murray Yi Xing
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BMC Genomics
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Characterization of the longissimus lumborum transcriptome response to adding propionate to the diet of growing Angus beef steers.
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2012-03-27
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Jennifer Thomson Cong-Jun Li
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Ransom L Baldwin Robert W Li Brian J Bequette
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Physiological Genomics
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Alternative splicing networks regulated by signaling in human T cells.
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2012-03-27
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Nicole M Martinez
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Qun Pan Brian S Cole Christopher A Yarosh Grace A Babcock Florian Heyd William Zhu Sandya Ajith Benjamin J Blencowe Kristen W Lynch
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RNA
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RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts
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2012-03-28
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Francisco Peñagaricano
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Ashley M Driver Wen Huang Khawaja R Ahmad Katie S Hackbart Milo C Wiltbank Hasan Khatib
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BMC Genomics
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A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-Seq and conservation analysis
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2012-03-28
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Paolo Miotto Alessandro Ambrosi
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Danilo Pellin Daniela Maria Cirillo Clelia Di Serio
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PLOS ONE
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Identification of allele-specific alternative mRNA processing via transcriptome sequencing.
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2012-03-29
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Jae-Hyung Lee Guangdun Peng Xinshu Xiao
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Gang Li Jae Hoon Bahn Zugen Chen Stanley F Nelson
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Nucleic Acids Research
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Comparative analyses of H3K4 and H3K27 trimethylations between the mouse cerebrum and testis.
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2012-04-01
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Songnian Hu
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Peng Cui Wanfei Liu Yuhui Zhao Qiang Lin Daoyong Zhang Feng Ding Chengqi Xin Zhang Zhang Shuhui Song Fanglin Sun Jun Yu
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Genomics Proteomics and Bioinformatics
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Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.
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2012-04-01
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Ellen V. Rothenberg
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Jingli A Zhang Ali Mortazavi Brian A Williams Barbara J Wold
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Cell
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A zinc-finger-family transcription factor, AbVf19, is required for the induction of a gene subset important for virulence in Alternaria brassicicola.
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2012-04-01
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Igor V Grigoriev
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Akhil Srivastava Robin A Ohm Lindsay Oxiles Fred Brooks Christopher B Lawrence Yangrae Cho
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Molecular Plant-Microbe Interactions
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Identification of shortened 3' untranslated regions from expression arrays.
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2012-04-01
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Andrei Zinovyev Loredana Martignetti Emmanuel Barillot
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Journal of Bioinformatics and Computational Biology
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Improving RNA-Seq Precision with MapAl.
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2012-04-02
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D Kreil
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Paweł P Labaj Bryan E Linggi H Steven Wiley
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Frontiers in Genetics
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RNA-Seq analysis of developing nasturtium seeds (Tropaeolum majus): identification and characterization of an additional galactosyltransferase involved in xyloglucan biosynthesis
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2012-04-02
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Alex Schultink Jacob K Jensen Markus Pauly
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Kenneth Keegstra Curtis G Wilkerson
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Plant Physiology Journal
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Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
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2012-04-03
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Gregory R Grant
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Michael E Hughes Christina Paquin Jack Qian Michael N Nitabach
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Genome Research
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The clonal and mutational evolution spectrum of primary triple-negative breast cancers
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2012-04-04
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Gavin Ha D Yap Daniel Lai Inanc Birol Malachi Griffith Gregg B Morin Suet-feung Chin Christina Curtis Mackey JR Wyeth W Wasserman Steven Jones
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Sohrab P Shah Andrew Roth Rodrigo Goya Arusha Oloumi Yongjun Zhao Gulisa Turashvili Jiarui Ding Kane Tse Gholamreza Haffari Ali Bashashati Leah M Prentice Jaswinder Khattra Angela Burleigh Virginie Bernard Andrew McPherson Karey Shumansky Anamaria Crisan Ryan Giuliany Alireza Heravi-Moussavi Jamie Rosner Richard Varhol Angela Tam Noreen Dhalla Thomas Zeng Kevin Ma Simon K Chan Annie Moradian S-W Grace Cheng Peter Watson Karen Gelmon Stephen Chia Oscar M Rueda Paul D Pharoah Sambasivarao Damaraju Kelly Hoon Timothy Harkins Vasisht Tadigotla Mahvash Sigaroudinia Philippe Gascard Thea Tlsty Joseph F Costello Irmtraud M Meyer Connie J Eaves David Huntsman Martin Hirst Carlos Caldas Marco A Marra Samuel Aparicio
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Nature
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Spatial proximity and similarity of the epigenetic state of genome domains.
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2012-04-04
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Ekaterina E Khrameeva Gennady G Fedonin Mikhail S Gelfand
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Andrey A Mironov Philipp Khaitovich
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PLOS ONE
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Computational inference of mRNA stability from histone modification and transcriptome profiles
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2012-04-10
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Yong Zhang
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Chengyang Wang Rui Tian Qian Zhao Han Xu Clifford A Meyer Cheng Li X Shirley Liu
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Nucleic Acids Research
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Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data.
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2012-04-12
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J Duitama
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Pramod K Srivastava Ion I Măndoiu
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BMC Genomics
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Rapid de novo evolution of X chromosome dosage compensation in Silene latifolia, a plant with young sex chromosomes.
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2012-04-17
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Niklaus Zemp
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Aline Muyle Clothilde Deschamps Sylvain Mousset Alex Widmer Gabriel A B Marais
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PLOS Biology
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KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
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2012-04-19
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Pierre Peterlongo Marie-France Sagot
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Gustavo A T Sacomoto Janice Kielbassa Rayan Chikhi Raluca Uricaru Pavlos Antoniou Vincent Lacroix
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BMC Bioinformatics
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A context-based approach to identify the most likely mapping for RNA-seq experiments.
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2012-04-19
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Ralf Zimmer
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Thomas Bonfert Gergely Csaba Caroline C Friedel
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BMC Bioinformatics
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A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy
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2012-04-24
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Daniel S. Rokhsar Kranthi Varala
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Kankshita Swaminathan Won Byoung Chae Therese Mitros Liang Xie Adam Barling Katarzyna Glowacka Megan Hall Stanislaw Jezowski Ray Ming Matthew Hudson John A Juvik Stephen P Moose
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BMC Genomics
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RNA-SeQC: RNA-seq metrics for quality control and process optimization
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2012-04-25
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Gad Getz Wendy Winckler
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David S DeLuca Joshua Z Levin Andrey Sivachenko Timothy Fennell Marc-Danie Nazaire Chris Williams Michael Reich
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Bioinformatics
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Transcriptome profiling of the intoxication response of Tenebrio molitor larvae to Bacillus thuringiensis Cry3Aa protoxin
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2012-04-25
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Ana Conesa Diana Huestis Jeffrey A Fabrick Juan Luis Jurat-Fuentes
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Brenda Oppert Scot E Dowd Pascal Bouffard Lewyn Li Marcé D Lorenzen Michelle Toutges Jeremy Marshall Cris Oppert
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PLOS ONE
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Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution.
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2012-04-26
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Ralf Zimmer
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Lukas Windhager Thomas Bonfert Kaspar Burger Zsolt Ruzsics Stefan Krebs Stefanie Kaufmann Georg Malterer Anne L'Hernault Markus Schilhabel Stefan Schreiber Philip Rosenstiel Dirk Eick Caroline C Friedel Lars Dölken
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Genome Research
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Transcriptome sequencing revealed significant alteration of cortical promoter usage and splicing in schizophrenia.
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2012-04-27
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Jingqin Wu Xi Wang Murray J Cairns
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Natalie J Beveridge Paul A Tooney Rodney J Scott Vaughan J Carr
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PLOS ONE
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Comprehensive Genomic Profiling Of The Lung Transcriptome In Emphysema And IPF Using RNA-Seq
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2012-05
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John Quackenbush Naftali Kaminski
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Rebecca L. Kusko John Brothers II Gang Liu Lingqi Luo Brenda J. Guardela John R. Tedrow Yuriy Aleksyev Ivana V. Yang Mick Correll Mark Geraci Frank C. Sciurba Marc Lenburg David A. Schwartz Jennifer Beane Avrum Spira
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Concordant signaling pathways produced by pesticide exposure in mice correspond to pathways identified in human Parkinson's disease
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2012-05-01
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Olivier Elemento
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Seema Gollamudi Ashu Johri Noel Y Calingasan Lichuan Yang M Flint Beal
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PLOS ONE
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Utilizing RNA-Seq data for de novo coexpression network inference
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2012-05-03
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Shannon K McWeeney
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Ovidiu D Iancu Sunita Kawane Daniel Bottomly Robert Searles Robert Hitzemann
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Bioinformatics
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Identifying differentially expressed transcripts from RNA-seq data with biological variation.
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2012-05-03
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Magnus Rattray Antti Honkela
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Peter Glaus Antti Honkela
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Bioinformatics
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PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
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2012-05-04
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Douwe Molenaar
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Jumamurat R Bayjanov Vesela Tzeneva Roland J Siezen Sacha A F T van Hijum
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BMC Genomics
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RNA-Seq identifies SNP markers for growth traits in rainbow trout
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2012-05-04
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Timothy D Leeds
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Mohamed Salem Roger L Vallejo Yniv Palti Sixin Liu Annas Sabbagh Caird E Rexroad Jianbo Yao
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PLOS ONE
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Gene mapping via bulked segregant RNA-Seq (BSR-Seq).
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2012-05-07
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Cheng-Ting Yeh Dan Nettleton Patrick S Schnable
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Sanzhen Liu Ho Man Tang
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PLOS ONE
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A simple strand-specific RNA-Seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.
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2012-05-15
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Marie-Laure Yaspo Hans Lehrach
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Marc Sultan Simon Dökel Vyacheslav Amstislavskiy Daniela Wuttig Holger Sültmann Marie-Laure Yaspo
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Biochemical and Biophysical Research Communications
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Transcriptome characterization by RNA-seq unravels the mechanisms of butyrate-induced epigenomic regulation in bovine cells.
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2012-05-15
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Weizhong Li
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Sitao Wu Robert W Li Cong-Jun Li
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PLOS ONE
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Transcriptome sequencing of and microarray development for a Helicoverpa zea cell line to investigate in vitro insect cell-baculovirus interactions
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2012-05-18
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Lars K. Nielsen Robin William Palfreyman Quan Nguyen
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Leslie C L Chan Steven Reid
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PLOS ONE
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RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance.
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2012-05-20
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David J. Lynn Christopher J. Creevey David A Kenny
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Matthew McCabe Sinéad Waters Dermot Morris
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BMC Genomics
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Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns
|
2012-05-24
|
Anders Krogh Jun Wang Johannes Waage Joachim Weischenfeldt Bo Torben Porse Janus Schou Jakobsen Karsten Kristiansen
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Geng Tian Jing Zhao Inge Damgaard
|
Genome Biology
|
Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
|
2012-05-25
|
Gavin Ha Daniel Lai Suet-feung Chin
|
Andrew Roth Ali Bashashati Jiarui Ding Rodrigo Goya Ryan Giuliany Jamie Rosner Arusha Oloumi Karey Shumansky Gulisa Turashvili Martin Hirst Marco A Marra Samuel Aparicio Sohrab P Shah Carlos Caldas
|
Genome Research
|
Dissect: detection and characterization of novel structural alterations in transcribed sequences
|
2012-06-01
|
Inanc Birol
|
Deniz Yorukoglu Faraz Hach Lucas Swanson Colin C Collins S Cenk Sahinalp
|
Bioinformatics
|
Trehalose-enhanced isolation of neuronal sub-types from adult mouse brain.
|
2012-06-01
|
Piero Carninci Yukihiko Noro
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Alka Saxena Akiko Wagatsuma Takenobu Kuji Atsuko Asaka-Oba Akira Watahiki Cecile Gurnot Michela Fagiolini Takao K Hensch
|
BioTechniques
|
Transcriptomic signatures of attachment, NF-κB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection.
|
2012-06-02
|
Eric Peatman Shikai Liu
|
Fanyue Sun Chao Li Yanliang Jiang Zunchun Zhou Zhanjiang Liu
|
Developmental and Comparative Immunology
|
RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
|
2012-06-08
|
John E. Lunn Björn Usadel Alisdair R Fernie Mark Stitt
|
Marc Lohse Anthony M Bolger Axel Nagel
|
Nucleic Acids Research
|
Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites
|
2012-06-08
|
Gabriel Kreiman Nicole Cloonan Sean M. Grimmond
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Martin Hemberg Jesse M Gray Scott Kuersten Michael E Greenberg
|
Nucleic Acids Research
|
Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray.
|
2012-06-10
|
Marek Żywicki Marcel Scheideler Mathieu Rederstorff
|
Konstantinia Skreka Michael Karbiener Alexander Hüttenhofer
|
Journal of Nucleic Acids
|
Modeling gene expression using chromatin features in various cellular contexts
|
2012-06-13
|
Roderic Guigó i Serra Mark Bender Gerstein Ewan Birney Sarah Djebali Xianjun Dong Anshul Kundaje Thomas R. Gingeras
|
Melissa C Greven James B Brown Chao Cheng Zhiping Weng
|
Genome Biology
|
Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma.
|
2012-06-13
|
Stephanie Ma Li Fu Xin-Yuan Guan Xin-Yuan Guan
|
Jessie Y J Bao Pak Shing Kwan Yuen Piu Chan Carol M Tong Na Zhang Amy H Y Tong Yan-Ru Qin Sai Wah Tsao Kwok Wah Chan Si Lok
|
Gastroenterology
|
Alternative splicing regulated by butyrate in bovine epithelial cells.
|
2012-06-14
|
Wen Huang Weizhong Li
|
Sitao Wu Congjun Li Robert W Li
|
PLOS ONE
|
Bellerophontes: an RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model.
|
2012-06-17
|
Alberto Ferrarini Elisa Ficarra Simona Soverini Giovanni Martinelli Ilaria Iacobucci
|
Francesco Abate Andrea Acquaviva Giulia Paciello Carmelo Foti Massimo Delledonne Enrico Macii
|
Bioinformatics
|
Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology.
|
2012-06-18
|
Sean Doyle David J. Lynn Bernadette Earley
|
Aran O'Loughlin Mark McGee Matthew McCabe
|
BMC Genomics
|
Detecting differential usage of exons from RNA-seq data
|
2012-06-21
|
Alejandro Reyes Simon Anders Wolfgang Huber
|
|
Genome Research
|
PM-Seq: Using Finite Poisson Mixture Models for RNA-Seq Data Analysis and Transcript Expression Level Quantification
|
2012-06-21
|
Zhaohui Steve Qin
|
Han Wu Yu Zhu
|
Statistics in biosciences
|
Expressed pseudogenes in the transcriptional landscape of human cancers
|
2012-06-22
|
John R. Prensner Shanker Kalyana-Sundaram Chandan Kumar-Sinha Irfan Asangani Nallasivam Palanisamy
|
Sunita Shankar Dan R Robinson Yi-Mi Wu Xuhong Cao Vishal Kothari Robert J Lonigro Matthew K Iyer Terrence Barrette Achiraman Shanmugam Saravana M Dhanasekaran Arul M Chinnaiyan
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Cell
|
RNA-Seq and human complex diseases: recent accomplishments and future perspectives.
|
2012-06-27
|
Valerio Costa
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Marianna Aprile Roberta Esposito Alfredo Ciccodicola
|
European Journal of Human Genetics
|
FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data.
|
2012-06-27
|
Richard W Francis Kim Carter Denise Anderson Alex H. Beesley
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Katherine Thompson-Wicking Ursula R Kees
|
PLOS ONE
|
A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.
|
2012-06-29
|
Gregory J. Kato
|
Nalini Raghavachari Jennifer Barb Yanqin Yang Poching Liu Kimberly Woodhouse Daniel Levy Christopher J O'Donnell Peter J Munson
|
BMC Medical Genomics
|
SAVoR: a server for sequencing annotation and visualization of RNA structures
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2012-07
|
Otto Valladares Fan Li
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Paul Ryvkin Daniel M Childress Brian D Gregory Li-San Wang
|
Nucleic Acids Research
|
Digging in the RNA-seq Garbage: Evaluating the Characteristics of Unmapped RNA-seq Reads in Normal Tissues
|
2012-07
|
Federica Cavallo
|
Matteo Carrara Maddalena Arigoni Raffaele A. Calogero
|
|
Molecular and developmental contributions to divergent pigment patterns in marine and freshwater sticklebacks
|
2012-07-01
|
Catherine L Peichel
|
Anna K Greenwood Jennifer N Cech
|
Evolution & Development
|
Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions
|
2012-07-01
|
Iros Barozzi Gioacchino Natoli
|
Dev M Bhatt Amy Pandya-Jones Ann-Jay Tong Michelle M Lissner Douglas L Black Stephen T Smale
|
Cell
|
RNA-seq analysis of the C. briggsae transcriptome.
|
2012-07-06
|
Bora Uyar
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Jeffrey S C Chu Ismael A Vergara Shu Yi Chua Martin R Jones Tammy Wong David L Baillie Nansheng Chen
|
Genome Research
|
Incorporating RNA-seq data into the zebrafish Ensembl genebuild
|
2012-07-12
|
Simon White
|
John E Collins Stephen M J Searle Derek L Stemple
|
Genome Research
|
Paired-end sequencing of Fosmid libraries by Illumina.
|
2012-07-16
|
Gad Getz Chad Nusbaum Yotam Drier
|
Louise J S Williams Diana G Tabbaa Na Li Aaron M Berlin Terrance P Shea Iain Maccallum Michael S Lawrence Sarah K Young David B Jaffe Andreas Gnirke
|
Genome Research
|
Inflammatory priming predisposes mice to age-related retinal degeneration.
|
2012-07-17
|
Krzysztof Palczewski
|
Debarshi Mustafi Tadao Maeda Hideo Kohno Joseph H Nadeau
|
Journal of Clinical Investigation
|
RNA processing in the minimal organism Nanoarchaeum equitans
|
2012-07-18
|
L Randau
|
Lennart Randau
|
Genome Biology
|
Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton
|
2012-07-20
|
Daojun Yuan
|
Xiyan Yang Xianlong Zhang Fangyan Jin Yunchao Zhang Jiao Xu
|
BMC Plant Biology
|
Genomic imprinting absent in Drosophila melanogaster adult females.
|
2012-07-20
|
C Joel McManus Brenton R. Graveley
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Joseph D Coolon Kraig R Stevenson Patricia J Wittkopp
|
Cell Reports
|
Differential gene expression in tamoxifen-resistant breast cancer cells revealed by a new analytical model of RNA-Seq data
|
2012-07-23
|
Willard M. Freeman Kent Vrana
|
Kathryn J Huber-Keener Xiuping Liu Zhong Wang Yaqun Wang Song Wu Maricarmen D Planas-Silva Xingcong Ren Yan Cheng Yi Zhang Chang-Gong Liu Jin-Ming Yang Rongling Wu
|
PLOS ONE
|
Metabolic Regulation of "Ca. Methylacidiphilum Fumariolicum" SolV Cells Grown Under Different Nitrogen and Oxygen Limitations.
|
2012-07-25
|
Huub J.M. Op den Camp
|
Ahmad F Khadem Arjan Pol Adam S Wieczorek Mike S M Jetten
|
Frontiers in Microbiology
|
Effects of drought on gene expression in maize reproductive and leaf meristem tissue revealed by RNA-Seq.
|
2012-07-26
|
Akshay Kakumanu Andy Pereira
|
Madana M R Ambavaram Curtis Klumas Arjun Krishnan Utlwang Batlang Elijah Myers Ruth Grene
|
Plant Physiology
|
Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells.
|
2012-07-27
|
Guoping Fan
|
Ganlu Hu Kevin Huang Juehua Yu Sailesh Gopalakrishna-Pillai Jun Kong He Xu Zhenshan Liu Kunshan Zhang Jun Xu Yuping Luo Siguang Li Yi E Sun Linda E Iverson Zhigang Xue
|
PLOS ONE
|
Identification of novel transcripts deregulated in buccal cancer by RNA-seq.
|
2012-07-27
|
Ajai K. Tripathi Subhash J Jakhesara Chaitanya G. Joshi
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Manisha R Sajnani Amrutlal K Patel Vaibhav D Bhatt Viral B Ahir Vangipuram Shankar Siddharth Shah Tejas M Shah Prakash G Koringa
|
Gene
|
Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis
|
2012-07-29
|
Anastassios Vourekas Panagiotis Alexiou Manolis Maragkakis Yohei Kirino Zissimos Mourelatos
|
Qi Zheng Brian D Gregory
|
Nature Structural & Molecular Biology
|
A mutation in the PP2C phosphatase gene in a Staphylococcus aureus USA300 clinical isolate with reduced susceptibility to vancomycin and daptomycin.
|
2012-07-30
|
Karla D Passalacqua
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Sarah W Satola Emily K Crispell Timothy D Read
|
Antimicrobial Agents and Chemotherapy
|
easyRNASeq: a bioconductor package for processing RNA-Seq data
|
2012-07-30
|
Eileen E. M. Furlong Lars M Steinmetz
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Nicolas Delhomme Ismaël Padioleau
|
Bioinformatics
|
RNASeq profiling of UTR expression during neuronal plasticity.
|
2012-07-31
|
Robert M. Flight Jeffrey C. Petruska
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Benjamin J Harrison Abdallah Eteleeb Eric C Rouchka
|
BMC Bioinformatics
|
Recurrent R-spondin fusions in colon cancer.
|
2012-08-01
|
Robert Gentleman
|
Somasekar Seshagiri Eric W Stawiski Steffen Durinck Zora Modrusan Elaine E Storm Caitlin B Conboy Subhra Chaudhuri Yinghui Guan Vasantharajan Janakiraman Bijay S Jaiswal Joseph Guillory Connie Ha Gerrit J P Dijkgraaf Jeremy Stinson Florian Gnad Melanie A Huntley Jeremiah D Degenhardt Peter M Haverty Richard Bourgon Weiru Wang Hartmut Koeppen Timothy K Starr Zemin Zhang David A Largaespada Thomas D Wu Frederic J de Sauvage
|
Nature
|
Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.
|
2012-08-04
|
Stéphane Poulain Andrew Paul Hutchins Hodaka Fujii
|
Diego Miranda-Saavedra
|
Genomics
|
Transcriptome profiling of resistant and susceptible Cavendish banana roots following inoculation with Fusarium oxysporum f. sp. cubense tropical race 4.
|
2012-08-05
|
Altus Viljoen
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Chun-Yu Li Gui-Ming Deng Jing Yang Yan Jin Rui-Bin Kuang Cun-Wu Zuo Zhi-Cheng Lv Qiao-Song Yang Ou Sheng Yue-Rong Wei Chun-Hua Hu Tao Dong Gan-Jun Yi
|
BMC Genomics
|
Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples.
|
2012-08-08
|
Vincent Lynch
|
Günter P Wagner Koryu Kin
|
Theory in Biosciences
|
RNA-Seq provides new insights in the transcriptome responses induced by the carcinogen benzo[a]pyrene.
|
2012-08-13
|
Stan Gaj Hans Lehrach Ralf Herwig Jos Kleinjans
|
Joost van Delft Stan Gaj Matthias Lienhard Marcus W Albrecht Alexander Kirpiy Karen Brauers Sandra Claessen Daneida Lizarraga
|
Toxicological Sciences
|
Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish.
|
2012-08-13
|
Ian A Johnston
|
Graham R Scott
|
Proceedings of the National Academy of Sciences of the United States of America
|
Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins.
|
2012-08-16
|
Peter A. DiMaggio Barry M Zee
|
Gary LeRoy Iouri Chepelev Mario A Blanco Keji Zhao Benjamin A Garcia
|
Genome Biology
|
Proteomics and deep sequencing comparison of seasonally active venom glands in the platypus reveals novel venom peptides and distinct expression profiles.
|
2012-08-16
|
Marilyn Renfree Anthony T. Papenfuss Emily S Wong Camilla M Whittington Glenn F King
|
David Morgenstern Ehtesham Mofiz Sara Gombert Katrina M Morris Peter Temple-Smith Wesley C Warren Katherine Belov
|
Molecular & Cellular Proteomics
|
RNA-seq transcriptome analysis of male and female zebra finch cell lines
|
2012-08-21
|
Christopher N. Balakrishnan Ya-Chi Lin Sarah E London David F. Clayton
|
Christopher N Balakrishnan Ya-Chi Lin Sarah E London David F Clayton
|
Genomics
|
Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data
|
2012-08-21
|
Shaojie Zhang
|
Peter Tonner Vinodh Srinivasasainagendra Degui Zhi
|
BMC Genomics
|
Research resource: RNA-Seq reveals unique features of the pancreatic β-cell transcriptome.
|
2012-08-21
|
Michael McManus Hail Kim
|
Gregory M Ku Ian W Vaughn Matthew J Hangauer Chang Myung Oh Michael S German
|
Molecular Endocrinology
|
shortran: a pipeline for small RNA-seq data analysis.
|
2012-08-22
|
Stig Uggerhøj Andersen Jens Stougaard
|
Vikas Gupta Katharina Markmann Christian N S Pedersen
|
Bioinformatics
|
Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis
|
2012-08-22
|
Karla D Passalacqua
|
Anjana Varadarajan Charlotte Weist Brian D Ondov Benjamin Byrd Timothy D Read Nicholas H Bergman
|
PLOS ONE
|
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.
|
2012-08-24
|
Yong Zhang
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Jianxing Feng Clifford A Meyer Qian Wang Jun S Liu X Shirley Liu
|
Bioinformatics
|
An injury-response mechanism conserved across kingdoms determines entry of the fungus Trichoderma atroviride into development.
|
2012-08-27
|
Miguel Hernández-Oñate Alfredo Herrera-Estrella
|
Edgardo U Esquivel-Naranjo Artemio Mendoza-Mendoza Alison Stewart
|
Proceedings of the National Academy of Sciences of the United States of America
|
A simple and novel method for RNA-seq library preparation of single cell cDNA analysis by hyperactive Tn5 transposase.
|
2012-08-28
|
Anna Terry Niall G. Campbell Charles Mein
|
Scott Brouilette Scott Kuersten Monika Bozek Kerith-Rae Dias Leena Bhaw-Rosun Yasunori Shintani Steven Coppen Chiho Ikebe Vinit Sawhney Masahiro Kaneko Nobuko Tano Hidekazu Ishida Ken Suzuki Kenta Yashiro
|
Developmental Dynamics
|
A putative role for amino acid permeases in sink-source communication of barley tissues uncovered by RNA-seq.
|
2012-08-30
|
Winfriede Weschke
|
Stefan Kohl Julien Hollmann Frank R Blattner Volodymyr Radchuk Franka Andersch Burkhard Steuernagel Thomas Schmutzer Uwe Scholz Karin Krupinska Hans Weber
|
BMC Plant Biology
|
Allele-biased expression in differentiating human neurons: implications for neuropsychiatric disorders
|
2012-08-30
|
Deyou Zheng
|
Mingyan Lin Anastasia Hrabovsky Erika Pedrosa Tao Wang Herbert M Lachman
|
PLOS ONE
|
RNA-Seq of early-infected poplar leaves by the rust pathogen Melampsora larici-populina uncovers PtSultr3;5, a fungal-induced host sulfate transporter
|
2012-08-30
|
Nicolas Rouhier Julie Poulain Benjamin Petre Sébastien Duplessis Corinne Da Silva Francis Martin Emmanuelle Morin Annegret Kohler
|
Emilie Tisserant Stéphane Hacquard Christine Delaruelle
|
PLOS ONE
|
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
|
2012-09
|
Roderic Guigó i Serra Sarah Djebali Rory Johnson Thomas R. Gingeras
|
Hagen Tilgner David G Knowles Carrie A Davis Sudipto Chakrabortty João Curado Michael Snyder
|
Genome Research
|
Dual RNA-seq of pathogen and host.
|
2012-09-01
|
Alexander Westermann Jörg Vogel
|
Stanislaw A Gorski
|
Nature Reviews Microbiology
|
Long noncoding RNAs are rarely translated in two human cell lines
|
2012-09-01
|
Yanbao Yu Anshul Kundaje Brian D Strahl Krzysztof Krajewski
|
Balázs Bánfai Hui Jia Jainab Khatun Emily Wood Brian Risk William E Gundling Harsha P Gunawardena Ling Xie Xian Chen Peter Bickel Morgan C Giddings James B Brown Leonard Lipovich
|
Genome Research
|
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.
|
2012-09-01
|
Andrea Tanzer Jose M Gonzalez Bronwen Aken Tim Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Cédric Howald Thibaut Hourlier Thomas Derrien Alexandre Reymond Simon White Adam Frankish
|
Jacqueline Chrast Nathalie Walters Jan-Hinnerk Vogel Stephen Searle
|
Genome Research
|
Initial characterization of shade avoidance response suggests functional diversity between Populus phytochrome B genes.
|
2012-09-03
|
Xiaohan Yang Gerald A Tuskan Sara S Jawdy Lee Gunter Stan D Wullschleger
|
Abhijit A Karve Sara M Allen David J Weston
|
New Phytologist
|
The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program.
|
2012-09-04
|
Silvia Dal Santo Giovanni Battista Tornielli Vittorio Murino Luca Venturini Lorenzo Farina
|
Marianna Fasoli Sara Zenoni Anita Zamboni Andrea Porceddu Manuele Bicego Alberto Ferrarini Massimo Delledonne Mario Pezzotti
|
The Plant Cell
|
A novel computational strategy to identify A-to-I RNA editing sites by RNA-Seq data: de novo detection in human spinal cord tissue
|
2012-09-05
|
Graziano Pesole Angela Gallo Ernesto Picardi
|
Federica Galeano Sara Tomaselli
|
PLOS ONE
|
Modelling and simulating generic RNA-Seq experiments with the flux simulator.
|
2012-09-07
|
Roderic Guigó i Serra Michael Sammeth
|
Thasso Griebel Benedikt Zacher Paolo Ribeca Emanuele Raineri Vincent Lacroix
|
Nucleic Acids Research
|
Comparative transcriptome analyses of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from Kenya by RNA-Seq
|
2012-09-07
|
Mariangela Bonnizoni Guiyun Yan
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Yaw Afrane William Augustine Dunn Francis K Atieli Goufa Zhou Daibin Zhong Jun Li Andrew Githeko
|
PLOS ONE
|
Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis.
|
2012-09-08
|
Taejoon Kwon Rosa A Uribe Jeffrey M Gross
|
|
Developmental Biology
|
A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
|
2012-09-10
|
Jens Nielsen Natapol Pornputtapong Linn Fagerberg Intawat Nookaew
|
Marta Papini Gionata Scalcinati Matthias Uhlén
|
Nucleic Acids Research
|
Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production.
|
2012-09-11
|
Todd P Michael
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Chongyuan Luo David J Sidote Yi Zhang Randall A Kerstetter Eric Lam
|
The Plant Journal
|
The bench scientist's guide to statistical analysis of RNA-Seq data.
|
2012-09-14
|
Craig R Yendrek
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Elizabeth A Ainsworth Jyothi Thimmapuram
|
BMC Research Notes
|
Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide.
|
2012-09-17
|
Georgi K Marinov Peter Dervan
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Jevgenij A Raskatov Nicholas G Nickols Amanda E Hargrove Barbara Wold
|
Proceedings of the National Academy of Sciences of the United States of America
|
Heterogeneous nuclear ribonucleoprotein L-like (hnRNPLL) and elongation factor, RNA polymerase II, 2 (ELL2) are regulators of mRNA processing in plasma cells
|
2012-09-18
|
Harri Lähdesmäki Vivek Anantharaman Lakshminarayanan Aravind Tarmo Aijö John Gagnon Xing Chang
|
Micah J Benson Tarmo Aijö Utz J Pape Juha-Pekka Pursiheimo Shalini Oberdoerffer X Shirley Liu Riitta Lahesmaa Anjana Rao
|
Proceedings of the National Academy of Sciences of the United States of America
|
Functional transcriptomics of a migrating cell in Caenorhabditis elegans.
|
2012-09-18
|
Erich M Schwarz Paul W. Sternberg
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Mihoko Kato
|
Proceedings of the National Academy of Sciences of the United States of America
|
Differential Expression Analysis for RNA-Seq Data.
|
2012-09-20
|
Alok Bhattacharya
|
Rashi Gupta Isha Dewan Richa Bharti
|
ISRN bioinformatics
|
A cost-effective method for Illumina small RNA-Seq library preparation using T4 RNA ligase 1 adenylated adapters
|
2012-09-20
|
Yi Zheng
|
Yun-Ru Chen Bao Liu Silin Zhong Jim Giovannoni Zhangjun Fei
|
Plant Methods
|
High-resolution transcriptome of human macrophages.
|
2012-09-21
|
Joachim Schultze Andrea Nino-Castro
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Marc Beyer Michael R Mallmann Jia Xue Andrea Staratschek-Jox Daniela Vorholt Wolfgang Krebs Daniel Sommer Jil Sander Christina Mertens Susanne V Schmidt
|
PLOS ONE
|
A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.
|
2012-09-22
|
Hao Wu Zhijin Wu
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Chi Wang
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Biostatistics
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Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.
|
2012-09-24
|
Axel Künstner
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Nagarjun Vijay Jelmer W Poelstra Jochen B W Wolf
|
Molecular Ecology
|
RNA-Seq Assembly - Are We There Yet?
|
2012-09-25
|
Andrea Bräutigam
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Simon Schliesky Udo Gowik Andreas P M Weber
|
Frontiers in Plant Science
|
Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3.
|
2012-09-26
|
Peggy Farnham
|
Seth Frietze Rui Wang Lijing Yao Yu Gyoung Tak Zhenqing Ye Malaina Gaddis Heather Witt Victor X Jin
|
Genome Biology
|
A next-generation sequencing approach to study the transcriptomic changes during the differentiation of physarum at the single-cell level.
|
2012-10-01
|
Israel Barrantes Jeremy Leipzig
|
Wolfgang Marwan
|
Gene Regulation and Systems Biology
|
The Snail family member Worniu is continuously required in neuroblasts to prevent Elav-induced premature differentiation
|
2012-10-01
|
Sen-Lin Lai
|
Michael R Miller Kristin J Robinson Chris Q Doe
|
Developmental Cell
|
Dual lineage-specific expression of Sox17 during mouse embryogenesis.
|
2012-10-01
|
Momoko Yoshimoto Mark A. Magnuson Elisabetta Manduchi Anne Grapin-Botton
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Eunyoung Choi Marine R C Kraus Laurence A Lemaire Sasidhar Vemula Leah A Potter Christian J Stoeckert
|
Stem Cells
|
Comprehensive genomic profiling of the lung transcriptome in emphysema and idiopathic pulmonary fibrosis using RNA-Seq.
|
2012-10-01
|
Jennifer Beane John Quackenbush Naftali Kaminski
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Rebecca L Kusko John Brothers Gang Liu Lingqi Luo Brenda Juan Guardela John Tedrow Yuriy Aleksyev Ivana V Yang Mick Correll Mark Geraci Frank Sciurba Marc Lenburg David A Schwartz Avrum Spira
|
BMC Proceedings
|
SERE: single-parameter quality control and sample comparison for RNA-Seq.
|
2012-10-03
|
Rahul Kanwar
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Stefan K Schulze Meike Gölzenleuchter Terry M Therneau Andreas S Beutler
|
BMC Genomics
|
Evaluation of different reference based annotation strategies using RNA-Seq - a case study in Drososphila pseudoobscura.
|
2012-10-03
|
Anton Suvorov
|
Nicola Palmieri Viola Nolte Carolin Kosiol Christian Schlötterer
|
PLOS ONE
|
Systems and trans-system level analysis identifies conserved iron deficiency responses in the plant lineage.
|
2012-10-05
|
David Casero Eugen Urzica Crysten E Blaby-Haas Matteo Pellegrini Sabeeha Merchant
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Hiroaki Yamasaki Scott I Hsieh Lital N Adler Steven J Karpowicz Steven G Clarke Joseph A Loo
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The Plant Cell
|
Identification of novel splice variants in horn cancer by RNA-Seq analysis in Zebu cattle.
|
2012-10-10
|
Subhash J Jakhesara Chaitanya G. Joshi Ajai K. Tripathi
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Amrutlal K Patel Vaibhav D Bhatt Manisha R Sajnani Prakash G Koringa
|
Genomics
|
New partners in regulation of gene expression: the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain.
|
2012-10-11
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Julien Rougeot Anne Coléno-Costes Jean-Michel Gibert Frédérique Peronnet Stéphane Le Crom
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Suk Min Jang Augustin de Vanssay Tahar Bouceba Neel B Randsholt Emmanuèle Mouchel-Vielh Sébastien Bloyer
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PLOS Genetics
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Faster-X evolution of gene expression in Drosophila
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2012-10-11
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Richard P Meisel
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John H Malone Andrew G Clark
|
PLOS Genetics
|
Transcriptome assembly and isoform expression level estimation from biased RNA-Seq reads.
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2012-10-11
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Wei Li
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Tao Jiang
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Bioinformatics
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Identification of hundreds of novel UPF1 target transcripts by direct determination of whole transcriptome stability.
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2012-10-12
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Naoto Imamachi Hidenori Tani
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Kazi Abdus Salam Rena Mizutani Kenichi Ijiri Takuma Irie Tetsushi Yada Yutaka Suzuki Nobuyoshi Akimitsu
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RNA Biology
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The proteome of copper, iron, zinc, and manganese micronutrient deficiency in Chlamydomonas reinhardtii.
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2012-10-13
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Eugen Urzica David Casero Matteo Pellegrini Sabeeha Merchant
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Scott I Hsieh Madeli Castruita Davin Malasarn Jonathan Erde M Dudley Page Hiroaki Yamasaki Joseph A Loo
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Molecular & Cellular Proteomics
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High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.
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2012-10-15
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Hans Ellegren
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Benoit Nabholz Jochen B W Wolf
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Molecular Biology and Evolution
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The biology of nematode- and IL4Rα-dependent murine macrophage polarization in vivo as defined by RNA-Seq and targeted lipidomics.
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2012-10-16
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Graham D Thomas Dominik Ruckerl Phillip D. Whitfield Mark Blaxter Judith Allen
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Benjamin H Maskrey
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Blood
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A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites.
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2012-10-17
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David R. Colquhoun Jürgen Hartler Gerhard G Thallinger Jesus Martinez-Barnetche Antonis Rokas Rhoel Dinglasan
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Ceereena Ubaida Mohien Derrick K Mathias John G Gibbons Jennifer S Armistead Maria C Rodriguez Mario Henry Rodriguez Nathan J Edwards David R Graham
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Molecular & Cellular Proteomics
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Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.
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2012-10-23
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Matteo Benelli Marco Severgnini Alberto Magi
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Chiara Pescucci Giuseppina Marseglia Francesca Torricelli
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Bioinformatics
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Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period.
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2012-10-23
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Paul A McGettigan Jane A Irwin Alan Baird Brendan Loftus
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Katarzyna Pluta Colm J Reid John A Browne Tharmala Tharmalingam Anthony Corfield Alexander C O Evans Stephen D Carrington
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Physiological Genomics
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Transcriptomic profiling of the oyster pathogen Vibrio splendidus opens a window on the evolutionary dynamics of the small RNA repertoire in the Vibrio genus
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2012-10-24
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Daniel Gautheret Philippe Bouloc Annick Jacq
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Claire Toffano-Nioche An N Nguyen Claire Kuchly Alban Ott
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RNA
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STAR: ultrafast universal RNA-seq aligner
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2012-10-25
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Philippe Batut Thomas R. Gingeras
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Alexander Dobin Carrie A Davis Felix Schlesinger Jorg Drenkow Chris Zaleski Sonali Jha Mark Chaisson
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Bioinformatics
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Transcription factor Amr1 induces melanin biosynthesis and suppresses virulence in Alternaria brassicicola
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2012-10-25
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Igor V Grigoriev
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Yangrae Cho Akhil Srivastava Robin A Ohm Christopher B Lawrence Koon-Hui Wang Sharadchandra P Marahatta
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PLOS Pathogens
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RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.
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2012-10-25
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Matthew Berriman
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Jonathan D Stoltzfus Samuel Minot Thomas J Nolan James B Lok
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PLOS Neglected Tropical Diseases
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The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq.
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2012-10-25
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Nolan Kane Brook T Moyers Sébastien Renaut Loren H. Rieseberg
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Christopher J Grassa
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Biology
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Identification of cold-responsive genes in a New Zealand alpine stick insect using RNA-Seq.
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2012-10-27
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Richard D Newcomb Thomas R. Buckley Duckchul Park Brent J Sinclair Alice B Dennis Luke T Dunning
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
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Identification of PADI2 as a potential breast cancer biomarker and therapeutic target.
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2012-10-30
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Obi Griffith Venkataraman Subramanian John L. McElwee Brian D Cherrington Louise R Howe
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Sunish Mohanan Heike C Breuer Lynne J Anguish Ashley M Palmer Corey P Causey Paul R Thompson Joe W Gray Scott A Coonrod
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BMC Cancer
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Interaction of cyclin-dependent kinase 12/CrkRS with cyclin K1 is required for the phosphorylation of the C-terminal domain of RNA polymerase II
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2012-11
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Jerry F. Tien Malachi Griffith Gregg B Morin
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S-W Grace Cheng Michael A Kuzyk Annie Moradian Taka-Aki Ichu Vicky C-D Chang Sarah E Vollett Marco A Marra
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Molecular and Cellular Biology
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Age-related changes of gene expression in the neocortex: preliminary data on RNA-Seq of the transcriptome in three functionally distinct cortical areas.
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2012-11-01
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Dean Palejev Flora M. Vaccarino
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Oksana Yu Naumova Natalia V Vlasova Maria Lee Sergei Yu Rychkov Olga N Babich Elena L Grigorenko
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Development and Psychopathology
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Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses
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2012-11-05
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Andrew M Carroll Caroline Meharg David J Vandenbergh
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Arimantas Lionikas Jonathan Mj Derry Aivaras Ratkevicius David A Blizard
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BMC Genomics
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Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote
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2012-11-05
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Shikai Liu Eric Peatman Geoff Waldbieser Huseyin Kucuktas
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Yu Zhang Zunchun Zhou Geoff Waldbieser Fanyue Sun Jianguo Lu Jiaren Zhang Yanliang Jiang Hao Zhang Xiuli Wang K V Rajendran Lester Khoo Zhanjiang Liu
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BMC Genomics
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Novel BRD4-NUT fusion isoforms increase the pathogenic complexity in NUT midline carcinoma.
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2012-11-05
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Adrian K. Charles Alex H. Beesley
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K Thompson-Wicking R W Francis A Stirnweiss E Ferrari M D Welch E Baker A R Murch A M Gout K W Carter M B Phillips U R Kees
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Oncogene
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Prediction of altered 3'- UTR miRNA-binding sites from RNA-Seq data: the swine leukocyte antigen complex (SLA) as a model region
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2012-11-06
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Marie-Laure Endale Ahanda Dario Beraldi Jordi Estellé Claire Rogel-Gaillard James M Reecy
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Eric R Fritz Zhi-Liang Hu Ole Madsen Martien A M Groenen Ronan Kapetanovic David A Hume Robert R R Rowland Joan K Lunney Elisabetta Giuffra
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PLOS ONE
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Simultaneous RNA-seq analysis of a mixed transcriptome of rice and blast fungus interaction.
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2012-11-06
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Takeshi Itoh
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Yoshihiro Kawahara Youko Oono Hiroyuki Kanamori Takashi Matsumoto Eiichi Minami
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PLOS ONE
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DiffSplice: the genome-wide detection of differential splicing events with RNA-seq.
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2012-11-15
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D. Neil Hayes
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Yin Hu Yan Huang Ying Du Christian F Orellana Darshan Singh Amy R Johnson Anaïs Monroy Pei-Fen Kuan Scott M Hammond Liza Makowski Scott H Randell Derek Y Chiang Corbin Jones Yufeng Liu Jan F Prins Jinze Liu
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Nucleic Acids Research
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Methods, Challenges and Potentials of Single Cell RNA-seq.
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2012-11-16
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Daniel Hebenstreit
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Biology
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The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.
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2012-11-20
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Aurelien L Carlier Christian H Ahrens Ulrich Omasits Gabriella Pessi
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Nadine Schmid Yinyue Deng Claudio Aguilar Alexander Grunau Lian-Hui Zhang Leo Eberl
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PLOS ONE
|
Intron-centric estimation of alternative splicing from RNA-seq data.
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2012-11-21
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Roderic Guigó i Serra
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Dmitri D Pervouchine David G Knowles
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Bioinformatics
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High-throughput sequencing of the melanoma genome.
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2012-11-22
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Janet Kelso
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Manfred Kunz Michael Dannemann
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Experimental Dermatology
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A comprehensive analysis of the Manduca sexta immunotranscriptome.
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2012-11-23
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Haobo Jiang
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Ramesh T Gunaratna
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Developmental and Comparative Immunology
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Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching.
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2012-11-24
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Charles Plessy Piero Carninci
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Dave T P Tang Md Salimullah Ana Maria Suzuki Raffaella Calligaris Stefano Gustincich
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Nucleic Acids Research
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iReckon: simultaneous isoform discovery and abundance estimation from RNA-seq data
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2012-11-29
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Derek Y Chiang Michael Brudno
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Aziz M Mezlini Eric J M Smith Marc Fiume Orion Buske Gleb L Savich Sohrab Shah Sam Aparicio Anna Goldenberg
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Genome Research
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Nuclear RNA sequencing of the mouse erythroid cell transcriptome
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2012-11-29
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Chih-Yu Chen Jennifer A. Mitchell Ieuan Clay Peter Fraser
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David Umlauf Catherine A Moir Christopher H Eskiw Stefan Schoenfelder Lyubomira Chakalova Takashi Nagano
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PLOS ONE
|
The diverse applications of RNA-seq for functional genomic studies in Aspergillus fumigatus.
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2012-12-01
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Xiaofan Zhou Antonis Rokas
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John G Gibbons Anne Beauvais Jean-Paul Latgé
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Annals of the New York Academy of Sciences
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An RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells.
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2012-12-04
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Songnian Hu
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Lina Ma Linghu Nie Jing Liu Bing Zhang Shuhui Song Min Sun Jin Yang Yadong Yang Xiangdong Fang Yongliang Zhao Jun Yu
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Genomics Proteomics and Bioinformatics
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A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.
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2012-12-06
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Alexander Stark Denes Hnisz Karl Kuchler
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Anaïs F Bardet Clarissa J Nobile Andriy Petryshyn Walter Glaser Ulrike Schöck
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PLOS Genetics
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The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells.
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2012-12-06
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Wolf Reik Felix Krueger Bernard Thienpont Julia Arand
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Stefanie Seisenberger Simon Andrews Jörn Walter Fátima Santos Christian Popp Wendy Dean
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Molecular Cell
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RNA-Seq vs dual- and single-channel microarray data: sensitivity analysis for differential expression and clustering
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2012-12-10
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Martin Crane
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Alina Sîrbu Gráinne Kerr Heather J Ruskin
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PLOS ONE
|
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.
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2012-12-13
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Andrew C Perkins Timothy L. Bailey
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Lei Sun Zhihua Zhang Michael R Tallack Zhao Xu Hui Liu
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BMC Bioinformatics
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Chromatin is an ancient innovation conserved between Archaea and Eukarya.
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2012-12-13
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Corey Nislow Gary D. Bader
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Ron Ammar Dax Torti Kyle Tsui Marinella Gebbia Tanja Durbic Guri Giaever
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eLife
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RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia
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2012-12-17
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Xiangning Chen
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Junzhe Xu Jingchun Sun Jingchun Chen Lily Wang Anna Li Matthew Helm Steven L Dubovsky Silviu-Alin Bacanu Zhongming Zhao
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BMC Genomics
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A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance to Grosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees.
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2012-12-17
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Jörg Bohlmann
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Ye Wang Lynette Lim Scott DiGuistini Gordon Robertson Colette Breuil
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New Phytologist
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Circular RNAs are abundant, conserved, and associated with ALU repeats.
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2012-12-18
|
Norman Sharpless
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William R Jeck Jessica A Sorrentino Kai Wang Michael K Slevin Christin E Burd Jinze Liu William F Marzluff
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RNA
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HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency.
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2012-12-20
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Jeremy Luban
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Federico A Santoni Jessica Guerra
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Retrovirology
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Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice.
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2012-12-22
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Guojun Lu
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Tingting Lu Chuanrang Zhu Yunli Guo Yan Zhou Zhiyong Zhang Yan Zhao Wenjun Li Ying Lu Weihua Tang Qi Feng Bin Han
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BMC Genomics
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A comprehensive evaluation of alignment algorithms in the context of RNA-seq
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2012-12-26
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Caroline C Friedel
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Robert Lindner
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PLOS ONE
|
How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?
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2012-12-27
|
Chad Nusbaum
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Brian J Haas Melissa Chin Bruce W Birren Jonathan Livny
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BMC Genomics
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Correlates of relative resistance against low-dose rectal simian immunodeficiency virus challenges in peripheral blood mononuclear cells of vaccinated rhesus macaques.
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2012-12-27
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Sarah J. Ratcliffe
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Raj Kurupati Steve Tuyishime Andrew V Kossenkov Marina Sazanovich Larissa H Haut Marcio O Lasaro Steven E Bosinger Diane G Carnathan Mark Lewis Louise C Showe Guido Silvestri Hildegund C J Ertl
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Journal of Leukocyte Biology
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Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data
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2013
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Matthias Kretzler Gil Omenn
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Ridvan Eksi Hong-Dong Li Rajasree Menon Yuchen Wen Yuanfang Guan
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PLOS Computational Biology
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Whole-genome DNA/RNA sequencing identifies truncating mutations in RBCK1 in a novel Mendelian disease with neuromuscular and cardiac involvement
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2013
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Cecilia Kim Hakon Hakonarson
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Kai Wang Jonathan Bradfield Yunfei Guo Elina Toskala Frederick G Otieno Cuiping Hou Kelly Thomas Christopher Cardinale Gholson J Lyon Ryan Golhar
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Genome Medicine
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Molecular and cellular mechanisms of neutral lipid accumulation in diatom following nitrogen deprivation
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2013
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Hong-Ye Li
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Zhi-Kai Yang Ying-Fang Niu Yu-Han Ma Jiao Xue Meng-Han Zhang Wei-Dong Yang Jie-Sheng Liu Song-Hui Lu Yuanfang Guan
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Biotechnology for Biofuels
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"A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids"
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2013
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Jennifer Ann Harikrishna
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Mark W Davey Ranganath Gudimella Lee Wan Sin Norzulaani Khalid Johan Keulemans
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BMC Genomics
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RNA-Seq Differentiates Tumour and Host mRNA Expression Changes Induced by Treatment of Human Tumour Xenografts with the VEGFR Tyrosine Kinase Inhibitor Cediranib
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2013
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James R. Bradford
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Matthew Farren Steve J Powell Sarah Runswick Susie L Weston Helen Brown Oona Delpuech Mark Wappett Neil R Smith T Hedley Carr Jonathan R Dry Neil J Gibson Simon T Barry
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PLOS ONE
|
RNA-Seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse
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2013
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Arthur L. Horwich Justin Cotney
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Urmi Bandyopadhyay Maria Nagy Sunghee Oh Jing Leng Milind Mahajan Shrikant Mane Wayne A Fenton James P Noonan
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PLOS ONE
|
Transcriptome sequencing of tumor subpopulations reveals a spectrum of therapeutic options for squamous cell lung cancer
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2013
|
Olivier Harismendy
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Christian L Barrett Richard B Schwab HyunChul Jung Brian Crain Daniel J Goff Catriona H M Jamieson Patricia A Thistlethwaite Dennis A Carson Kelly A Frazer
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PLOS ONE
|
RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches
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2013
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Yaodong Yang Annaliese S Mason
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Haikuo Fan Yong Xiao Wei Xia Zhihui Xia Fei Qiao Songlin Zhao Haoru Tang
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PLOS ONE
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Integrative approach reveals composition of endoparasitoid wasp venoms
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2013
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Todd A Schlenke Nathan T Mortimer James Taylor
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Jeremy Goecks James A Mobley Gregory J Bowersock
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PLOS ONE
|
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing
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2013
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Yinglong Chen
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Yan Wang Liang Xu Hong Shen Yiqin Gong Cecilia Limera Liwang Liu
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PLOS ONE
|
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data
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2013
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Philip D Dunne Darragh G McArt Shu-Dong Zhang
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Jaine K Blayney Manuel Salto-Tellez Sandra Van Schaeybroeck Peter W Hamilton
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PLOS ONE
|
Unique transcriptome patterns of the white and grey matter corroborate structural and functional heterogeneity in the human frontal lobe
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2013
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Michael Janitz Glenda Halliday
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James D Mills Tomas Kavanagh Woojin S Kim Bei Jun Chen Yoshihiro Kawahara
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PLOS ONE
|
Computational identification of diverse mechanisms underlying transcription factor-DNA occupancy
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2013
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Majid Kazemian
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Qiong Cheng Hannah Pham Charles Blatti Susan E Celniker Scot A Wolfe Michael H Brodsky Saurabh Sinha
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PLOS Genetics
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Putative sugar transporters of the mustard leaf beetle Phaedon cochleariae: their phylogeny and role for nutrient supply in larval defensive glands
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2013
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Wilhelm Boland René R Bodemann Marco Groth
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Magdalena Stock Simone Eiserloh Antje Burse
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PLOS ONE
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MicroRNA discovery by similarity search to a database of RNA-seq profiles
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2013
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Jan Gorodkin Sachin Pundhir
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Frontiers in Genetics
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Differential analysis of gene regulation at transcript resolution with RNA-seq
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2013-01
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John L. Rinn
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Trapnell C Hendrickson DG Sauvageau M Goff L Pachter L
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Nature Biotechnology
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Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data
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2013-01-01
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Yves A. Lussier
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Alan Perez-Rathke Haiquan Li
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Pacific Symposium on Biocomputing
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Analysis of RNA-Seq data with TopHat and Cufflinks for genome-wide expression analysis of jasmonate-treated plants and plant cultures.
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2013-01-01
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Stephane Rombauts Alain Goossens
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Jacob Pollier
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Methods in Molecular Biology
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High occurrence of functional new chimeric genes in survey of rice chromosome 3 short arm genome sequences
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2013-01-01
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Rod A. Wing
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Chengjun Zhang Jun Wang Nicholas C Marowsky Manyuan Long Chuanzhu Fan
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Genome Biology and Evolution
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RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations.
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2013-01-01
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Loren H. Rieseberg
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Graeme D M Bell Nolan C Kane Keith L Adams
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Genome Biology and Evolution
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Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers.
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2013-01-01
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Hans Ellegren
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Severin Uebbing Axel Künstner Hannu Mäkinen
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Genome Biology and Evolution
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Genomic, RNAseq, and molecular modeling evidence suggests that the major allergen domain in insects evolved from a homodimeric origin
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2013-01-01
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Thomas A Randall Geoffrey A Mueller Lalith Perera
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Robert E London
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Genome Biology and Evolution
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Transcriptome sequencing of neonatal thymic epithelial cells.
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2013-01-01
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Claude Perreault
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Charles St-Pierre Sylvie Brochu Juan Ruiz Vanegas Maude Dumont-Lagacé Sébastien Lemieux
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Scientific Reports
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In vitro expansion of fetal neural progenitors as adherent cell lines.
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2013-01-01
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Steven M Pollard
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Methods in Molecular Biology
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Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics.
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2013-01-07
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Ching-Chia Yang Tsuyoshi Tanaka Takeshi Itoh
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Hiroaki Sakai Sung Shin Lee Hisataka Numa Jungsok Kim Yoshihiro Kawahara Hironobu Wakimoto Masao Iwamoto Takashi Abe Yuko Yamada Akira Muto Hachiro Inokuchi Toshimichi Ikemura Takashi Matsumoto Takuji Sasaki
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Plant and Cell Physiology
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RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism.
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2013-01-07
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Pingzhao Hu Michael Janitz
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James D Mills Thomas Nalpathamkalam Heidi I L Jacobs Caroline Janitz Daniele Merico
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Neuroscience Letters
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Dual functions of TAF7L in adipocyte differentiation.
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2013-01-08
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Michael Eisen Ivan Grubisic Tommy Kaplan Haiying Zhou Yan Li Zhengjian Zhang P Jeremy Wang Robert Tjian
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eLife
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MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.
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2013-01-08
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Jonathon T Hill
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Bradley L Demarest Brent W Bisgrove Bushra Gorsi Yi-Chu Su H Joseph Yost
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Genome Research
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SIBER: systematic identification of bimodally expressed genes using RNAseq data
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2013-01-09
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Kevin R. Coombes
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Pan Tong Yong Chen Xiao Su
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Bioinformatics
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Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls.
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2013-01-11
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Frank Baas
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Ching Yong Yick Aeilko H Zwinderman Peter W Kunst Katrien Grünberg Thais Mauad Annemiek Dijkhuis Elisabeth H Bel René Lutter Peter J Sterk
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European Respiratory Journal
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ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
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2013-01-12
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Raymond Wan
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Jing-Woei Li Chi-Shing Yu Ngai Na Co Nathalie Wong Ting-Fung Chan
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Bioinformatics
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Comparative RNA-seq analysis of early-infected peach leaves by the invasive phytopathogen Xanthomonas arboricola pv. pruni.
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2013-01-14
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Joël F. Pothier A Patocchi
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Didier Socquet-Juglard Tim Kamber Danilo Christen Cesare Gessler Brion Duffy
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PLOS ONE
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Dynamic DNA methylation across diverse human cell lines and tissues
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2013-01-16
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Gregory E Crawford John A Stamatoyannopoulos
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Katherine E Varley Jason Gertz Kevin M Bowling Stephanie L Parker Timothy E Reddy Florencia Pauli-Behn Marie K Cross Brian A Williams Devin M Absher Barbara J Wold Richard M Myers
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Genome Research
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RNA-Seq data: a goldmine for organelle research.
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2013-01-18
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David Roy Smith
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Briefings in functional genomics
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Efficient and comprehensive representation of uniqueness for next-generation sequencing by minimum unique length analyses.
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2013-01-18
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Daniel Ramsköld Rickard Sandberg
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Helena Storvall
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PLOS ONE
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Analysis of RNA-Seq data reveals involvement of JAK/STAT signalling during leg regeneration in the cricket Gryllus bimaculatus.
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2013-01-23
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Taro Nakamura
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Tetsuya Bando Yoshiyasu Ishimaru Takuro Kida Yoshimasa Hamada Yuji Matsuoka Hideyo Ohuchi Sumihare Noji Taro Mito
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Development
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Conserved gene regulatory function of the carboxy-terminal domain of dictyostelid C-module-binding factor.
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2013-01-25
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Gernot Glöckner
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Anika Schmith Marco Groth Josephine Ratka Sara Gatz Thomas Spaller Oliver Siol Thomas Winckler
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Eukaryotic Cell
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Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data
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2013-01-28
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John C Marioni Jong Kyoung Kim
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Genome Biology
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Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
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2013-01-31
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Jozef Gécz Lam S Nguyen James F. Gusella
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Hyung-Goo Kim Jill A Rosenfeld Yiping Shen Yves Lacassie Lawrence C Layman Lisa G Shaffer
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Human Molecular Genetics
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The evolutionary causes and consequences of sex-biased gene expression.
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2013-02-01
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Hans Ellegren
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John Parsch
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Nature Reviews Genetics
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Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.
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2013-02-01
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Cristian Del Fabbro
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Federico M Giorgi Francesco Licausi
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Bioinformatics
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puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis.
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2013-02-05
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Magnus Rattray
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Xuejun Liu Zhenzhu Gao Li Zhang
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BMC Bioinformatics
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Genetic screens: RNA-seq into the toolkit.
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2013-02-05
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Darren J. Burgess
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Nature Reviews Genetics
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Expression profile of ectopic olfactory receptors determined by deep sequencing.
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2013-02-06
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Hanns Hatt Günter Gisselmann
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Caroline Flegel Stavros Manteniotis Sandra Osthold Günter Gisselmann
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PLOS ONE
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A high-dimensional, deep-sequencing study of lung adenocarcinoma in female never-smokers
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2013-02-06
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Wan Kyu Kim Namshin Kim
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Sang Cheol Kim Yeonjoo Jung Jinah Park Sooyoung Cho Chaehwa Seo Jaesang Kim Pora Kim Jehwan Park Jihae Seo Jiwoong Kim Seongjin Park Insu Jang Jin Ok Yang Byungwook Lee Kyoohyoung Rho Yeonhwa Jung Juhee Keum Jinseon Lee Jungho Han Sangeun Kang Sujin Bae So-Jung Choi Sujin Kim Jong-Eun Lee Jhingook Kim Sanghyuk Lee
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PLOS ONE
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FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns.
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2013-02-06
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Zissimos Mourelatos Manolis Maragkakis Panagiotis Alexiou
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Tadashi Nakaya Alexandra Chang
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RNA
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SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data.
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2013-02-14
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Jun Wang Wenlong Jia
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Kunlong Qiu Minghui He Pengfei Song Quan Zhou Feng Zhou Yuan Yu Dandan Zhu Michael L Nickerson Shengqing Wan Xiangke Liao Xiaoqian Zhu Shaoliang Peng Yingrui Li Guangwu Guo
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Genome Biology
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The draft genome and transcriptome of Panagrellus redivivus are shaped by the harsh demands of a free-living lifestyle
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2013-02-14
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Paul W. Sternberg
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Jagan Srinivasan Adler R Dillman Marissa G Macchietto Liisa Heikkinen Merja Lakso Kelley M Fracchia Igor Antoshechkin Ali Mortazavi Garry Wong
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Genetics
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mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex.
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2013-02-17
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Dagmar Galter David N Hauser Mark R Cookson
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Allissa A Dillman J Raphael Gibbs Michael A Nalls Melissa K McCoy Iakov N Rudenko
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Nature Neuroscience
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EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments.
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2013-02-21
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Christina Kendziorski
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Ning Leng John A Dawson James A Thomson Victor Ruotti Anna I Rissman Bart M G Smits Jill D Haag Michael N Gould Ron M Stewart
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Bioinformatics
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Zinc deficiency impacts CO2 assimilation and disrupts copper homeostasis in Chlamydomonas reinhardtii.
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2013-02-25
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Sabeeha Merchant Matteo Pellegrini David Casero
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Davin Malasarn Janette Kropat Scott I Hsieh Giovanni Finazzi Joseph A Loo Francis-André Wollman
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Journal of Biological Chemistry
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Activity of a Py-Im polyamide targeted to the estrogen response element.
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2013-02-26
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Jerzy O Szablowski Peter Dervan
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Nicholas G Nickols Amanda E Hargrove Benjamin C Li Jevgenij A Raskatov
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Molecular Cancer Therapeutics
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Perturbations of Plasmodium Puf2 expression and RNA-seq of Puf2-deficient sporozoites reveal a critical role in maintaining RNA homeostasis and parasite transmissibility.
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2013-02-27
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Scott E. Lindner Sebastian A. Mikolajczak
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Ashley M Vaughan Wonjong Moon Brad R Joyce William J Sullivan Stefan H I Kappe
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Cellular Microbiology
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SplicingCompass: differential splicing detection using RNA-seq data.
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2013-02-28
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Roland Eils
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Moritz Aschoff Agnes Hotz-Wagenblatt Karl-Heinz Glatting Matthias Fischer Rainer König
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Bioinformatics
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Epstein - Barr virus transforming protein LMP-1 alters B cells gene expression by promoting accumulation of the oncoprotein ΔNp73α
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2013-03
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Florence Le Calvez-Kelm Birke Bartosch Evelyne Manet Hector Hernandez-Vargas
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Rosita Accardi Ikbal Fathallah Henri Gruffat Giuseppe Mariggiò Catherine Voegele James McKay Bakary S Sylla Massimo Tommasino
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PLOS Pathogens
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WNT5A inhibits metastasis and alters splicing of Cd44 in breast cancer cells.
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2013-03-06
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David K. Crossman
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Wen Jiang Elizabeth H Mitchell Philip Sohn Michael R Crowley Rosa Serra
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PLOS ONE
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RNA-seq reveals activation of both common and cytokine-specific pathways following neutrophil priming.
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2013-03-06
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Huw B Thomas Helen L Wright
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Robert J Moots Steven W Edwards
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PLOS ONE
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Regulation of viral and cellular gene expression by Kaposi's sarcoma-associated herpesvirus polyadenylated nuclear RNA.
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2013-03-06
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Cyprian Rossetto Subhash Verma Gregory S. Pari
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Margaret Tarrant-Elorza Pravinkumar Purushothaman
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Journal of Virology
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RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1α depletion in Medicago truncatula.
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2013-03-06
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Anca Macovei Daniela Carbonera Alma Balestrazzi
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Mattia Donà Massimo Confalonieri Andrea Minio Marco Biggiogera Armando Buttafava Elena Raimondi Massimo Delledonne Lorenzo Ventura Maria Elisa Sabatini Giorgio Giraffa
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Journal of Experimental Botany
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Comparative RNA-seq analysis in the unsequenced axolotl: the oncogene burst highlights early gene expression in the blastema.
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2013-03-07
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Bianca Habermann Elly M Tanaka
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Ron Stewart Cynthia Alexander Rascón Shulan Tian Jeff Nie Chris Barry Li-Fang Chu Hamisha Ardalani Ryan J Wagner Mitchell D Probasco Jennifer M Bolin Ning Leng Srikumar Sengupta Michael Volkmer James A Thomson Colin N Dewey
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PLOS Computational Biology
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Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR).
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2013-03-08
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Jasmine Jacob-Hirsch
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Oz Solomon Shirley Oren Michal Safran Naamit Deshet-Unger Pinchas Akiva Jasmine Jacob-Hirsch Karen Cesarkas Reut Kabesa Ninette Amariglio Ron Unger Gideon Rechavi Eran Eyal
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RNA
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A comparison of methods for differential expression analysis of RNA-seq data
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2013-03-09
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Charlotte Soneson
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Mauro Delorenzi
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BMC Bioinformatics
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Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405.
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2013-03-13
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Susan Fanayan Ling Yen Lee
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Joshua T Smith Fangfei Yan Michael Snyder William S Hancock Edouard Nice
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Journal of Proteome Research
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CathaCyc, a metabolic pathway database built from Catharanthus roseus RNA-Seq data.
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2013-03-14
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Stephane Rombauts Kirsi-Marja Oksman-Caldentey Michele Fabris Alex Van Moerkercke Jacob Pollier Johan Memelink Alain Goossens
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Gino J E Baart Ghulam Hasnain Heiko Rischer
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Plant and Cell Physiology
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Isolation of Blastomyces dermatitidis yeast from lung tissue during murine infection for in vivo transcriptional profiling
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2013-03-14
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Christina A Cuomo
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Amber J Marty Marcel Wüthrich John C Carmen Thomas D Sullivan Bruce S Klein Gregory M Gauthier
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Fungal Genetics and Biology
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TDP-43 high throughput screening analyses in neurodegeneration: advantages and pitfalls.
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2013-03-14
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Emanuele Buratti Maurizio Romano
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Francisco E Baralle
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Molecular and Cellular Neuroscience
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Interpretation, stratification and evidence for sequence variants affecting mRNA splicing in complete human genome sequences.
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2013-03-14
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Peter K. Rogan Paul I Costea
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Ben C Shirley Eliseos J Mucaki Tyson Whitehead Pelin Akan
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Genomics Proteomics and Bioinformatics
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Identification of novel exons and transcripts by comprehensive RNA-Seq of horn cancer transcriptome in Bos indicus.
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2013-03-14
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Subhash J Jakhesara Chaitanya G. Joshi
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Prakash G Koringa
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Journal of Biotechnology
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The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels.
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2013-03-16
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Matthias Platzer
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Andreas Petzold Kathrin Reichwald Marco Groth Stefan Taudien Nils Hartmann Steffen Priebe Dmitry Shagin Christoph Englert
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BMC Genomics
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A multifaceted study of Pseudomonas aeruginosa shutdown by virulent podovirus LUZ19.
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2013-03-19
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Rob Lavigne
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Elke Lecoutere Jeroen Wagemans William Cenens Abram Aertsen Liliane Schoofs Bart Landuyt Jan Paeshuyse Maurice Scheer Max Schobert Pieter-Jan Ceyssens
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mBio
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Zinc-mediated RNA fragmentation allows robust transcript reassembly upon whole transcriptome RNA-Seq.
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2013-03-21
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Maxime Wery Daniel Gautheret
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Marc Descrimes Claude Thermes Antonin Morillon
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Methods
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Investigation of radiation-induced transcriptome profile of radioresistant non-small cell lung cancer A549 cells using RNA-seq
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2013-03-22
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Namshin Kim
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Hee Jung Yang Ki Moon Seong HyeSook Youn BuHyun Youn
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PLOS ONE
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Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation
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2013-03-24
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Jun Wang Junyi Wang Klaus Mayer Thomas Wicker Huanming Yang
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Jizeng Jia Shancen Zhao Xiuying Kong Yingrui Li Guangyao Zhao Weiming He Rudi Appels Matthias Pfeifer Yong Tao Xueyong Zhang Ruilian Jing Chi Zhang Youzhi Ma Lifeng Gao Chuan Gao Manuel Spannagl Dong Li Shengkai Pan Fengya Zheng Qun Hu Xianchun Xia Jianwen Li Qinsi Liang Jie Chen Caiyun Gou Hanhui Kuang Genyun He Yadan Luo Beat Keller Qiuju Xia Peng Lu Hongfeng Zou Rongzhi Zhang Junyang Xu Jinlong Gao Christopher Middleton Zhiwu Quan Guangming Liu Jian Wang Xu Liu Zhonghu He Long Mao
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Nature
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RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome
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2013-03-25
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Brigitte Galliot
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Yvan Wenger
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BMC Genomics
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RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome.
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2013-03-25
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Alicia Oshlack Nadia M Davidson Craig A. Smith
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Katie L Ayers Diana Demiyah Kelly N Roeszler Frank Grützner Andrew H Sinclair
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Genome Biology
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Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data
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2013-03-26
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Michael Gill Elaine M Kenny Richard Anney Derek W. Morris Aiden Corvin
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Emma M Quinn Paul Cormican Matthew Hill
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PLOS ONE
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Differential expression analysis for paired RNA-Seq data
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2013-03-27
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Ruth R Montgomery
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Lisa M Chung John P Ferguson Wei Zheng Feng Qian Vincent Bruno Hongyu Zhao
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BMC Bioinformatics
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Predicting long non-coding RNAs using RNA sequencing.
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2013-03-27
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Chris Ponting Nicholas E Ilott
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Methods
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Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
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2013-03-28
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Jon Jerlström-Hultqvist Staffan G Svärd
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Oscar Franzén Elin Einarsson Johan Ankarklev Marcela Ferella Björn Andersson
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PLOS Computational Biology
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Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans
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2013-03-28
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Adam C. Siepel Robert A Burne
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Lin Zeng Sang Chul Choi Charles G Danko Michael J Stanhope
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PLOS ONE
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Comprehensive molecular screening: from the RT-PCR to the RNA-seq.
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2013-04-01
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Rafael Rosell
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Carlota Costa Ana Giménez-Capitán Niki Karachaliou
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Translational lung cancer research
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Spatial transcriptional profile of the chick and mouse endocardial cushions identify novel regulators of endocardial EMT in vitro.
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2013-04-01
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Daniel M DeLaughter
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Daniel M DeLaughter Danos C Christodoulou Jamille Y Robinson Christine E Seidman H Scott Baldwin J G Seidman Joey V Barnett
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Journal of Molecular and Cellular Cardiology
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Frogs and estivation: transcriptional insights into metabolism and cell survival in a natural model of extended muscle disuse.
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2013-04-02
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Craig E. Franklin David I Schlipalius Paul R Ebert Rebecca L. Cramp
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Beau D Reilly
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Physiological Genomics
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New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics.
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2013-04-03
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Patrick May Alexander Goesmann
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Jörg Toepel Maike Illmer-Kephalides Sebastian Jaenicke Jasmin Straube Olaf Kruse
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Plant Biotechnology Journal
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Comparative RNA-Seq and microarray analysis of gene expression changes in B-cell lymphomas of Canis familiaris.
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2013-04-04
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Noel Monks
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Marie Mooney Jeffrey Bond Emily Eugster David Cherba Pamela Berlinski Steve Kamerling Keith Marotti Heather Simpson Tony Rusk Waibhav Tembe Christophe Legendre Hollie Benson Winnie Liang Craig Paul Webb
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PLOS ONE
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The transcriptome of Leishmania major in the axenic promastigote stage: transcript annotation and relative expression levels by RNA-seq.
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2013-04-04
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A Rastrojo Rosa M. Reguera
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Fernando Carrasco-Ramiro Diana Martín Antonio Crespillo Begoña Aguado Jose M Requena
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BMC Genomics
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Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro.
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2013-04-08
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Amanda J Lohan Kévin Rue-Albrecht Karsten Hokamp Brendan Loftus Eamonn Gormley David E. MacHugh Stephen V. Gordon Kate Killick
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Nicolas C Nalpas Stephen D E Park David A Magee Maria Taraktsoglou John A Browne Kevin M Conlon
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BMC Genomics
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Characterization of FUS mutations in amyotrophic lateral sclerosis using RNA-Seq.
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2013-04-08
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Marka van Blitterswijk Brad Friedman Leonard H van den Berg Jan H Veldink
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Eric T Wang Pamela J Keagle Patrick Lowe Ashley Lyn Leclerc David E Housman John E Landers
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PLOS ONE
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Functional genomics based understanding of rice endosperm development.
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2013-04-10
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Shi-Rong Zhou
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Lin-Lin Yin Hong-Wei Xue
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Current Opinion in Plant Biology
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Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo.
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2013-04-11
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Abhinav Nellore
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Alexander D Ramos Aaron Diaz Ryan N Delgado Ki-Youb Park Gabriel Gonzales-Roybal Michael C Oldham Jun S Song Daniel A Lim
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Cell Stem Cell
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Accurate detection of differential RNA processing.
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2013-04-12
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Oliver Stegle Gunnar Rätsch Karsten M Borgwardt
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Philipp Drewe Lisa Hartmann André Kahles Regina Bohnert Andreas Wachter
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Nucleic Acids Research
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Exome-based analysis for RNA epigenome sequencing data.
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2013-04-14
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Jia Meng
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Xiaodong Cui Manjeet K Rao Yidong Chen Yufei Huang
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Bioinformatics
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Glycyrrhiza uralensis transcriptome landscape and study of phytochemicals.
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2013-04-14
|
Keiichi Mochida Tetsuya Sakurai Carsten O Daub Toshiya Muranaka Kazuki Saito
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Jordan A Ramilowski Satoru Sawai Hikaru Seki Takuhiro Yoshida
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Plant and Cell Physiology
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Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.
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2013-04-14
|
Wolfgang Huber
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Danni Yu Olga Vitek
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Bioinformatics
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Faculty of 1000 evaluation for Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-Seq
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2013-04-16
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Christen Rune Stensvold
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C Graham Clark
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Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity
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2013-04-17
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Yohei Sasagawa Tetsutaro Hayashi Itoshi Nikaido Takeshi Imai Hiroki R Ueda
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Hiroki Danno Kenichiro D Uno
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Genome Biology
|
Sprouts of RNA epigenetics: the discovery of mammalian RNA demethylases.
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2013-04-17
|
Arne Klungland
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Guanqun Zheng John Arne Dahl Yamei Niu Ye Fu Yun-Gui Yang Chuan He
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RNA Biology
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Characterization of differential transcript abundance through time during Nematostella vectensis development.
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2013-04-19
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Sarah Tulin Joel Smith Casey W. Dunn
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Rebecca Rae Helm Stefan Siebert
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BMC Genomics
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Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish
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2013-04-23
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Ingo Braasch
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Fanwei Meng Jennifer B Phillips Xiwen Lin Tom Titus Chunguang Zhang John H Postlethwait
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Molecular Biology and Evolution
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Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.
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2013-04-23
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Elaine Ostrander Agata Smogorzewska Arleen D. Auerbach NISC Comparative Sequencing Program
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Settara C Chandrasekharappa Francis P Lach Danielle C Kimble Aparna Kamat Jamie K Teer Frank X Donovan Elizabeth Flynn Shurjo K Sen Supawat Thongthip Erica Sanborn
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Blood
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A model based criterion for gene expression calls using RNA-seq data.
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2013-04-25
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Vincent Lynch
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Günter P Wagner Koryu Kin
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Theory in Biosciences
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Transcriptome analysis of Japanese pear (Pyrus pyrifolia Nakai) flower buds transitioning through endodormancy.
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2013-04-26
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Songling Bai
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Takanori Saito Daisuke Sakamoto Akiko Ito Hiroshi Fujii Takaya Moriguchi
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Plant and Cell Physiology
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RNAseq-based transcriptome analysis of Lactuca sativa infected by the fungal necrotroph Botrytis cinerea.
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2013-04-26
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Barbara De Coninck
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Kaat De Cremer Janick Mathys Christine Vos Lutz Froenicke Richard W Michelmore Bruno P A Cammue
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Plant, Cell and Environment
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Prediction of transcribed PIWI-interacting RNAs from CHO RNAseq data.
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2013-04-29
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Johannes Grillari Alexandra B Graf Matthias Hackl Nicole Borth
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Matthias Peter Gerstl
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Journal of Biotechnology
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RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding, and degradation in response to heat stress in catfish.
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2013-04-30
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Shikai Liu Eric Peatman Huseyin Kucuktas Ludmilla Kaltenboeck Luyang Sun Yu Zhang
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Xiuli Wang Fanyue Sun Jiaren Zhang Jianbin Feng Hong Liu K V Rajendran Yanliang Jiang Zhanjiang Liu
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Physiological Genomics
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Erratum: RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings
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2013-05
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Jun Wang Huanming Yang
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Shancheng Ren Zhiyu Peng Jian-Hua Mao Yongwei Yu Changjun Yin Xin Gao Zilian Cui Jibin Zhang Kang Yi Weidong Xu Chao Chen Fubo Wang Xinwu Guo Ji Lu Jun Yang Min Wei Zhijian Tian Yinghui Guan Liang Tang Chuanliang Xu Linhui Wang Xu Gao Wei Tian Jian Wang Yinghao Sun
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Cell Research
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Glucocorticoid-induced changes in gene expression of airway smooth muscle in patients with asthma.
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2013-05-01
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Frank Baas Kees Fluiter
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Ching Yong Yick Aeilko H Zwinderman Peter W Kunst Katrien Grünberg Thais Mauad Elisabeth H Bel René Lutter Peter J Sterk
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American Journal of Respiratory and Critical Care Medicine
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Transcription factors that convert adult cell identity are differentially polycomb repressed
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2013-05-01
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Sean Eddy Davis FP
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PLOS ONE
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Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans
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2013-05-04
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Stuart J Macdonald
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Joel V Tamayo Mahekta Gujar Erik A Lundquist
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BMC Genomics
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Research resource: small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes.
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2013-05-09
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Agne Velthut Madis Metsis Andres Salumets
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Jaak Simm Timo Tuuri Juha S Tapanainen
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Molecular Endocrinology
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Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy.
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2013-05-09
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Melody Baddoo Michelle Lacey Erik K Flemington
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Michael J Strong Guorong Xu Joseph Coco Carl Baribault Dass S Vinay Amy L Strong Teresa A Lehman Michael B Seddon Zhen Lin Monica Concha Melody Baddoo Marybeth Ferris Kenneth F Swan Deborah E Sullivan Matthew E Burow Christopher M Taylor
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PLOS Pathogens
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In vitro-differentiated neural cell cultures progress towards donor-identical brain tissue
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2013-05-10
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Thomas G Beach
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Brooke E Hjelm Bodour Salhia Ahmet Kurdoglu Szabolcs Szelinger Rebecca A Reiman Lucia I Sue Matthew J Huentelman David W Craig
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Human Molecular Genetics
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Global detection and identification of developmental stage specific transcripts in mouse brain using subtractive cross-screening algorithm.
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2013-05-12
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Zhixiang Zuo
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Yi Lv Xiao Xu
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Genomics
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Mapping the RNA-Seq trash bin: unusual transcripts in prokaryotic transcriptome sequencing data.
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2013-05-13
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Peter F. Stadler David Langenberger
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Gero Doose Maria Alexis Rebecca Kirsch Sven Findeiß Rainer Machné Mario Mörl Steve Hoffmann
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RNA Biology
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Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.
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2013-05-14
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Stephen A. Smith
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Ya Yang
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BMC Genomics
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OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis.
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2013-05-15
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Tesfaye Wubet Martin Schädler Mika T Tarkka Stefan Scheu François Buscot
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Sylvie Herrmann Lasse Feldhahn Sabine Recht Florence Kurth Sarah Mailänder Markus Bönn Maren Neef Oguzhan Angay Michael Bacht Marcel Graf Hazel Maboreke Frank Fleischmann Thorsten E E Grams Liliane Ruess Roland Brandl Silvia D Schrey Ivo Grosse
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New Phytologist
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Complexities of gammaherpesvirus transcription revealed by microarrays and RNAseq.
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2013-05-16
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Laurie T. Krug
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Current opinion in virology
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Comparative analysis of RNA sequencing methods for degraded or low-input samples.
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2013-05-19
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Aviv Regev Rahul Satija Nathalie Pochet
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Xian Adiconis Diego Borges-Rivera David S DeLuca Michele A Busby Aaron M Berlin Andrey Sivachenko Dawn Anne Thompson Alec Wysoker Timothy Fennell Andreas Gnirke Joshua Z Levin
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Nature Methods
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Evaluation of higher plant virus resistance genes in the green alga, Chlorella variabilis NC64A, during the early phase of infection with Paramecium bursaria chlorella virus-1
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2013-05-21
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Guillaume Blanc
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Janet M Rowe David D Dunigan James R Gurnon Yuannan Xia James L Van Etten
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Virology
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Genome wide proteomics of ERBB2 and EGFR and other oncogenic pathways in inflammatory breast cancer.
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2013-05-22
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Gil Omenn Susan Fanayan
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Emma Yue Zhang Massimo Cristofanilli Fredika Robertson James M Reuben Zhaomei Mu Ronald C Beavis Hogune Im Michael Snyder Matan Hofree Trey Ideker Seul-Ki Jeong Young-Ki Paik Anna Fan Zhang Shiaw-Lin Wu William S Hancock
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Journal of Proteome Research
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Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing
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2013-05-22
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Ryan D Morin Andrew Mungall Steven Jones
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Karen Mungall Erin Pleasance Rodrigo Goya Ryan D Huff David W Scott Jiarui Ding Andrew Roth Readman Chiu Richard D Corbett Fong Chun Chan Maria Mendez-Lago Diane L Trinh Madison Bolger-Munro Greg Taylor Alireza Hadj Khodabakhshi Susana Ben-Neriah Julia Pon Barbara Meissner Bruce Woolcock Noushin Farnoud Sanja Rogic Emilia L Lim Nathalie A Johnson Sohrab Shah Christian Steidl Robert Holt Inanc Birol Richard Moore Joseph M Connors Randy D Gascoyne Marco A Marra
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Blood
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A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells.
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2013-05-26
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Nina Papavasiliou Thomas Tuschl
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Eric L Fritz Brad R Rosenberg Kenneth Lay Aleksandra Mihailović F Nina Papavasiliou
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Nature Immunology
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Identification of the zebrafish maternal and paternal transcriptomes
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2013-05-29
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James Cuthbert Smith
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Steven A Harvey Ian Sealy Ross Kettleborough Fruzsina Fenyes Richard White Derek Stemple
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Development
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Transcriptome sequencing (RNA-seq) analysis of the effects of metal nanoparticle exposure on the transcriptome of Chlamydomonas reinhardtii.
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2013-05-31
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Rute F. Domingos William Zerges Kevin J Wilkinson
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Dana F Simon Charles Hauser Colin M Hutchins
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Applied and Environmental Microbiology
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Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs
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2013-06
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Michael McManus
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Matthew J Hangauer Ian W Vaughn
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PLOS Genetics
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The gene desert mammary carcinoma susceptibility locus Mcs1a regulates Nr2f1 modifying mammary epithelial cell differentiation and proliferation
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2013-06
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Christina Kendziorski
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Bart M G Smits Jill D Haag Anna I Rissman Deepak Sharma Ann Tran Alexi A Schoenborn Rachael C Baird Dan S Peiffer David Q Leinweber Matthew J Muelbl Amanda L Meilahn Mark R Eichelberg Ning Leng Manorama C John Patricia A Powers Caroline M Alexander Michael N Gould
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PLOS Genetics
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Distinctive expansion of potential virulence genes in the genome of the oomycete fish pathogen Saprolegnia parasitica
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2013-06
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Chad Nusbaum Carsten Russ Berend Snel Stephan Wawra Sucheta Tripathy Irene de Bruijn Michael F. Seidl Guido Van den Ackerveken Pieter van West Francine Govers Stan Oome Neil Horner Bernard Dumas Marcia Saraiva Julio C Vega-Arreguín Paul F Morris
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Rays H Y Jiang Brian J Haas Rodrigo Belmonte Lars Löbach James Christie Arnaud Bottin Vincent Bulone Sara M Díaz-Moreno Lin Fan Elodie Gaulin Laura J Grenville-Briggs Joshua Z Levin Marco Mammella Harold J G Meijer Stan Oome Andrew J Phillips David van Rooyen Elzbieta Rzeszutek Chris J Secombes Joost H M Stassen Sean Sykes Herbert van den Berg Sarah K Young Qiandong Zeng Javier Dieguez-Uribeondo Brett M Tyler
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PLOS Genetics
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RNA-seq analysis reveals extensive transcriptional plasticity to temperature stress in a freshwater fish species.
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2013-06-05
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Steve Smith Luciano B. Beheregaray
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Louis Bernatchez
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BMC Genomics
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Landscape of DNA virus associations across human malignant cancers: analysis of 3,775 cases using RNA-Seq
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2013-06-05
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Michelle D Williams Funda Meric-Bernstam
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Joseph D Khoury Nizar M Tannir Yunxin Chen Hui Yao Jianping Zhang Erika J Thompson TCGA Network L Jeffrey Medeiros John N Weinstein Xiaoping Su
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Journal of Virology
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A meta-analysis of the genomic and transcriptomic composition of complex life.
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2013-06-06
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John Mattick
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Ganqiang Liu Ryan J Taft
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Cell Cycle
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Discovery of diversity in xylan biosynthetic genes by transcriptional profiling of a heteroxylan containing mucilaginous tissue.
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2013-06-07
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Jacob K Jensen
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Nathan Johnson Curtis G Wilkerson
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Frontiers in Plant Science
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A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples
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2013-06-10
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Paolo Piazza Elizabeth M Batty Tanya Golubchik Kate E Dingle Paul Klenerman Daniel Wilson Eleanor Barnes
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T H Nicholas Wong Amy Trebes Karène Argoud Moustafa Attar David Buck Camilla L C Ip Madeleine Cule Rory Bowden Charis Manganis A Sarah Walker David H Wyllie Tim E A Peto Derrick W Crook
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PLOS ONE
|
Assessment of gene expression in peripheral blood using RNAseq before and after weight restoration in anorexia nervosa
|
2013-06-15
|
Cynthia M. Bulik
|
Yunjung Kim Sara E Trace James J Crowley Kimberly A Brownley Robert M Hamer David S Pisetsky Patrick F Sullivan
|
Psychiatry Research
|
Comprehensive High-Resolution Analysis of the Role of an Arabidopsis Gene Family in RNA Editing
|
2013-06-20
|
Stéphane Bentolila Maureen R. Hanson
|
Julyun Oh Robert Bukowski
|
PLOS Genetics
|
RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism
|
2013-06-20
|
Erin Osborne
|
Nirav M Amin Panna Tandon Frank L Conlon
|
Methods
|
Cellular source and mechanisms of high transcriptome complexity in the mammalian testis.
|
2013-06-20
|
Anamaria Necsulea
|
Magali Soumillon Manuela Weier David Brawand Xiaolan Zhang Hongcang Gu Pauline Barthès Maria Kokkinaki Serge Nef Andreas Gnirke Martin Dym Bernard de Massy Tarjei S Mikkelsen Henrik Kaessmann
|
Cell Reports
|
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.
|
2013-06-21
|
Avi Ma'ayan Caroline Baroukh
|
Huilei Xu Ruth Dannenfelser Edward Y Chen Christopher M Tan Yan Kou Yujin E Kim Ihor R Lemischka
|
Database
|
Global transcriptome profiles of Camellia sinensis during cold acclimation
|
2013-06-22
|
Qiong-Yi Zhao
|
Xin-Chao Wang Chun-Lei Ma Zong-Hong Zhang Hong-Li Cao Yi-Meng Kong Chuan Yue Xin-Yuan Hao Liang Chen Jian-Qiang Ma Ji-Qiang Jin Xuan Li Ya-Jun Yang
|
BMC Genomics
|
Evaluating the impact of sequencing depth on transcriptome profiling in human adipose
|
2013-06-24
|
Jane Ferguson Muredach P. Reilly
|
Yichuan Liu Chenyi Xue Ian M Silverman Brian Gregory Mingyao Li
|
PLOS ONE
|
Parallel comparison of Illumina RNA-Seq and Affymetrix microarray platforms on transcriptomic profiles generated from 5-aza-deoxy-cytidine treated HT-29 colon cancer cells and simulated datasets
|
2013-06-28
|
W. Richard McCombie
|
Xiao Xu Yuanhao Zhang Jennie Williams Eric Antoniou Song Wu Wei Zhu Nicholas O Davidson Paula Denoya Ellen Li
|
BMC Bioinformatics
|
Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.
|
2013-07-01
|
Sayan Mukherjee Uwe Ohler
|
Dina Hafez Ting Ni Jun Zhu
|
Bioinformatics
|
Classification of topological domains based on gene expression and regulation.
|
2013-07-01
|
Nadav Ahituv
|
Jingjing Zhao Hongbo Shi
|
Genome
|
RNA-Seq-based analysis of the physiologic cold shock-induced changes in Moraxella catarrhalis gene expression.
|
2013-07-02
|
Stefan Wyder Christoph Aebi
|
Violeta Spaniol
|
PLOS ONE
|
Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA
|
2013-07-03
|
Andrzej Dziembowski Rafał Tomecki Torben Heick Jensen Dominik Cysewski
|
Michal Lubas Christian K Damgaard
|
The EMBO Journal
|
RNaseIII and T4 polynucleotide Kinase sequence biases and solutions during RNA-seq library construction
|
2013-07-04
|
Claus O. Wilke
|
Changhoon Lee R Adron Harris Jason K Wall R Dayne Mayfield
|
Biology Direct
|
Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution
|
2013-07-05
|
Mark Bender Gerstein
|
Gang Fang Karla D Passalacqua Jason Hocking Paula Montero Llopis Nicholas H Bergman Christine Jacobs-Wagner
|
BMC Genomics
|
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases
|
2013-07-07
|
Carlo Gambacorti-Passerini Vera Magistroni
|
Roberta Spinelli Alessandra Pirola Sara Redaelli Nitesh Sharma Hima Raman Simona Valletta Rocco Piazza
|
Molecular genetics & genomic medicine
|
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis.
|
2013-07-08
|
Sebastian Kurscheid Ruth R Montgomery Erol Fikrig Mark Bender Gerstein
|
Feng Qian Lisa Chung Wei Zheng Vincent Bruno Roger P Alexander Zhong Wang Xiaomei Wang Hongyu Zhao Michael Snyder
|
Viruses
|
Clear cell renal cell carcinoma associated microRNA expression signatures identified by an integrated bioinformatics analysis.
|
2013-07-10
|
Wenying Yan
|
Jiajia Chen Daqing Zhang Wenyu Zhang Yifei Tang Lingchuan Guo Bairong Shen
|
Journal of Translational Medicine
|
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease
|
2013-07-12
|
Geir Kjetil Sandve Gavin Giovannoni
|
Adam E Handel Giulio Disanto Antonio J Berlanga-Taylor Giuseppe Gallone Heather Hanwell Finn Drabløs George C Ebers Sreeram V Ramagopalan
|
BMC Medicine
|
Male-biased genes in catfish as revealed by RNA-Seq analysis of the testis transcriptome.
|
2013-07-12
|
Shikai Liu Ludmilla Kaltenboeck Luyang Sun Rex Dunham
|
Fanyue Sun Xiaoyu Gao Yanliang Jiang Dayan Perera Xiuli Wang Chao Li Jiaren Zhang Zhanjiang Liu
|
PLOS ONE
|
Senescence-associated lncRNAs: senescence-associated long noncoding RNAs.
|
2013-07-14
|
Kevin G. Becker Myriam Gorospe Kotb Abdelmohsen
|
Amaresh Panda Min-Ju Kang Jason Xu Roza Selimyan Je-Hyun Yoon Jennifer L Martindale Supriyo De William H Wood
|
Aging Cell
|
Transcriptome analysis of mouse brain infected with Toxoplasma gondii.
|
2013-07-15
|
Yoshifumi Nishikawa
|
Sachi Tanaka Maki Nishimura Fumiaki Ihara Junya Yamagishi Yutaka Suzuki
|
Infection and Immunity
|
Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles.
|
2013-07-16
|
Hirokazu Handa Takeshi Itoh
|
Youko Oono Yoshihiro Kawahara Takayuki Yazawa Hiroyuki Kanamori Masato Kuramata Harumi Yamagata Satomi Hosokawa Hiroshi Minami Satoru Ishikawa Jianzhong Wu Baltazar Antonio Takashi Matsumoto
|
Plant Molecular Biology
|
Proteogenomic database construction driven from large scale RNA-seq data.
|
2013-07-17
|
Vineet Bafna
|
Sunghee Woo Seong Won Cha Gennifer Merrihew Yupeng He Natalie Castellana Clark Guest Michael MacCoss
|
Journal of Proteome Research
|
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes
|
2013-07-18
|
Jennifer Doudna Lei S Qi Jonathan Weissman Noam Stern-Ginossar
|
Luke A Gilbert Matthew H Larson Leonardo Morsut Zairan Liu Gloria A Brar Sandra E Torres Onn Brandman Evan H Whitehead Wendell A Lim
|
Cell
|
Methylmercury exposure increases lipocalin related (lpr) and decreases activated in blocked unfolded protein response (abu) genes and specific miRNAs in Caenorhabditis elegans
|
2013-07-18
|
Natalia Vanduyn
|
Martina Rudgalvyte Vuokko Aarnio Liisa Heikkinen Juhani Peltonen Merja Lakso Richard Nass Garry Wong
|
Toxicology Letters
|
Using a periclinal chimera to unravel layer-specific gene expression in plants.
|
2013-07-19
|
James Abbott
|
Ioannis Filippis Rosa Lopez-Cobollo Sarah Butcher Gerard J Bishop
|
The Plant Journal
|
Gene networks and chromatin and transcriptional regulation of the phaseolin promoter in Arabidopsis.
|
2013-07-19
|
Lakshminarayan M. Iyer
|
Sabarinath Sundaram Sunee Kertbundit Eugene V Shakirov Lakshminarayan M Iyer Miloslav Jurícek Timothy C Hall
|
The Plant Cell
|
Enhanced expression of codon optimized interferon gamma in CHO cells.
|
2013-07-19
|
Dong-Yup Lee
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Bevan Kai-Sheng Chung Faraaz N K Yusufi Mariati Yuansheng Yang
|
Journal of Biotechnology
|
GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data.
|
2013-07-22
|
Zhi-xiang Lu
|
Keyan Zhao Juw Won Park Qing Zhou Yi Xing
|
Genome Biology
|
Replication protein A subunit 3 and the iron efficiency response in soybean.
|
2013-07-22
|
Dianne Cook
|
Sarah E Atwood Jamie A O'Rourke Gregory A Peiffer Tengfei Yin Mahbubul Majumder Chunquan Zhang Silvia R Cianzio John H Hill Steven A Whitham Randy C Shoemaker Michelle A Graham
|
Plant, Cell and Environment
|
Knockdown of CDKN1C (p57(kip2)) and PHLDA2 results in developmental changes in bovine pre-implantation embryos
|
2013-07-22
|
Francisco Peñagaricano Wen Huang
|
Ashley M Driver Jenna Kropp Hasan Khatib
|
PLOS ONE
|
Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.
|
2013-07-22
|
Ulrich Omasits Christian H Ahrens Mark D. Robinson Christoph Dehio
|
Maxime Quebatte Daniel J Stekhoven Claudia Fortes Bernd Roschitzki
|
Genome Research
|
Pairwise comparisons of ten porcine tissues identify differential transcriptional regulation at the gene, isoform, promoter and transcription start site level.
|
2013-07-27
|
Christian Bendixen
|
Leila Farajzadeh Henrik Hornshøj Jamal Momeni Bo Thomsen Knud Larsen Jakob Hedegaard Lone Bruhn Madsen
|
Biochemical and Biophysical Research Communications
|
Basal polarization of the mucosal compartment in Flavobacterium columnare susceptible and resistant channel catfish (Ictalurus punctatus).
|
2013-07-27
|
Eric Peatman
|
Chao Li Brian C Peterson David L Straus Bradley D Farmer Benjamin H Beck
|
Molecular Immunology
|
Differential programming of B cells in AID deficient mice
|
2013-07-29
|
Bas van Steensel
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Marc A Hogenbirk Marinus R Heideman Arno Velds Paul C M van den Berk Ron M Kerkhoven Heinz Jacobs
|
PLOS ONE
|
DNA methylation, genotype and gene expression: who is driving and who is along for the ride?
|
2013-07-29
|
Meaghan J Jones Michael S Kobor
|
Anthony P Fejes
|
Genome Biology
|
Global gene expression response of a population exposed to benzene: a pilot study exploring the use of RNA-sequencing technology
|
2013-08
|
Nathaniel Rothman
|
Reuben Thomas Cliona M McHale Qing Lan Alan E Hubbard Luoping Zhang Roel Vermeulen Guilan Li Stephen M Rappaport Songnian Yin Martyn T Smith
|
Environmental and Molecular Mutagenesis
|
Computational analysis of bacterial RNA-Seq data
|
2013-08
|
Paul Sumby
|
Ryan McClure Divya Balasubramanian Yan Sun Maksym Bobrovskyy Caroline A Genco Carin K Vanderpool Brian Tjaden
|
Nucleic Acids Research
|
The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line
|
2013-08-01
|
Jay Shendure Joshua N Burton
|
Andrew Adey Jacob O Kitzman Joseph B Hiatt Alexandra P Lewis Beth K Martin Ruolan Qiu Choli Lee
|
Nature
|
Increased BCAR1 predicts poor outcomes of non-small cell lung cancer in multiple-center patients.
|
2013-08-01
|
Zhifu Sun
|
Bo Deng Wampfler Jason Ping Yang
|
Annals of Surgical Oncology
|
RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus
|
2013-08-02
|
Christine G Elsik Monica F Poelchau
|
Julie A Reynolds David L Denlinger Peter A Armbruster
|
The Journal of Experimental Biology
|
Photoreceptor phagocytosis is mediated by phosphoinositide signaling.
|
2013-08-02
|
Krzysztof Palczewski
|
Debarshi Mustafi Brian M Kevany Christel Genoud Xiaodong Bai
|
FASEB Journal
|
Simultaneous profiling of 194 distinct receptor transcripts in human cells
|
2013-08-06
|
Kevin A. Janes
|
Byong H Kang Karin J Jensen Jaime A Hatch
|
Science Signaling
|
Masculinization of the x chromosome in the pea aphid.
|
2013-08-08
|
Solenn Stoeckel Fabrice Legeai Gaël Le Trionnaire Julie Jaquiéry Nathalie Prunier-Leterme Béatrice Ségurens Julie Poulain Denis Tagu Corinne Da Silva Claude Rispe
|
Denis Roze Lucie Mieuzet Béatrice Ségurens Jean-Christophe Simon
|
PLOS Genetics
|
BlackOPs: increasing confidence in variant detection through mappability filtering.
|
2013-08-08
|
Charles M. Perou
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Christopher R Cabanski Matthew D Wilkerson Matthew Soloway Joel S Parker Jinze Liu Jan F Prins J S Marron D Neil Hayes
|
Nucleic Acids Research
|
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger
|
2013-08-09
|
Stéphane Delmas Steven T. Pullan
|
Laure Ries Sunir Malla Martin J Blythe David B Archer
|
BMC Genomics
|
Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons.
|
2013-08-12
|
Cameron Brennan David Haussler Lynda Chin
|
J Zachary Sanborn Sofie R Salama Mia Grifford Tom Mikkelsen Suresh Jhanwar Sol Katzman
|
Cancer Research
|
Developing nuclear DNA phylogenetic markers in the angiosperm genus Leucadendron (Proteaceae): a next-generation sequencing transcriptomic approach.
|
2013-08-13
|
Emmanuel J. P. Douzery
|
Jeanne Tonnabel Isabelle Olivieri Agnès Mignot Anthony Rebelo Fabienne Justy Sylvain Santoni Stéfanie Caroli Laure Sauné Olivier Bouchez
|
Molecular Phylogenetics and Evolution
|
Comparative genomic and transcriptome analyses of pathotypes of Xanthomonas citri subsp. citri provide insights into mechanisms of bacterial virulence and host range.
|
2013-08-14
|
Joao Carlos Setubal Maxuel O Andrade
|
Neha Jalan Dibyendu Kumar Fahong Yu Jeffrey B Jones James H Graham Frank F White Nian Wang
|
BMC Genomics
|
Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy.
|
2013-08-14
|
Owen J Sansom Chris Ponting Andreas Heger Ian Sudbery Imran Ahmad Joanne Edwards Hing Y Leung Prabhakar Rajan
|
M Eugenia M Villasevil Ernest Mui Janis Fleming Mark Davis David Sims Rhona M McMenemin Ian D Pedley
|
European Urology
|
Adaptive responses to glucose restriction enhance cell survival, antioxidant capability, and autophagy of the protozoan parasite Trichomonas vaginalis.
|
2013-08-17
|
Petrus Tang
|
Kuo-Yang Huang Yi-Ywan Margaret Chen Yi-Kai Fang Wei-Hung Cheng Chih-Chieh Cheng Yu-Chuen Chen Tiffany E Wu Fu-Man Ku Shih-Chieh Chen Rose Lin
|
Biochimica et Biophysica Acta
|
Shaping development through mechanical strain: the transcriptional basis of diet-induced phenotypic plasticity in a cichlid fish.
|
2013-08-19
|
Helen M Gunter Paolo Franchini Axel Meyer Carmelo Fruciano
|
Shaohua Fan Fan Xiong
|
Molecular Ecology
|
Mechanisms of macroevolution: polyphagous plasticity in butterfly larvae revealed by RNA-Seq.
|
2013-08-19
|
Niklas Janz Sören Nylin Maria de la Paz Celorio-Mancera
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Christopher W Wheat Heiko Vogel Lina Söderlind
|
Molecular Ecology
|
Large scale comparison of gene expression levels by microarrays and RNAseq using TCGA data.
|
2013-08-20
|
Quanhu Sheng David C Samuels
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Yan Guo Jiang Li Fei Ye Yu Shyr
|
PLOS ONE
|
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.
|
2013-08-21
|
Pedro Puig
|
Mikel Esnaola David Gonzalez Robert Castelo Juan R Gonzalez
|
BMC Bioinformatics
|
Whole transcriptome RNA-Seq allelic expression in human brain
|
2013-08-22
|
Wolfgang Sadee
|
Ryan M Smith Amy Webb Audrey C Papp Leslie C Newman Samuel K Handelman Adam Suhy Roshan Mascarenhas John Oberdick
|
BMC Genomics
|
Jumping and gliding rodents: mitogenomic affinities of Pedetidae and Anomaluridae deduced from an RNA-Seq approach.
|
2013-08-23
|
Knud A. Jønsson Emmanuel J. P. Douzery
|
Pierre-Henri Fabre
|
Gene
|
Profiling microRNA expression in bovine alveolar macrophages using RNA-seq.
|
2013-08-24
|
Daniel G. Bradley Peter Vegh David J. Lynn David E. MacHugh Stephen V. Gordon
|
Amir B K Foroushani David A Magee Matthew S McCabe John A Browne Nicolas C Nalpas Kevin M Conlon
|
Veterinary Immunology and Immunopathology
|
Transcriptome analysis and SNP identification in SCC of horn in (Bos indicus) Indian cattle.
|
2013-08-24
|
Subhash J Jakhesara Chaitanya G. Joshi
|
Prakash G Koringa Vaibhav D Bhatt Anand B Patel Debabrata Dash
|
Gene
|
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples.
|
2013-08-25
|
Gunnar Rätsch
|
Jonas Behr André Kahles Yi Zhong Vipin T Sreedharan Philipp Drewe
|
Bioinformatics
|
Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum
|
2013-08-26
|
Jianhui Zhang
|
Jianqin Li Haimei Chen Xiangdong Chen Jin Lan Chang Liu
|
PLOS ONE
|
Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis.
|
2013-08-26
|
Isabelle Janoueix-Lerosey Valérie Combaret Valentina Boeva Emmanuel Barillot Olivier Delattre
|
Stéphanie Jouannet Romain Daveau Cécile Pierre-Eugène Alex Cazes Caroline Louis-Brennetot Gudrun Schleiermacher Sandrine Ferrand Gaëlle Pierron Alban Lermine Thomas Rio Frio Virginie Raynal Gilles Vassal
|
PLOS ONE
|
Remodeling of membrane lipids in iron-starved Chlamydomonas.
|
2013-08-27
|
David Casero Sabeeha Merchant Matteo Pellegrini Eugen Urzica Sean D Gallaher Astrid Vieler Christoph Benning
|
Anne Hong-Hermesdorf M Dudley Page Janette Kropat
|
Journal of Biological Chemistry
|
Characterization and comparative analyses of muscle transcriptomes in Dorper and small-tailed Han sheep using RNA-Seq technique.
|
2013-08-30
|
Jianmin Wang
|
Chunlan Zhang Guizhi Wang Zhibin Ji Zhaohuan Liu Xiushuang Pi Cunxian Chen
|
PLOS ONE
|
SNP development from RNA-seq data in a nonmodel fish: how many individuals are needed for accurate allele frequency prediction?
|
2013-08-31
|
Enrique Macpherson
|
C Schunter J C Garza M Pascual
|
Molecular Ecology Resources
|
SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization
|
2013-08-31
|
Shintaro Katayama Juha Kere Sten Linnarsson
|
Virpi Töhönen
|
Bioinformatics
|
Editorial for “Diversity of the non-coding transcriptomes revealed by RNA-seq technologies”
|
2013-09
|
Jean-Christophe Andrau
|
Antonin Morillon
|
Methods
|
Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineage divergence.
|
2013-09-01
|
Nuria Cerdá-Esteban Nancy Mah Francesca Spagnoli
|
Elisa Rodríguez-Seguel Heike Naumann Igor M Pongrac Jean-Fred Fontaine Yongbo Wang Wei Chen Miguel A Andrade-Navarro
|
Genes & Development
|
Mining RNA-seq data for infections and contaminations.
|
2013-09-03
|
Caroline C Friedel Ralf Zimmer
|
Thomas Bonfert Gergely Csaba
|
PLOS ONE
|
RNA-Seq reveals infection-related gene expression changes in Phytophthora capsici.
|
2013-09-03
|
Xiao-Ren Chen
|
Yu-Ping Xing Yan-Peng Li Yun-Hui Tong Jing-You Xu
|
PLOS ONE
|
Trametes versicolor protein YZP activates regulatory B lymphocytes - gene identification through de novo assembly and function analysis in a murine acute colitis model.
|
2013-09-03
|
Fuu Sheu
|
Yen-Chou Kuan Ying-Jou Wu Chih-Liang Hung
|
PLOS ONE
|
Short-term feed deprivation alters immune status of surface mucosa in channel catfish (Ictalurus punctatus).
|
2013-09-04
|
Eric Peatman Lisa Liu
|
Chao Li Baofeng Su Benjamin H Beck
|
PLOS ONE
|
Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia.
|
2013-09-06
|
David Casero Thomas Happe Sabeeha Merchant Matteo Pellegrini Anja Hemschemeier Christoph Benning
|
Bensheng Liu
|
The Plant Cell
|
Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.
|
2013-09-08
|
Yiqi Seow Shahrouz Amini Ali Miserez
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Paul A Guerette Shawn Hoon Manfred Raida Admir Masic Fong T Wong Vincent H B Ho Kiat Whye Kong Melik C Demirel Abdon Pena-Francesch Gavin Z Tay Dawei Ding
|
Nature Biotechnology
|
Beta cell 5'-shifted isomiRs are candidate regulatory hubs in type 2 diabetes.
|
2013-09-09
|
Jeanette Baran-Gale
|
Emily E Fannin C Lisa Kurtz Praveen Sethupathy
|
PLOS ONE
|
U1 small nuclear ribonucleoprotein complex and RNA splicing alterations in Alzheimer's disease.
|
2013-09-10
|
Yuxin Li Drew R Jones Hao Wu Eric B Dammer David A Bennett
|
Bing Bai Chadwick M Hales Ping-Chung Chen Yair Gozal Jason J Fritz Xusheng Wang Qiangwei Xia Duc M Duong Craig Street Gloria Cantero Dongmei Cheng Zhiping Wu Ian Diner Craig J Heilman Howard D Rees Li Lin Keith E Szulwach Marla Gearing Elliott J Mufson Thomas J Montine Nicholas T Seyfried Thomas S Wingo Yi E Sun Peng Jin John Hanfelt Donna M Willcock Allan Levey James J Lah Junmin Peng
|
Proceedings of the National Academy of Sciences of the United States of America
|
Analysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with Cis-eQTL identified using genetic linkage.
|
2013-09-11
|
Aldons Jake Lusis Eleazar Eskin Pierre-François Roux Sandrine Lagarrigue
|
Lisa Martin Farhad Hormozdiari Calvin Pan Atila van Nas Olivier Demeure Rita Cantor Anatole Ghazalpour
|
Genetics
|
Androgen receptor signaling regulates DNA repair in prostate cancers.
|
2013-09-11
|
Deyou Zheng Daniel E. Spratt Michael J Zelefsky
|
William R Polkinghorn Joel S Parker Man X Lee Elizabeth M Kass Phillip J Iaquinta Vivek K Arora Wei-Feng Yen Ling Cai Brett S Carver Yu Chen Philip A Watson Neel P Shah Sho Fujisawa Alexander G Goglia Anuradha Gopalan Haley Hieronymus John Wongvipat Peter T Scardino Maria Jasin Jayanta Chaudhuri Simon N Powell Charles L Sawyers
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Cancer Discovery
|
A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease
|
2013-09-14
|
Kenneth J McDowall
|
Yu-fei Lin David Romero A Shuang Guan Lira Mamanova
|
BMC Genomics
|
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
|
2013-09-15
|
Ann-Christine Syvänen Michael Sammeth Tuuli Lappalainen Xavier Estivill i Pallejà Peter A.C. 't Hoen Marc Friedlander Jeroen Laros
|
Jonas Almlöf Irina Pulyakhina Seyed Yahya Anvar Henk P J Buermans Olof Karlberg Mathias Brännvall GEUVADIS Consortium Johan T den Dunnen Gert-Jan B van Ommen Ivo G Gut Roderic Guigó Emmanouil T Dermitzakis
|
Nature Biotechnology
|
Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy
|
2013-09-16
|
Niles A. Pierce Xinning Zhang Vikas Trivedi
|
Adam Z Rosenthal Kaitlyn S Lucey Elizabeth A Ottesen Harry M T Choi Niles A Pierce Jared R Leadbetter
|
Proceedings of the National Academy of Sciences of the United States of America
|
RNA-Seq analysis of Mycobacterium avium non-coding transcriptome
|
2013-09-16
|
Dmitriy Ignatov Timofey Skvortsov Alexander S Apt
|
Sofia Malakho Konstantin Majorov Tatyana Azhikina
|
PLOS ONE
|
DEXUS: identifying differential expression in RNA-Seq studies with unknown conditions
|
2013-09-17
|
Sepp Hochreiter Günter Klambauer Thomas Unterthiner
|
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Nucleic Acids Research
|
Analysis of the host transcriptome from demyelinating spinal cord of murine coronavirus-infected mice.
|
2013-09-18
|
Fan Li
|
Ruth Elliott Isabelle Dragomir Ming Ming W Chua Brian D Gregory Susan R Weiss
|
PLOS ONE
|
Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens.
|
2013-09-18
|
John Quackenbush
|
Xuanhui Sharron Lin Lan Hu Kirley Sandy Mick Correll Chin-Lee Wu William Scott McDougal
|
Urologic Oncology
|
Epstein-Barr virus and human herpesvirus 6 detection in a non-Hodgkin's diffuse large B-cell lymphoma cohort by using RNA sequencing.
|
2013-09-18
|
Melody Baddoo Tina O'Grady Erik K Flemington
|
Michael J Strong Zhen Lin Guorong Xu Melody Baddoo Chris Parsons Kun Zhang Christopher M Taylor
|
Journal of Virology
|
Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.
|
2013-09-20
|
Jens Nielsen Mathias Uhlén Elton P. Hudson
|
Josefine Anfelt Björn Hallström
|
Applied and Environmental Microbiology
|
Accounting for technical noise in single-cell RNA-seq experiments.
|
2013-09-22
|
Simon Anders Vladimir Benes Sarah Teichmann John C Marioni Valentina Proserpio Marcus Heisler Jong Kyoung Kim
|
Philip Brennecke Aleksandra A Kołodziejczyk Xiuwei Zhang Bianka Baying
|
Nature Methods
|
Cryptic FUS-ERG fusion identified by RNA-sequencing in childhood acute myeloid leukemia.
|
2013-09-25
|
Sverre Heim Ioannis Panagopoulos
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Ludmila Gorunova Bernward Zeller Anne Tierens
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Oncology Reports
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Next-generation sequence analysis of cancer xenograft models.
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2013-09-26
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Fernando J Rossello Kara L. Britt Richard W. Tothill Luciano G. Martelotto Jason Li Luigi Marchionni
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Kieren D Marini Jeanette Falzon David M Thomas Craig D Peacock Samara Bennett Erwin Tantoso Tracey Brown Philip Chan D Neil Watkins
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PLOS ONE
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Taf7l cooperates with Trf2 to regulate spermiogenesis.
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2013-09-30
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Ke Zheng Ivan Grubisic Tommy Kaplan Robert Tjian
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Haiying Zhou Ying He P Jeremy Wang
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Proceedings of the National Academy of Sciences of the United States of America
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Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria.
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2013-09-30
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Margaret F Romine Ronald Taylor
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Bobbie-Jo M Webb Robertson Lye Meng Markillie Margrethe H Serres Bryan E Linggi Joshua T Aldrich Eric A Hill Mary S Lipton H Steven Wiley
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Integrative Biology
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Human housekeeping genes, revisited
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2013-10
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Eli Eisenberg
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Erez Y. Levanon
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Trends in Genetics
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Evaluation of the effectiveness of semen storage and sperm purification methods for spermatozoa transcript profiling
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2013-10
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Russ Hauser Zhen Chen
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Shihong Mao Robert J Goodrich Steven M Schrader Stephen A Krawetz
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Systems Biology in Reproductive Medicine
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RNA-Seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation
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2013-10-01
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Heiko Liesegang Sandra Wiegand Rolf Daniel
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Sascha Dietrich Robert Hertel Johannes Bongaerts Stefan Evers Sonja Volland
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BMC Genomics
|
RNA-Seq analysis of Citrus reticulata in the early stages of Xylella fastidiosa infection reveals auxin-related genes as a defense response.
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2013-10-03
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Luciano T. Kishi
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Carolina M Rodrigues Alessandra A de Souza Marco A Takita Marcos A Machado
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BMC Genomics
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Transcriptome comparison of human neurons generated using induced pluripotent stem cells derived from dental pulp and skin fibroblasts
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2013-10-03
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Deyou Zheng John J. Foxe
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Jian Chen Mingyan Lin Erika Pedrosa Anastasia Hrabovsky Reed Carroll Herbert M Lachman
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PLOS ONE
|
Transcriptomics of the rice blast fungus Magnaporthe oryzae in response to the bacterial antagonist Lysobacter enzymogenes reveals candidate fungal defense response genes
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2013-10-03
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Bradley I. Hillman
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Sandra M Mathioni Nrupali Patel Bianca Riddick James A Sweigard Kirk J Czymmek Jeffrey L Caplan Sridhara G Kunjeti Saritha Kunjeti Vidhyavathi Raman Donald Y Kobayashi Nicole M Donofrio
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PLOS ONE
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Function of lncRNAs and approaches to lncRNA-protein interactions.
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2013-10-05
|
Hanjiang Fu
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Juanjuan Zhu Yongge Wu Xiaofei Zheng
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Science in China. Series C: Life Sciences
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In vitro grown pollen tubes of Nicotiana alata actively synthesise a fucosylated xyloglucan.
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2013-10-08
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Edwin R. Lampugnani Ed Newbigin Antony Bacic
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Isabel E Moller Andrew Cassin Daniel F Jones Poh Ling Koh Sunil Ratnayake Cherie T Beahan Sarah M Wilson
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PLOS ONE
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Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study
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2013-10-09
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Gregory Poland
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Brooke L Fridley Gregory D Jenkins Diane E Grill Richard B Kennedy Ann L Oberg
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Scientific Reports
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mirCoX: a database of miRNA-mRNA expression correlations derived from RNA-seq meta-analysis.
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2013-10-09
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Mikhail G Dozmorov
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Cory B Giles Reshmi Girija-Devi Jonathan D Wren
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BMC Bioinformatics
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Towards the integration, annotation and association of historical microarray experiments with RNA-seq
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2013-10-09
|
Michael A Bauer
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Shweta S Chavan Erich A Peterson Christoph J Heuck Donald J Johann
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BMC Bioinformatics
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Host-Mycobacterium avium subsp. paratuberculosis interactome reveals a novel iron assimilation mechanism linked to nitric oxide stress during early infection.
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2013-10-10
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Srinand Sreevatsan
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Elise A Lamont Wayne W Xu
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BMC Genomics
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Histoplasma yeast and mycelial transcriptomes reveal pathogenic-phase and lineage-specific gene expression profiles.
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2013-10-10
|
Chad Rappleye
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Jessica A Edwards Chenxi Chen Megan M Kemski Jinnan Hu Thomas K Mitchell
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BMC Genomics
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Transcriptome comparison between porcine subcutaneous and intramuscular stromal vascular cells during adipogenic differentiation.
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2013-10-10
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Hongkui Wei
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Shuzhong Jiang Tongxing Song Yang Yang Jian Peng Siwen Jiang
|
PLOS ONE
|
Modeling the next generation sequencing sample processing pipeline for the purposes of classification.
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2013-10-11
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Charles D. Johnson Edward R. Dougherty
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Noushin Ghaffari Mohammadmahdi R Yousefi Ivan Ivanov
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BMC Bioinformatics
|
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots.
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2013-10-11
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W. Richard McCombie Elena A Vidal Gabriel Krouk Milos Tanurdzic Rodrigo A Gutiérrez
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Tomás C Moyano Manpreet S Katari Gloria M Coruzzi
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BMC Genomics
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GIIRA--RNA-Seq driven gene finding incorporating ambiguous reads.
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2013-10-11
|
Bernhard Y Renard
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Franziska Zickmann Martin S Lindner
|
Bioinformatics
|
F11R is a novel monocyte prognostic biomarker for malignant glioma
|
2013-10-11
|
Xi Feng Winnie W Pong Jaebok Choi Malachi Griffith Obi Griffith Greg N. Fuller David H Gutmann
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Jason Walker Todd Wylie Vincent Magrini Jingqin Luo Ryan J Emnett Matthew L Cooper Joshua B Rubin David Piwnica-Worms Dolores Hambardzumyan John F DiPersio Elaine R Mardis
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PLOS ONE
|
SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads.
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2013-10-11
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Tak-Wah Lam Jun Wang Jikun Wu Zhiyu Peng
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Wenqian Zhang Songbo Huang Zengquan He Yanbing Cheng Siu-Ming Yiu
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Bioinformatics
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Profiling the molecular mechanism of fullerene cytotoxicity on tumor cells by RNA-seq.
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2013-10-12
|
Marco Gerdol Alberto Pallavicini Marianna Lucafò Gianni Sava Sabrina Pacor Maurizio Prato
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Sonia Zorzet Tatiana Da Ros
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Toxicology
|
Use of a capture-based pathogen transcript enrichment strategy for RNA-Seq analysis of the Francisella tularensis LVS transcriptome during infection of murine macrophages.
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2013-10-14
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David M Brazel
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Zachary W Bent Mary B Tran-Gyamfi Rachelle Y Hamblin Victoria A VanderNoot Steven S Branda
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PLOS ONE
|
Ribosomal protein S6 mRNA is a biomarker upregulated in multiple sclerosis, downregulated by interferon treatment, and affected by season.
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2013-10-14
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Peter M. Visscher Mark Slee Joseph E. Powell Grant W. Montgomery Fiona C McKay
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Grant P Parnell Prudence N Gatt Stephen Schibeci Malgorzata Krupa Jeannette Lechner-Scott Simon Broadley Christopher Liddle Steve Vucic Graeme J Stewart David R Booth
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Multiple Sclerosis Journal
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An RNA-seq transcriptome analysis of histone modifiers and RNA silencing genes in soybean during floral initiation process.
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2013-10-16
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Lim Chee Liew Mohan B. Singh Prem L. Bhalla
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PLOS ONE
|
Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network
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2013-10-16
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Marcel E. Dinger John Mattick Animesh Ray Shaojie Zhang
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Jian-Liang Li Joseph Mazar Cuncong Zhong Geoffrey J Faulkner Subramaniam S Govindarajan Zhan Zhang Gavin Meredith Christopher Adams Ranjan J Perera
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Scientific Reports
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A novel intra-U1 snRNP cross-regulation mechanism: alternative splicing switch links U1C and U1-70K expression.
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2013-10-17
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Ekaterina E Khrameeva
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Tanja Dorothe Rösel-Hillgärtner Lee-Hsueh Hung Patrick Le Querrec Mikhail S Gelfand Albrecht Bindereif
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PLOS Genetics
|
A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.
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2013-10-17
|
Liming Xiong Shoudong Zhang
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Tao Chen Peng Cui Hao Chen Shahjahan Ali
|
PLOS Genetics
|
Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032
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2013-10-19
|
Alfred Pühler Jörn Kalinowski
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Almut Mentz Armin Neshat Katharina Pfeifer-Sancar Christian Rückert
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BMC Genomics
|
Quantitative assessment of single-cell RNA-sequencing methods.
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2013-10-20
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Barbara Treutlein Piero Dalerba
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Angela R Wu Norma F Neff Tomer Kalisky Michael E Rothenberg Francis M Mburu Gary L Mantalas Sopheak Sim Michael F Clarke Stephen R Quake
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Nature Methods
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HAMR: high-throughput annotation of modified ribonucleotides.
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2013-10-22
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Otto Valladares
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Paul Ryvkin Yuk Yee Leung Ian M Silverman Micah Childress Isabelle Dragomir Brian D Gregory Li-San Wang
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RNA
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Genome-wide analysis of poly(A) site selection in Schizosaccharomyces pombe.
|
2013-10-23
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Monika Gullerova Jürg Bähler Nicholas Jarvis Proudfoot
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Margarita Schlackow Samuel Marguerat Jürg Bähler Radek Erban
|
RNA
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Parallel deep transcriptome and proteome analysis of zebrafish larvae
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2013-10-24
|
Christiaan V. Henkel Magnus Palmblad Herman P Spaink
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Ron P Dirks Annemarie H Meijer André M Deelder
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BMC Research Notes
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Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress.
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2013-10-24
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Alistair C. Darby Dong Xia
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A Christina Gill Stuart D Armstrong Catherine S Hartley Jonathan M Wastling Benjamin L Makepeace
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The ISME Journal
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IMG 4 version of the integrated microbial genomes comparative analysis system.
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2013-10-27
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Natalia N. Ivanova Nikos C. Kyrpides Tanja Woyke Neha Varghese Konstantinos Billis Amrita Pati Marcel Huntemann Iain J. Anderson Konstantinos Mavromatis Krishna Palaniappan
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Victor M Markowitz I-Min A Chen Ken Chu Ernest Szeto Manoj Pillay Anna Ratner Jinghua Huang
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Nucleic Acids Research
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Differential expression of olfactory genes in the southern house mosquito and insights into unique odorant receptor gene isoforms.
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2013-10-28
|
Walter S Leal
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Young-Moo Choo Pingxi Xu Cherre S B da Silva Carlos Ueira-Vieira
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Proceedings of the National Academy of Sciences of the United States of America
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Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps.
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2013-10-29
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Ross C Hardison Manolis Kellis
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Ali Mortazavi Shirley Pepke Camden Jansen Georgi K Marinov Jason Ernst Richard M Myers Barbara J Wold
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Genome Research
|
A unified model for yeast transcript definition.
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2013-10-29
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Harm van Bakel Corey Nislow Carl G de Boer Quaid D Morris
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Kyle Tsui Joyce Li Jack F Greenblatt Timothy R Hughes
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Genome Research
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Inferring polymorphism-induced regulatory gene networks active in human lymphocyte cell lines by weighted linear mixed model analysis of multiple RNA-Seq datasets.
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2013-10-30
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Erik K Flemington
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Wensheng Zhang Andrea Edwards Kun Zhang
|
PLOS ONE
|
Probing bacterial metabolism during infection using high-resolution transcriptomics
|
2013-11
|
Marvin Whiteley
|
Peter Jorth Urvish Trivedi Kendra Rumbaugh
|
Journal of Bacteriology
|
An integrated model of the transcriptome of HER2-positive breast cancer.
|
2013-11-01
|
Kevin J Thompson Xiaojia Tang Krishna R Kalari Richard W. Joseph Zhifu Sun
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Brian M Necela Melissa Lau Jeanette E Eckel-Passow Jennifer M Kachergus S Keith Anderson Saurabh Baheti Jennifer M Carr Tiffany R Baker Poulami Barman Derek C Radisky Sarah A McLaughlin High-seng Chai Stephan Camille David Rossell Yan W Asmann E Aubrey Thompson Edith A Perez
|
PLOS ONE
|
Identification of molecular tumor markers in renal cell carcinomas with TFE3 protein expression by RNA sequencing.
|
2013-11-01
|
Mark Rubin
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Dorothee Pflueger Andrea Sboner Martina Storz Jasmine Roth Eva Compérat Elisabeth Bruder Peter Schraml Holger Moch
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Neoplasia
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RNA-seq-based comparative transcriptome analysis of the syngas-utilizing bacterium Clostridium ljungdahlii DSM 13528 grown autotrophically and heterotrophically.
|
2013-11-01
|
Fuli Li
|
Yang Tan Juanjuan Liu Xiaohua Chen Huajun Zheng
|
Molecular BioSystems
|
Global aspects of pacC regulation of pathogenicity genes in Colletotrichum gloeosporioides as revealed by transcriptome analysis.
|
2013-11-01
|
Michael Thon Serenella Sukno
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Noam Alkan Xiangchun Meng Gilgi Friedlander Eli Reuveni Amir Sherman Robert Fluhr Dov Prusky
|
Molecular Plant-Microbe Interactions
|
Systematic evaluation of spliced alignment programs for RNA-seq data
|
2013-11-03
|
Jennifer Harrow Roderic Guigó i Serra Tamara Steijger Pär G Engström Gregory R Grant Gunnar Rätsch Nick Goldman Paul Bertone
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Botond Sipos André Kahles Tim J Hubbard RGASP Consortium
|
Nature Methods
|
Assessment of transcript reconstruction methods for RNA-seq.
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2013-11-03
|
Tim Hubbard Jennifer Harrow Felix Kokocinski Roderic Guigó i Serra Tamara Steijger Pär G Engström Josep F. Abril Paul Bertone
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RGASP Consortium
|
Nature Methods
|
Model-based clustering for RNA-seq data.
|
2013-11-04
|
Thomas Brutnell
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Yaqing Si Peng Liu Pinghua Li
|
Bioinformatics
|
The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations
|
2013-11-04
|
Gavin Sherlock Jennifer R Wortman Diane Inglis
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Gustavo C Cerqueira Martha B Arnaud Marek S Skrzypek Gail Binkley Matt Simison Stuart R Miyasato Jonathan Binkley Joshua Orvis Prachi Shah Farrell Wymore
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Nucleic Acids Research
|
Dysregulation of synaptogenesis genes antecedes motor neuron pathology in spinal muscular atrophy.
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2013-11-04
|
Anna Maria Pinto Christopher Dengler
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Zhenxi Zhang Lili Wan Wei Wang Michael G Berg Isabela Oliva Larry N Singh Zhi Wei Gideon Dreyfuss
|
Proceedings of the National Academy of Sciences of the United States of America
|
Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments.
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2013-11-05
|
Russell S. Thomas Michael B Black
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Bethany B Parks Linda Pluta Tzu-Ming Chu Bruce C Allen Russell D Wolfinger
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Toxicological Sciences
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Serotonergic neuron regulation informed by in vivo single-cell transcriptomics.
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2013-11-05
|
Tamas Bartfai
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Jennifer M Spaethling David Piel Hannah Dueck Peter T Buckley Jacqueline F Morris Stephen A Fisher Jaehee Lee Jai-Yoon Sul Junhyong Kim Sheryl G Beck James H Eberwine
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FASEB Journal
|
Surfing transcriptomic landscapes. A step beyond the annotation of chromosome 16 proteome.
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2013-11-05
|
Miguel Marcilla Cristina Ruiz-Romero Joan J Bech-Serra Oscar Gallardo Gorka Prieto Concha Gil Joaquín Abian Marta Mendes Irene Orera Noelia Dasilva Kerman Aloria María I Mora Manuel Fuentes José M Mato
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Víctor Segura Juan Alberto Medina-Aunon Salvador Martínez-Bartolomé Oreto Antúnez Jesús M Arizmendi Mikel Azkargorta Silvia Barceló-Batllori Jabier Beaskoetxea Francisco Blanco Mariana B Monteiro David Cáceres Francesc Canals Monserrat Carrascal José Ignacio Casal Felipe Clemente Nuria Colomé Paula Díaz Félix Elortza Patricia Fernández-Puente Severine I Gharbi Carmen González-Tejedo María Luisa Hernáez Manuel Lombardía Maria Lopez-Lucendo Eliandre Oliveira Alberto Pascual-Montano Manuel M Sánchez del Pino Daniel Tabas-Madrid Maria L Valero Vital Vialas Joan Villanueva Juan Pablo Albar Fernando J Corrales
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Journal of Proteome Research
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Modeling alternative splicing variants from RNA-Seq data with isoform graphs.
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2013-11-07
|
Gianluca Della Vedova
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Stefano Beretta Paola Bonizzoni Yuri Pirola Raffaella Rizzi
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Journal of Computational Biology
|
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation.
|
2013-11-07
|
Alexander van Oudenaarden Wenqian Hu Jiahai Shi Harvey Lodish
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Juan R Alvarez-Dominguez Bingbing Yuan Staphany S Park Austin A Gromatzky
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Blood
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Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes
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2013-11-07
|
Gil Omenn
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Rajasree Menon Hogune Im Emma Yue Zhang Shiaw-Lin Wu Rui Chen Michael Snyder William S Hancock
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Journal of Proteome Research
|
Comprehensive RNA-Seq expression analysis of sensory ganglia with a focus on ion channels and GPCRs in Trigeminal ganglia
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2013-11-08
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Hanns Hatt Günter Gisselmann
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Stavros Manteniotis Ramona Lehmann Caroline Flegel Felix Vogel Adrian Hofreuter Benjamin S P Schreiner Janine Altmüller Christian Becker Nicole Schöbel Günter Gisselmann
|
PLOS ONE
|
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki)
|
2013-11-09
|
David Sturgill
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John H Malone Xia Sun Harold E Smith Leonard Rabinow Marie-Laure Samson Brian Oliver
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BMC Bioinformatics
|
Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo
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2013-11-11
|
Jinfeng Liu Xinyang Zhao Eunhee Kim Omar Abdel-Wahab
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Jie Gao Mazhar Adli Anwesha Dey Thomas Trimarchi Young Rock Chung Cem Kuscu Todd Hricik Delphine Ndiaye-Lobry Lindsay M Lafave Richard Koche Alan H Shih Olga A Guryanova Sheng Li Suveg Pandey Joseph Y Shin Leon Telis Parva K Bhatt Sebastien Monette Christopher E Mason Christopher Y Park Bradley E Bernstein Iannis Aifantis Ross L Levine
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Journal of Experimental Medicine
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Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.
|
2013-11-13
|
Adam Ameur
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Ammar Zaghlool Linnea Nyberg Jonatan Halvardson Manfred Grabherr Lucia Cavelier Lars Feuk
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BMC Biotechnology
|
Mapping genetic modifiers of survival in a mouse model of Dravet syndrome.
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2013-11-14
|
Jennifer A Kearney
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A R Miller N A Hawkins C E McCollom
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Genes, Brain and Behavior
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Early T helper cell programming of gene expression in human
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2013-11-15
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Riitta Lahesmaa
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Soile Tuomela
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Seminars in Immunology
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Resolving chromosome-centric human proteome with translating mRNA analysis: a strategic demonstration.
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2013-11-15
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Yizhi Cui Qing-Yu He Gong Zhang Tong Wang
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Jiayong Zhong Jiahui Guo Zhipeng Chen Lijuan Yang
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Journal of Proteome Research
|
Accuracy of allele frequency estimation using pooled RNA-Seq.
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2013-11-16
|
Mateusz Konczal Wieslaw Babik Jacek Radwan Paweł Koteja
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M T Stuglik
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Molecular Ecology Resources
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Proteogenomic analysis reveals unanticipated adaptations of colorectal tumor cells to deficiencies in DNA mismatch repair.
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2013-11-18
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Daniel C. Liebler
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Patrick J Halvey Xiaojing Wang Jing Wang Ajaz A Bhat Punita Dhawan Ming Li Bing Zhang Robbert J C Slebos
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Cancer Research
|
Expression of Porphyromonas gingivalis small RNA in response to hemin availability identified using microarray and RNA-seq analysis.
|
2013-11-19
|
Ann Progulske-Fox
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Priscilla Phillips Scott Grieshaber Nicole Grieshaber
|
FEMS Microbiology Letters
|
Global analysis of differentially expressed genes and proteins in the wheat callus infected by Agrobacterium tumefaciens
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2013-11-20
|
Dongwen Lv
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Xiaohong Zhou Ke Wang Chengjun Wu Jiarui Li Pei Zhao Zhishan Lin Lipu Du Yueming Yan Xingguo Ye
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PLOS ONE
|
Phenotypic and transcriptional fidelity of patient-derived colon cancer xenografts in immune-deficient mice
|
2013-11-20
|
Edus H Warren
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Jeffrey Chou Matthew P Fitzgibbon Christie-Lynn L Mortales Andrea M H Towlerton Melissa P Upton Raymond S Yeung Martin W McIntosh
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PLOS ONE
|
Global bidirectional transcription of the Epstein-Barr virus genome during reactivation.
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2013-11-20
|
Melody Baddoo Tina O'Grady Erik K Flemington
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Subing Cao Michael J Strong Monica Concha Xia Wang Sandra Splinter Bondurant Marie Adams Melody Baddoo Sudesh K Srivastav Zhen Lin Claire Fewell Qinyan Yin
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Journal of Virology
|
Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.
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2013-11-21
|
Graham Rose Teresa Cortes Olga T Schubert Kristine B Arnvig Iñaki Comas Ruedi Aebersold
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Douglas B Young
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Cell Reports
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DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis.
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2013-11-21
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Zizhen Yao Silvère M van der Maarel
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Janet M Young Jennifer L Whiddon Bhavatharini Kasinathan Lauren Snider Linda N Geng Judit Balog Rabi Tawil Stephen J Tapscott
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PLOS Genetics
|
RNA-seq profiles of immune related genes in the staghorn coral Acropora cervicornis infected with white band disease
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2013-11-21
|
Silvia Libro
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Stefan T Kaluziak Steven V Vollmer
|
PLOS ONE
|
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.
|
2013-11-21
|
Víctor Quesada Núria López-Bigas Alfonso Valencia Carlos López Otín Roderic Guigó i Serra Jean Monlong Panagiotis Papasaikas Simone Ecker Guillem Clot Sarah Djebali Pedro G Ferreira Rory Johnson Daniel Rico Gonzalo Gómez-López Xose S. Puente David G. Pisano María Rozman José I Martín-Subero Dolors Colomer Elias Campo
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Pedro Jares Alejandra Martínez-Trillos Neus Villamor Abel González-Pérez David G Knowles Mónica López-Guerra Cristina Royo Maite Cazorla Magda Pinyol Marta Aymerich Marta Kulis David Tamborero Anaïs Gouin Julie Blanc Marta Gut Ivo Gut Armando López-Guillermo
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Genome Research
|
RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.
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2013-11-22
|
Adam J Reid Joshua P Ramsay Laurent Gatto Lars Barquist
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Nabil M Wilf Neil R Williamson Nicholas J Croucher Svenja S Hester David Goulding Kathryn S Lilley Robert A Kingsley Gordon Dougan George Pc Salmond
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BMC Genomics
|
Assessment of myometrial transcriptome changes associated with spontaneous human labour by high-throughput RNA-seq.
|
2013-11-22
|
Jonathan D. Moore Andrew M Blanks Siobhan Quenby
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Yi-Wah Chan Hugo A van den Berg
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Experimental Physiology
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MMDiff: quantitative testing for shape changes in ChIP-Seq data sets
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2013-11-24
|
Thomas Clouaire Adrian Peter Bird
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Gabriele Schweikert Botond Cseke Guido Sanguinetti
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BMC Genomics
|
Flexible analysis of RNA-seq data using mixed effects models.
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2013-11-26
|
Ernest Turro
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William J Astle Simon Tavaré
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Bioinformatics
|
Characterization of the human ESC transcriptome by hybrid sequencing.
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2013-11-26
|
Harm van Bakel Renee Reijo Pera
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Kin Fai Au Vittorio Sebastiano Pegah Tootoonchi Afshar Jens Durruthy Durruthy Lawrence Lee Brian A Williams Eric E Schadt Jason G Underwood Wing Hung Wong
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Proceedings of the National Academy of Sciences of the United States of America
|
Transcriptional regulation of two conceptus interferon tau genes expressed in Japanese black cattle during peri-implantation period.
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2013-11-27
|
So Nakagawa
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Toshihiro Sakurai Min-Su Kim Hanako Bai Rulan Bai Junyou Li Kwan-Sik Min Atsushi Ideta Yoshito Aoyagi Kazuhiko Imakawa
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PLOS ONE
|
RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns.
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2013-12-01
|
Judith Zoephel L Randau
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Judith Zoephel
|
Biochemical Society Transactions
|
An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.
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2013-12-01
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Carsten Kröger Shabarinath Srikumar Kristian Händler Karsten Hokamp
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Aoife Colgan Sathesh K Sivasankaran Disa L Hammarlöf Rocío Canals Joe E Grissom Tyrrell Conway Jay C D Hinton
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Cell Host & Microbe
|
The transcription-splicing protein NonO/p54nrb and three NonO-interacting proteins bind to distal enhancer region and augment rhodopsin expression.
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2013-12-02
|
Anand Swaroop Matthew Brooks
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Sharda P Yadav Hong Hao Hyun-Jin Yang Marie-Audrey I Kautzmann Jacob Nellissery Bernward Klocke Martin Seifert
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Human Molecular Genetics
|
Comparative N-glycan profiling of colorectal cancer cell lines reveals unique bisecting GlcNAc and α-2,3-linked sialic acid determinants are associated with membrane proteins of the more metastatic/aggressive cell lines.
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2013-12-02
|
Morten Thaysen-Andersen Susan Fanayan Mark Baker
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Manveen K Sethi Joshua T Smith Nicolle H Packer William S Hancock
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Journal of Proteome Research
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Comparison of software packages for detecting differential expression in RNA-seq studies.
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2013-12-02
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Laura L. Elo
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Fatemeh Seyednasrollah Asta Laiho
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Briefings in Bioinformatics
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Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines.
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2013-12-03
|
György Marko-Varga
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Cheryl F Lichti Huiling Liu Alexander S Shavkunov Ekaterina Mostovenko Erik P Sulman Ravesanker Ezhilarasan Qianghu Wang Roger A Kroes Joseph C Moskal David Fenyö Betül Akgöl Oksuz Charles A Conrad Frederick F Lang Frode S Berven Akos Végvári Melinda Rezeli Sophia Hober Carol L Nilsson
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Journal of Proteome Research
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Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data.
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2013-12-03
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Stefano Calza
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Chen Suo Agus Salim Yudi Pawitan
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Bioinformatics
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The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum
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2013-12-04
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Blake Meyers
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Keerthi P Venkataramanan Shawn W Jones Kevin P McCormick Sridhara G Kunjeti Matthew T Ralston Eleftherios T Papoutsakis
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BMC Genomics
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Simultaneous transcriptional profiling of bacteria and their host cells
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2013-12-04
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Claire M. Fraser Naomi Sengamalay Marcus C. Chibucos Amol C Shetty Todd Creasy
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Michael S Humphrys Yezhou Sun Elliott F Drabek Umar Farooq Naomi Sengamalay Sandy Ott Huizhong Shou Patrik M Bavoil Anup Mahurkar Garry S A Myers
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PLOS ONE
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Vespucci: a system for building annotated databases of nascent transcripts.
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2013-12-04
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Terry Gaasterland Minna U Kaikkonen Christopher K Glass
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Karmel A Allison
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Nucleic Acids Research
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A platform independent RNA-Seq protocol for the detection of transcriptome complexity.
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2013-12-05
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Graziano Pesole Flaviana Marzano Mariano Francesco Caratozzolo Ivana Kurelac D D'Elia Anna Maria D'Erchia Flavio Licciulli Ernesto Picardi
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Claudia Calabrese Marina Mangiulli Caterina Manzari Anna Maria Paluscio Sabino Liuni Marcella Attimonelli Giuseppe Gasparre Anna Maria Porcelli Elisabetta Sbisà Apollonia Tullo
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BMC Genomics
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Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.
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2013-12-05
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Jens Nielsen Mathias Uhlén Jenny Ottosson Takanen Cristina Al-Khalili Szigyarto Kalle von Feilitzen Linn Fagerberg Jan Mulder Mikael Huss Jochen Schwenk Jacob Odeberg Peter Nilsson Per Oksvold
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Björn M Hallström Caroline Kampf Dijana Djureinovic Masato Habuka Simin Tahmasebpoor Angelika Danielsson Karolina Edlund Anna Asplund Evelina Sjöstedt Emma Lundberg Marie Skogs Jenny Ottosson Takanen Holger Berling Hanna Tegel Cecilia Lindskog Frida Danielsson Adil Mardinoglu Asa Sivertsson Kalle von Feilitzen Mattias Forsberg Martin Zwahlen IngMarie Olsson Sanjay Navani Fredrik Ponten
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Molecular & Cellular Proteomics
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Fermentation stage-dependent adaptations of Bacillus licheniformis during enzyme production.
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2013-12-06
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Sandra Wiegand Heiko Liesegang Rolf Daniel
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Birgit Voigt Dirk Albrecht Johannes Bongaerts Stefan Evers Michael Hecker
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Microbial Cell Factories
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RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.
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2013-12-06
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Brian Scheffler Megan J Bowman Philip J Bauer
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Wonkeun Park Joshua A Udall Justin T Page Joshua Raney Don C Jones B Todd Campbell
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PLOS ONE
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Co-expression network analysis identifies Spleen Tyrosine Kinase (SYK) as a candidate oncogenic driver in a subset of small-cell lung cancer
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2013-12-09
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John K. Field
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Akshata R Udyavar Megan D Hoeksema Jonathan E Clark Yong Zou Zuojian Tang Zhiguo Li Ming Li Heidi Chen Alexander Statnikov Yu Shyr Daniel C Liebler Rosana Eisenberg Lourdes Estrada Pierre P Massion Vito Quaranta
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BMC Systems Biology
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ETV6-NTRK3 is a common chromosomal rearrangement in radiation-associated thyroid cancer.
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2013-12-10
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Tetiana Bogdanova Mark P Little
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Rebecca J Leeman-Neill Lindsey M Kelly Pengyuan Liu Alina V Brenner Viktoria N Evdokimova Maureen Hatch Liudmyla Y Zurnadzy Marina N Nikiforova Ning J Yue Miao Zhang Kiyohiko Mabuchi Mykola D Tronko Yuri E Nikiforov
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Cancer
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Next generation sequencing analysis of human platelet PolyA+ mRNAs and rRNA-depleted total RNA.
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2013-12-11
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Abdimajid Osman
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Antheia Kissopoulou Jon Jonasson Tomas L Lindahl
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PLOS ONE
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Transcriptome changes in the porcine endometrium during the preattachment phase.
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2013-12-12
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Susanne E. Ulbrich
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Anastazia Samborski Alexander Graf Stefan Krebs Barbara Kessler Myriam Reichenbach Horst-Dieter Reichenbach Stefan Bauersachs
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Biology of Reproduction
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TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes.
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2013-12-13
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Michiel Van Bel Klaas Vandepoele Yves Van de Peer
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Sebastian Proost Christophe Van Neste Dieter Deforce Yves Van de Peer
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Genome Biology
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Identification of two putative reference genes from grapevine suitable for gene expression analysis in berry and related tissues derived from RNA-Seq data
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2013-12-13
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Ariel Orellana
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Mauricio González-Agüero Miguel García-Rojas Alex Di Genova José Correa Alejandro Maass Patricio Hinrichsen
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BMC Genomics
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Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola.
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2013-12-16
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Jun-Jun Liu
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Rona N Sturrock Ross Benton
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BMC Genomics
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Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique
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2013-12-17
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Jörn Kalinowski
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Katharina Pfeifer-Sancar Almut Mentz Christian Rückert
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BMC Genomics
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RNA-Seq optimization with eQTL gold standards.
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2013-12-17
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Andrew B. West
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Shannon E Ellis Simone Gupta Foram N Ashar Joel S Bader Dan E Arking
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BMC Genomics
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Studying Culicoides vectors of BTV in the post-genomic era: resources, bottlenecks to progress and future directions.
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2013-12-17 2014-03-01
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Daniel Lawson Paul J Kersey
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Dana Nayduch Lee W Cohnstaedt Christopher Saski Mark Fife Simon Carpenter
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Virus Research
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Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome
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2013-12-18
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Eric Rivals
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Nicolas Philippe Elias Bou Samra Anthony Boureux Alban Mancheron Florence Rufflé Qiang Bai John De Vos Thérèse Commes
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Nucleic Acids Research
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Comprehensive analysis of transcriptome variation uncovers known and novel driver events in T-cell acute lymphoblastic leukemia
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2013-12-19
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Iwona Wlodarska Gert Hulselmans Zeynep Kalender Atak Kim De Keersmaecker Peter Vandenberghe Jan Cools Stein Aerts Robin Foà
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Valentina Gianfelici Arun George Devasia Ellen Geerdens Nicole Mentens Sabina Chiaretti Kaat Durinck Anne Uyttebroeck Jacqueline Cloos Frank Speleman
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PLOS Genetics
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An overview of gene expression dynamics during early ovarian folliculogenesis: specificity of follicular compartments and bi-directional dialog.
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2013-12-19
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Sylvain Foissac
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Agnes Bonnet Cedric Cabau Olivier Bouchez Julien Sarry Nathalie Marsaud Florent Woloszyn Philippe Mulsant Beatrice Mandon-Pepin
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BMC Genomics
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Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua
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2013-12-20
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Alain Goossens
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Sandra S A Soetaert Christophe M F Van Neste Mado L Vandewoestyne Steven R Head Filip C W Van Nieuwerburgh Dieter L D Deforce
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BMC Plant Biology
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PennSeq: accurate isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution
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2013-12-20
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Xianyun Mao Jane Ferguson Muredach P. Reilly
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Yu Hu Yichuan Liu Cheng Jia Chenyi Xue Hongzhe Li Mingyao Li
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Nucleic Acids Research
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Correction: RNA-Seq-Based Analysis of the Physiologic Cold Shock-Induced Changes in Moraxella catarrhalis Gene Expression.
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2013-12-20
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Stefan Wyder
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Violeta Spaniol Christoph Aebi
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PLOS ONE
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Quantitative single-cell RNA-seq with unique molecular identifiers.
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2013-12-22
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Sten Linnarsson Peter Lönnerberg
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Saiful Islam Amit Zeisel Simon Joost Gioele La Manno Pawel Zajac Maria Kasper
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Nature Methods
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Divergent transcription is associated with promoters of transcriptional regulators.
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2013-12-23
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Marc Garibal Jean-Christophe Andrau Jean Imbert Salvatore Spicuglia
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Cyrille Lepoivre Mohamed Belhocine Aurélie Bergon Aurélien Griffon Miriam Yammine Laurent Vanhille Joaquin Zacarias-Cabeza Frederic Koch Muhammad Ahmad Maqbool Romain Fenouil Beatrice Loriod Hélène Holota Marta Gut Ivo Gut Denis Puthier
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BMC Genomics
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Lsh regulates LTR retrotransposon repression independently of Dnmt3b function.
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2013-12-24
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Colin A. Semple Tracey Davey Ian R. Adams John Greally
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Donncha S Dunican Hazel A Cruickshanks Masako Suzuki Robert J Arceci Richard R Meehan
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Genome Biology
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Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching
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2013-12-24
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Lennart Opitz
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Hubert Rehrauer Ge Tan Lina Sieverling Ralph Schlapbach
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BMC Bioinformatics
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Computational analysis reveals a correlation of exon-skipping events with splicing, transcription and epigenetic factors.
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2013-12-24
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Laura Elnitski Zhong Chen
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Zhenqing Ye Xun Lan Stephen Hara Benjamin Sunkel Tim H-M Huang Qianben Wang Victor X Jin
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Nucleic Acids Research
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Mycorrhizal phosphate uptake pathway in maize: vital for growth and cob development on nutrient poor agricultural and greenhouse soils.
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2013-12-26
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Jan Jansa
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Martin Willmann Nina Gerlach Benjamin Buer Aleksandra Polatajko Réka Nagy Eva Koebke René Flisch Marcel Bucher
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Frontiers in Plant Science
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Nutritional impacts on gene expression in the surface mucosa of blue catfish (Ictalurus furcatus).
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2013-12-28
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Eric Peatman
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Chao Li Benjamin H Beck
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Developmental and Comparative Immunology
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Bulk segregant RNA-seq reveals expression and positional candidate genes and allele-specific expression for disease resistance against enteric septicemia of catfish.
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2013-12-30
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Luyang Sun Shikai Liu
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Ruijia Wang Lisui Bao Jiaren Zhang Yanliang Jiang Jun Yao Lin Song Jianbin Feng Zhanjiang Liu
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BMC Genomics
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Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
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2013-12-30
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Jean-Jack M Riethoven
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Yong Ding Ning Liu Laetitia Virlouvet Michael Fromm Zoya Avramova
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BMC Plant Biology
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Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure
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2014
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Christian Tamburini
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Amira Amrani Aurélie Bergon Hélène Holota Marc Garel Bernard Ollivier Jean Imbert Alain Dolla Nathalie Pradel
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PLOS ONE
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Melanocytes in the skin--comparative whole transcriptome analysis of main skin cell types
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2014
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Viljar Jaks Ene Reimann Q24546281 Eero Vasar Sulev Kõks
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Paula Reemann Sten Ilmjärv Orm Porosaar Helgi Silm
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PLOS ONE
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Deep RNA sequencing reveals hidden features and dynamics of early gene transcription in Paramecium bursaria chlorella virus 1
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2014
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Jean-Jack M Riethoven Guillaume Blanc David D. Dunigan
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Michael Mozar Irina V Agarkova James R Gurnon Giane Yanai-Balser Janet M Rowe Yuannan Xia James L Van Etten
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PLOS ONE
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De novo assembly and characterization of the transcriptome of the toxic dinoflagellate Karenia brevis
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2014
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Lisa Campbell
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Darcie E Ryan Alan E Pepper
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BMC Genomics
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Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains
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2014
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Helmut Denk Hans Lehrach Marie-Laure Yaspo Christina Grimm Kurt Zatloukal
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Vikash Pandey Marc Sultan Karl Kashofer Meryem Ralser Vyacheslav Amstislavskiy Julia Starmann Ingrid Osprian Hendrik Hache Holger Sültmann Michael Trauner Christoph Wierling
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PLOS ONE
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Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation
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2014
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Darya Peregudova Alexey A. Dmitriev Sergey V Mylnikov Peter O Fedichev Nataliya Melnikova Anna V Kudryavtseva Mikhail V Shaposhnikov Alexey A Moskalev
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Anastasia Snezhkina Valeria Kogan Ekaterina Plyusnina Leonid Uroshlev Sergey Plusnin
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PLOS ONE
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The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs
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2014
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Angela M Yu Patrícia Costa Reis Michelle A. Petri
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Lihua Shi Zhe Zhang Wei Wang Zhi Wei Ehtisham Akhter Kelly Maurer Li Song Kathleen E Sullivan
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PLOS ONE
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Establishment of highly tumorigenic human colorectal cancer cell line (CR4) with properties of putative cancer stem cells
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2014
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Iwao Ojima
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Rebecca A Rowehl Stephanie Burke Agnieszka B Bialkowska Donald W Pettet Leahana Rowehl Ellen Li Eric Antoniou Yuanhao Zhang Roberto Bergamaschi Kenneth R Shroyer Galina I Botchkina
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PLOS ONE
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RNA-sequencing analysis of HepG2 cells treated with atorvastatin
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2014
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Daniel Sachse Jens P. Berg
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Camilla Stormo Marianne K Kringen Robert Lyle Ole Kristoffer Olstad Armin P Piehler
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PLOS ONE
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The oncogenic MicroRNA Hsa-miR-155-5p targets the transcription factor ELK3 and links it to the hypoxia response
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2014
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Alain C Jung Bohdan Wasylyk
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E Douglas Robertson Christine Wasylyk Tao Ye
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PLOS ONE
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Genetics of gene expression in CNS
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2014
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Robert W. Williams
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Ashutosh K Pandey
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International Review of Neurobiology
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Towards a computational model of a methane producing archaeum
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2014
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Piyush Labhsetwar Zaida Luthey-Schulten
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Joseph R Peterson Jeremy R Ellermeier Petra R A Kohler Ankur Jain Taekjip Ha William W Metcalf
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Archaea
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Comparison between karyotyping-FISH-reverse transcription PCR and RNA-sequencing-fusion gene identification programs in the detection of KAT6A-CREBBP in acute myeloid leukemia
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2014
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Sverre Heim Ioannis Panagopoulos
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Synne Torkildsen Ludmila Gorunova Anne Tierens Geir E Tjønnfjord
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PLOS ONE
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RNA families in Epstein-Barr virus
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2014
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Joan A. Steitz
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Walter N Moss Nara Lee Genaro Pimienta
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RNA Biology
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Characterization of human pseudogene-derived non-coding RNAs for functional potential
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2014
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Deyou Zheng
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Xingyi Guo Mingyan Lin Shira Rockowitz Herbert M Lachman
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PLOS ONE
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Oqtans: a multifunctional workbench for RNA-seq data analysis
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2014
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Gunnar Rätsch
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Vipin T Sreedharan Sebastian J Schultheiss Géraldine Jean André Kahles Regina Bohnert Philipp Drewe Pramod Mudrakarta Nico Görnitz Georg Zeller
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BMC Bioinformatics
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Blood biomarkers of the late phase asthmatic response using RNA-Seq
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2014
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Louis-Philippe Boulet
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Amrit Singh Casey P Shannon Gail M Gauvreau Paul M O'Byrne J FitzGerald Scott J Tebbutt
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Allergy, Asthma & Clinical Immunology
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Emerging RNA-Seq Applications in Food Science
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2014
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Alberto Valdés Virginia García-Cañas Carolina Simó
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Clara Ibáñez
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Zinc finger transcription factors displaced SREBP proteins as the major Sterol regulators during Saccharomycotina evolution
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2014-01
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Sarah L Maguire Geraldine Butler Theodore C White Kenneth H. Wolfe Jean-Marc Nicaud Cécile Neuvéglise
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Can Wang Linda M Holland François Brunel Martin Zavrel
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PLOS Genetics
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CellFinder: a cell data repository
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2014-01
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Stefanie Seltmann Fritz Lekschas Mariana Lara Neves Harald Stachelscheid Nancy Mah Andreas Kurtz
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Jean-Fred Fontaine Miguel A Andrade-Navarro Ulf Leser
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Nucleic Acids Research
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A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells
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2014-01-01
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Michael Stratton
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Tony Ly Yasmeen Ahmad Adam Shlien Dominique Soroka Allie Mills Michael J Emanuele Angus I Lamond
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eLife
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Isl1 and Pou4f2 form a complex to regulate target genes in developing retinal ganglion cells
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2014-01-01
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Xiuqian Mu
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Renzhong Li Fuguo Wu Raili Ruonala Darshan Sapkota Zihua Hu
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PLOS ONE
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A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
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2014-01-01
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Danielle Thierry-Mieg Lee Lancashire Heng Luo Nan Mei Jean Thierry-Mieg
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Ying Yu James C Fuscoe Chen Zhao Chao Guo Meiwen Jia Tao Qing Desmond I Bannon Wenjun Bao Tingting Du Zhenqiang Su Wendell D Jones Carrie L Moland William S Branham Feng Qian Baitang Ning Yan Li Huixiao Hong Lei Guo Tieliu Shi Kevin Y Wang Russell D Wolfinger Yuri Nikolsky Stephen J Walker Penelope Duerksen-Hughes Christopher E Mason Weida Tong Leming Shi Charles Wang
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Nature Communications
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Correlating histone modification patterns with gene expression data during hematopoiesis.
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2014-01-01
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Gangqing Hu
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Keji Zhao
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Methods in Molecular Biology
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Domestic dogs and cancer research: a breed-based genomics approach.
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2014-01-01
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Elaine Ostrander
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Brian W Davis
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ILAR Journal
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Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq.
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2014-01-01
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Sten Linnarsson Peter Lönnerberg Sabrina Zechel
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Pawel Zajac Carlos F Ibáñez
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Genome Biology
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RNA-Seq reveals novel transcriptional reorganization in human alcoholic brain.
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2014-01-01
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Sean P Farris
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R Dayne Mayfield
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International Review of Neurobiology
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Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets
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2014-01-01
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Liang-Hu Qu
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Jun-Hao Li Shun Liu Ling-Ling Zheng Jie Wu Wen-Ju Sun Ze-Lin Wang Hui Zhou Jian-Hua Yang
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Frontiers in Bioengineering and Biotechnology
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Next-generation sequencing applied to flower development: RNA-seq.
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2014-01-01
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Yuling Jiao
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Jun He
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Methods in Molecular Biology
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Riboswitch discovery by combining RNA-seq and genome-wide identification of transcriptional start sites.
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2014-01-01
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Isabelle Rosinski-Chupin
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Olga Soutourina Isabelle Martin-Verstraete
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Methods in Enzymology
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Plant and fungal gene expression in mycorrhizal protocorms of the orchid Serapias vomeracea colonized by Tulasnella calospora.
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2014-01-01
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Fabiano Sillo Silvia Perotto Raffaella Balestrini
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Luca Nerva Mariangela Girlanda
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Plant Signaling and Behavior
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Shared transcription factors contribute to distinct cell fates
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2014-01-01
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Berthold Göttgens
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Felicia S L Ng Fernando J Calero-Nieto
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Transcription
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Transcriptomic changes in brain development.
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2014-01-01
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Mark R Cookson
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Allissa A Dillman
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International Review of Neurobiology
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RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines.
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2014-01-01
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Youping Deng
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Yan Li Omid Rouhi Hankui Chen Rolando Ramirez Jeffrey A Borgia
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Cancer Informatics
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Developmental analysis of spliceosomal snRNA isoform expression.
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2014-01-01
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Zhipeng Lu
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A Gregory Matera
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G3
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Deep sequencing of small chromatin-associated RNA: bioinformatic analysis.
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2014-01-01
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Sarah Diermeier Gernot Längst
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Methods in Molecular Biology
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Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
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2014-01-01
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Daniel Ramsköld Rickard Sandberg Qiaolin Deng Björn Reinius
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Science
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edgeR for differential RNA-seq and ChIP-seq analysis: an application to stem cell biology.
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2014-01-01
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Mark D. Robinson
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Olga Nikolayeva
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Methods in Molecular Biology
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Quantitative transcriptome analysis using RNA-seq.
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2014-01-01
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Andrea Bräutigam
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Canan Külahoglu
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Methods in Molecular Biology
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Full-length RNA-seq from single cells using Smart-seq2.
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2014-01-02
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Omid R Faridani Rickard Sandberg
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Simone Picelli Asa K Björklund Gösta Winberg Sven Sagasser
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Nature Protocols
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Variable suites of non-effector genes are co-regulated in the type III secretion virulence regulon across the Pseudomonas syringae phylogeny.
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2014-01-02
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Marc T Nishimura Jeff H. Chang David A. Baltrus
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Tatiana S Mucyn Scott Yourstone Abigail L Lind Surojit Biswas Jason S Cumbie Corbin D Jones Jeffery L Dangl Sarah R Grant
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PLOS Pathogens
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RNA-Seq analysis of the toxicant-induced transcriptome of the marine diatom, Ceratoneis closterium.
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2014-01-04
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Philippe Moncuquet
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Sharon E Hook Hannah L Osborn Francesca Gissi Natalie A Twine Marc R Wilkins Merrin S Adams
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Marine Genomics
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Differential expression analysis of RNA-seq data at single-base resolution
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2014-01-06
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Kasper D. Hansen Jeffrey T. Leek
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Alyssa C Frazee Sarven Sabunciyan Rafael A Irizarry
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Biostatistics
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A unique missense allele of BAF155, a core BAF chromatin remodeling complex protein, causes neural tube closure defects in mice.
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2014-01-09
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Dawn E Watkins-Chow William J Pavan Lee Niswander
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Laura Harmacek Jianfu Chen Kenneth L Jones J Michael Salbaum
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Developmental Neurobiology
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The histone-H3K4-specific demethylase KDM5B binds to its substrate and product through distinct PHD fingers.
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2014-01-09
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Brian D Strahl Scott B Rothbart
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Brianna J Klein Lianhua Piao Yuanxin Xi Hector Rincon-Arano Danni Peng Hong Wen Connie Larson Xi Zhang Xia Zheng Michael A Cortazar Pedro V Peña Anthony Mangan David L Bentley Mark Groudine Wei Li Xiaobing Shi Tatiana G Kutateladze
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Cell Reports
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Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis.
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2014-01-11
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Georg Zeller Gunnar Rätsch
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Vipin T Sreedharan Sebastian J Schultheiss Géraldine Jean André Kahles Regina Bohnert Philipp Drewe Pramod Mudrakarta Nico Görnitz
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Bioinformatics
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Differential protein occupancy profiling of the mRNA transcriptome.
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2014-01-13
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Markus Landthaler
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Markus Schueler Mathias Munschauer Lea Haarup Gregersen Ana Finzel Alexander Loewer Wei Chen Christoph Dieterich
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Genome Biology
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Production of RNA for transcriptomic analysis from mouse spinal cord motor neuron cell bodies by laser capture microdissection.
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2014-01-13
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Arthur L. Horwich
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Urmi Bandyopadhyay Wayne A Fenton Maria Nagy
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Journal of Visualized Experiments
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GuavaH: a compendium of host genomic data in HIV biology and disease.
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2014-01-15
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Paul J. McLaren Angela Ciuffi Jacques Fellay
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István Bartha Amalio Telenti
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Retrovirology
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Transciptome analysis of the gill and swimbladder of Takifugu rubripes by RNA-Seq.
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2014-01-16
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Shikai Liu
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Jun Cui Bing Zhang Hongdi Wang Hongjuan Sun Shuhui Song Xuemei Qiu Yang Liu Xiuli Wang Zhiqiang Jiang Zhanjiang Liu
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PLOS ONE
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Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms
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2014-01-17
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A Johnston Lam C. Tsoi
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Bingshan Li William R Swindell Johann E Gudjonsson Trilokraj Tejasvi Jun Ding Philip E Stuart Xianying Xing James J Kochkodan John J Voorhees Hyun M Kang Rajan P Nair Goncalo R Abecasis James T Elder
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Journal of Investigative Dermatology
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The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs.
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2014-01-17
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Matthew Baranski Nicholas A. Robinson
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Gopalapillay Gopikrishna Vinaya Kumar Katneni Mudagandur S Shekhar Jayakani Shanmugakarthik Sarangapani Jothivel Chavali Gopal Pitchaiyappan Ravichandran Matthew Kent Mariann Arnyasi Alphis G Ponniah
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PLOS ONE
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Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.
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2014-01-17
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Wenwu Wu James L. Manley
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Xuexia Zhou Huang Li Yuanming Cheng Ning Wei Jie Zong Xiaoyan Feng Zhiqin Xie Dai Chen Hui Wang Ying Feng
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Nucleic Acids Research
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A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis
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2014-01-17
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Lior Pachter Harold Pimentel Narla Mohandas Xiuli An
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Marilyn Parra Sherry Gee Dana Ghanem Jie Li John G Conboy
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Nucleic Acids Research
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Set5 and Set1 cooperate to repress gene expression at telomeres and retrotransposons.
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2014-01-17
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Sean R Collins Devin A King Ashby Morrison Or Gozani
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Glòria Mas Martín Erin M Green Pablo E Garcia-Nieto Richard Alexander Nevan J Krogan
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Epigenetics
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ALEA: a toolbox for allele-specific epigenomics analysis.
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2014-01-21
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Mohammad M Karimi Torsten Möller Matthew C. Lorincz
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Hamid Younesy Alireza Heravi-Moussavi Jeffrey B Cheng Joseph F Costello Steven J M Jones
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Bioinformatics
|
RNA-Seq analysis provides insights for understanding photoautotrophic polyhydroxyalkanoate production in recombinant Synechocystis Sp.
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2014-01-22
|
Kumar Sudesh
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Nyok-Sean Lau Choon Pin Foong Yukio Kurihara Kumar Sudesh Minami Matsui
|
PLOS ONE
|
RNA-Seq transcriptome analysis of Spirodela dormancy without reproduction.
|
2014-01-23
|
Wenqin Wang Joachim Messing
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Yongrui Wu
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BMC Genomics
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glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing data.
|
2014-01-24
|
Andrew Paul Hutchins
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Ralf Jauch Mateusz Dyla Diego Miranda-Saavedra
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Cell regeneration (London, England)
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A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat.
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2014-01-28
|
Christine Orengo James R Perkins Matthias Kohl Stephen B McMahon
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Ana Antunes-Martins Margarita Calvo John Grist Werner Rust Ramona Schmid Tobias Hildebrandt David L H Bennett
|
Molecular Pain
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The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA.
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2014-01-29
|
Anselm Enders
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Vicky Cho Yan Mei Arleen Sanny Stephanie Chan Edward M Bertram Andy Tan Christopher C Goodnow T Daniel Andrews
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Genome Biology
|
RNA-seq analysis of host and viral gene expression highlights interaction between varicella zoster virus and keratinocyte differentiation.
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2014-01-30
|
Judith Breuer Paul Kellam
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Meleri Jones Inga R Dry Dan Frampton Manuraj Singh Ravinder K Kanda Michael B Yee Michael Hollinshead Paul R Kinchington Edel A O'Toole
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PLOS Pathogens
|
bwtool: a tool for bigWig files.
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2014-01-30
|
Miguel Beato del Rosal
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Andy Pohl
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Bioinformatics
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A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events
|
2014-01-31
|
Matthew Meyerson Mara Rosenberg Marcin Imielinski Juliann Chmielecki Gad Getz Gordon Saksena
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Angela N Brooks Peter S Choi Luc de Waal Tanaz Sharifnia Chandra Sekhar Pedamallu Andrey Sivachenko Michael S Lawrence David S DeLuca
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PLOS ONE
|
Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
|
2014-02-01
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Naama Elefant Hadas Keren-Shaul Franziska Paul Alexander Mildner Steffen Jung
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Diego Adhemar Jaitin Ephraim Kenigsberg Hadas Keren-Shaul Naama Elefant Irina Zaretsky Nadav Cohen Amos Tanay Ido Amit
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Science
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SOX9: a stem cell transcriptional regulator of secreted niche signaling factors.
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2014-02-01
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Deyou Zheng Elaine Fuchs Maria Genander
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Meelis Kadaja Brice E Keyes Mingyan Lin H Amalia Pasolli Lisa Polak Nicole Stokes
|
Genes & Development
|
Faculty of 1000 evaluation for Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells
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2014-02-02
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Marc S. Williams
|
|
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voom: Precision weights unlock linear model analysis tools for RNA-seq read counts.
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2014-02-03
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Gordon K Smyth
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Charity W Law Yunshun Chen Wei Shi
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Genome Biology
|
Ultra deep sequencing of Listeria monocytogenes sRNA transcriptome revealed new antisense RNAs.
|
2014-02-03
|
Ramakanth Madhugiri Stefanie Widder Thomas Rattei
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Sebastian Behrens Gopala Krishna Mannala Xiaoxing Qing Nathalie Kefer Mobarak Abu Mraheil Torsten Hain
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PLOS ONE
|
The Cryptococcus neoformans transcriptome at the site of human meningitis.
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2014-02-04
|
Yuan Chen David R. Boulware
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Dena L Toffaletti Jennifer L Tenor Anastasia P Litvintseva Charles Fang Thomas G Mitchell Tami R McDonald Kirsten Nielsen Tihana Bicanic John R Perfect
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mBio
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Tissue-specific RNA-Seq in human evoked inflammation identifies blood and adipose LincRNA signatures of cardiometabolic diseases.
|
2014-02-06
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Rachel L Ballantyne Muredach P. Reilly
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Yichuan Liu Jane F Ferguson Chenyi Xue Ian M Silverman Sager J Gosai Jacquelyn Serfecz Michael P Morley Brian D Gregory Mingyao Li
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Arteriosclerosis, Thrombosis, and Vascular Biology
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RNA-seq reveals transcriptomic shock involving transposable elements reactivation in hybrids of young lake whitefish species.
|
2014-02-06
|
Sébastien Renaut Louis Bernatchez
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Anne-Marie Dion-Côté Eric Normandeau
|
Molecular Biology and Evolution
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Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems.
|
2014-02-07
|
Keywan Hassani-Pak Angela Karp Huw Dylan Jones
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Yongfang Wan Cristina Gritsch Theodora Tryfona Mike J Ray Ambrose Andongabo Paul Dupree Peter R Shewry Rowan A C Mitchell
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Planta
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Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq.
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2014-02-07
|
Rui Vitorino Gerald B Pier Manuel Vilanova
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Virginia Carvalhais Angela França Filipe Cerca Nuno Cerca
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Applied Microbiology and Biotechnology
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Analysis of 52 Rab GTPases from channel catfish and their involvement in immune responses after bacterial infections.
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2014-02-07
|
Luyang Sun Shikai Liu Yu Zhang
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Ruijia Wang Chao Li Lisui Bao Jianbin Feng Zhanjiang Liu
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Developmental and Comparative Immunology
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ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects.
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2014-02-10
|
Erik D. Roberson James Shorter Eric J Huang
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Haiyan Qiu Sebum Lee Yulei Shang Wen-Yuan Wang Kin Fai Au Sherry Kamiya Sami J Barmada Steven Finkbeiner Hansen Lui Caitlin E Carlton Amy A Tang Michael C Oldham Hejia Wang Anthony J Filiano Warren G Tourtellotte Bin Chen Li-Huei Tsai
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Journal of Clinical Investigation
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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.
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2014-02-13
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Gane Ka-Shu Wong Ruibang Luo Tak-Wah Lam Jun Wang
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Yinlong Xie Gengxiong Wu Jingbo Tang Jordan Patterson Shanlin Liu Weihua Huang Guangzhu He Shengchang Gu Shengkang Li Xin Zhou Yingrui Li Xun Xu
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Bioinformatics
|
Sequencing and functional analysis of the genome of a nematode egg-parasitic fungus, Pochonia chlamydosporia.
|
2014-02-13
|
Ana Conesa Corey Nislow Eduardo Larriba José Martín-Nieto Luis V Lopez-Llorca
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María D L A Jaime José Carbonell-Caballero Joaquín Dopazo
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Fungal Genetics and Biology
|
Condition-specific target prediction from motifs and expression.
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2014-02-14
|
Martin Vingron
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Guofeng Meng
|
Bioinformatics
|
Dynamic recruitment of amino acid transporters to the insect/symbiont interface.
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2014-02-16
|
John P. McCutcheon Rebecca P. Duncan Filip Husník
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James T Van Leuven Donald G Gilbert Liliana M Dávalos Alex C C Wilson
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Molecular Ecology
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SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-Seq data integrating differential expression and splicing.
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2014-02-17
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Xi Wang Murray J Cairns
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Bioinformatics
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Interaction of vitamin D with membrane-based signaling pathways
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2014-02-18
|
María Jesús Larriba
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José Manuel González-Sancho Félix Bonilla Alberto Muñoz
|
Frontiers in Physiology
|
Ammonium induces differential expression of methane and nitrogen metabolism-related genes in Methylocystis sp. strain SC2.
|
2014-02-18
|
Werner Liesack
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Bomba Dam Somasri Dam Yongkyu Kim
|
Environmental Microbiology
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Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle.
|
2014-02-19
|
Songnian Hu
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YuanYuan Zhou Wei Gong JingFa Xiao JiaYan Wu LinLin Pan XiaoNuan Li XuMin Wang WeiWei Wang Jun Yu
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Science in China. Series C: Life Sciences
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Insight into insulin secretion from transcriptome and genetic analysis of insulin-producing cells of Drosophila
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2014-02-20
|
Luis A Milla Wenxiu Ma Maria L Spletter
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Jian Cao Julie Ni Vanessa Shiu Sangbin Park Sheng Tang Jun Zhang Xing Wei Seung K Kim Matthew P Scott
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Genetics
|
Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq.
|
2014-02-24
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Jeremy A Miller Vilas Menon Jeff Goldy Ajamete Kaykas Chang-Kyu Lee Kimberly A Smith Elaine H Shen John W Phillips Ed S Lein Mike J Hawrylycz
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BMC Genomics
|
Context-selective death of acute myeloid leukemia cells triggered by the novel hybrid retinoid-HDAC inhibitor MC2392.
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2014-02-24
|
Dante Rotili Yves Collette Angela Nebbioso Antonello Mai Hugues de Thé Mariarosaria Conte Sergio Valente Lucia Altucci Julien Ablain Vincenzo Carafa
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Floriana De Bellis Francesca Petraglia Filomena Matarese Kees-Jan Françoijs Rèmy Castellano Armelle Goubard Amit Mandoli Joost H A Martens Hendrik G Stunnenberg
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Cancer Research
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RNA CoMPASS: a dual approach for pathogen and host transcriptome analysis of RNA-seq datasets
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2014-02-25
|
Erik K Flemington
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Guorong Xu Michael J Strong Michelle R Lacey Carl Baribault Christopher M Taylor
|
PLOS ONE
|
Transcriptomic profiling of differential responses to drought in two freshwater mussel species, the giant floater Pyganodon grandis and the pondhorn Uniomerus tetralasmus.
|
2014-02-25
|
Eric Peatman
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Yupeng Luo Chao Li Andrew Gascho Landis Guiling Wang James Stoeckel
|
PLOS ONE
|
FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.
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2014-02-25
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Carlos Torroja Francesco Mazzarotto Enrique Lara-Pezzi Alberto Gatto
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Stuart A Cook Paul J R Barton Fátima Sánchez-Cabo
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Nucleic Acids Research
|
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource.
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2014-02-25
|
Claudia Angelini Valerio Costa Maria Rosaria Ambrosio
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Margherita Scarpato Roberta Esposito Daniela Evangelista Marianna Aprile Alfredo Ciccodicola
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Database
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SnapShot-Seq: a method for extracting genome-wide, in vivo mRNA dynamics from a single total RNA sample
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2014-02-26
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Nimrod Miller Sarah A Boswell Yong-Chao Ma Nicole Cloonan Sean M. Grimmond
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Jesse M Gray David A Harmin Thomas E Mullen Joseph J Ling Scott Kuersten Steven A McCarroll Michael Springer
|
PLOS ONE
|
Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA.
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2014-02-27
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Deyou Zheng
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Robert D Bell Xiaochun Long Mingyan Lin Jan H Bergmann Vivek Nanda Sarah L Cowan Qian Zhou Yu Han David L Spector Joseph M Miano
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Arteriosclerosis, Thrombosis, and Vascular Biology
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Metabolic reprogramming during purine stress in the protozoan pathogen Leishmania donovani
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2014-02-27
|
Jessica L Martin Vladislav A Petyuk Kristin E Burnum Richard D. Smith
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Phillip A Yates Radika Soysa Joshua F Alfaro Feng Yang Karl K Weitz David G Camp Phillip A Wilmarth Larry L David Gowthaman Ramasamy Peter J Myler Nicola S Carter
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PLOS Pathogens
|
The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii.
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2014-02-28
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Sean D Gallaher Taylor L Weiss David Casero Shannon L Johnson Matteo Pellegrini Sabeeha Merchant Ursula Goodenough
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Ian Blaby Carrie Goodson Jae-Hyeok Lee Robyn Roth Jannette Rusch Manmilan Singh James G Umen Tuya Wulan
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Eukaryotic Cell
|
Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility
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2014-02-28
|
Stephan Schmitz-Esser Edward M Fox Aidan Coffey
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Aidan Casey Edward M Fox Aidan Coffey Olivia McAuliffe Kieran Jordan
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Frontiers in Microbiology
|
ChIP-Seq and RNA-Seq reveal an AmrZ-mediated mechanism for cyclic di-GMP synthesis and biofilm development by Pseudomonas aeruginosa
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2014-03-01
|
Yasuhiko Irie Peter White
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Christopher J. Jones David Newsom Benjamin Kelly Laura K. Jennings Binjie Xu Dominique H. Limoli Joe J. Harrison Matthew R. Parsek Daniel J. Wozniak
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PLOS Pathogens
|
The IncRNAs PCGEM1 and PRNCR1 are not implicated in castration resistant prostate cancer.
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2014-03-01
|
Elai Davicioni
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John R Prensner Anirban Sahu Matthew K Iyer Rohit Malik Benjamin Chandler Irfan A Asangani Anton Poliakov Ismael A Vergara Mohammed Alshalalfa Robert B Jenkins Felix Y Feng Arul M Chinnaiyan
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Oncotarget
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Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness
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2014-03-04
|
Eric Haugen
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R Kohen A Dobra J H Tracy
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Translational Psychiatry
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Differential transcriptomic analysis by RNA-Seq of GSNO-responsive genes between Arabidopsis roots and leaves.
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2014-03-04
|
Juan C Begara-Morales Francisco J. Corpas
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Beatriz Sánchez-Calvo Francisco Luque María O Leyva-Pérez Marina Leterrier Juan B Barroso
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Plant and Cell Physiology
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Relaxed functional constraints on triplicate α-globin gene in the bank vole suggest a different evolutionary history from other rodents.
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2014-03-05
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Jeremy Searle Petr Kotlík
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S Marková
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Heredity
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The human testis-specific proteome defined by transcriptomics and antibody-based profiling.
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2014-03-05
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Linn Fagerberg Mathias Uhlén
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D Djureinovic B Hallström A Danielsson C Lindskog F Pontén
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Molecular Human Reproduction
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Overexpression of molecular chaperone genes in nucleomorph genomes.
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2014-03-06
|
Patrick J. Keeling
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Yoshihisa Hirakawa Shigekatsu Suzuki John M Archibald Ken-ichiro Ishida
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Molecular Biology and Evolution
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Faculty of 1000 evaluation for SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads
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2014-03-06
|
Steven Salzberg
|
|
|
Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion.
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2014-03-07
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Casey P. Shannon Robert Balshaw
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Heesun Shin Nick Fishbane Jian Ruan Mi Zhou Janet E Wilson-McManus Raymond T Ng Bruce M McManus Scott J Tebbutt PROOF Centre of Excellence Team
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PLOS ONE
|
Vicinal: a method for the determination of ncRNA ends using chimeric reads from RNA-seq experiments.
|
2014-03-12
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Zhipeng Lu
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A Gregory Matera
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Nucleic Acids Research
|
RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.
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2014-03-12
|
Linn Fagerberg Mathias Uhlén Per Oksvold
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Charlotte Stadler Åsa Sivertsson Martin Zwahlen Björn M Hallström Emma Lundberg
|
Journal of Proteome Research
|
Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing.
|
2014-03-13
|
Hans-Ulrich Schildhaus Sabine Merkelbach-Bruse
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Evgeny A Moskalev Judith Frohnauer Arno Dimmler Thomas Schubert Carsten Boltze Helmut König Florian Fuchs Horia Sirbu Ralf J Rieker Abbas Agaimy Arndt Hartmann Florian Haller
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Lung Cancer
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Lacking alignments? The next-generation sequencing mapper segemehl revisited.
|
2014-03-13
|
Peter F. Stadler
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Christian Otto Steve Hoffmann
|
Bioinformatics
|
Identification of novel point mutations in splicing sites integrating whole-exome and RNA-seq data in myeloproliferative diseases.
|
2014-03-13
|
Carlo Gambacorti-Passerini
|
Roberta Spinelli Alessandra Pirola Sara Redaelli Nitesh Sharma Hima Raman Simona Valletta Vera Magistroni Rocco Piazza
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Molecular genetics & genomic medicine
|
Identification of candidate genes involved in coronary artery calcification by transcriptome sequencing of cell lines.
|
2014-03-14
|
NISC Comparative Sequencing Program Leslie G Biesecker Eric D. Green James C Mullikin
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Shurjo K Sen Jennifer J Barb Praveen F Cherukuri David S Accame Abdel G Elkahloun Larry N Singh Shih-Queen Lee-Lin Frank D Kolodgie Qi Cheng XiaoQing Zhao Marcus Y Chen Andrew E Arai Peter J Munson
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BMC Genomics
|
RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.
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2014-03-18
|
Hans J Nauwynck
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Bouabid Badaoui Teresa Rutigliano Anna Anselmo Merijn Vanhee Elisabetta Giuffra Sara Botti
|
PLOS ONE
|
The human liver-specific proteome defined by transcriptomics and antibody-based profiling.
|
2014-03-19
|
Jens Nielsen Linn Fagerberg Mathias Uhlén
|
Caroline Kampf Adil Mardinoglu Björn M Hallström Karolina Edlund Emma Lundberg Fredrik Pontén
|
FASEB Journal
|
SNP discovery from transcriptome of the swimbladder of Takifugu rubripes
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2014-03-20
|
Shikai Liu
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Jun Cui Hongdi Wang Lifu Zhu Xuemei Qiu Zhiqiang Jiang Xiuli Wang Zhanjiang Liu
|
PLOS ONE
|
The highly conserved MraZ protein is a transcriptional regulator in Escherichia coli.
|
2014-03-21
|
Jesus M Eraso Ronald Taylor
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Lye M Markillie Hugh D Mitchell Galya Orr William Margolin
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Journal of Bacteriology
|
Genomics of CpG methylation in developing and developed zebrafish
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2014-03-21
|
David M McGaughey
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Hatice Ozel Abaan Ryan M Miller Peter A Kropp Lawrence C Brody
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G3
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The characteristic direction: a geometrical approach to identify differentially expressed genes.
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2014-03-21
|
Avi Ma'ayan
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Neil R Clark Kevin S Hu Axel S Feldmann Yan Kou Edward Y Chen Qiaonan Duan
|
BMC Bioinformatics
|
From root to fruit: RNA-Seq analysis shows that arbuscular mycorrhizal symbiosis may affect tomato fruit metabolism
|
2014-03-21
|
Matteo Chialva Paola Bonfante
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Inès Zouari Alessandra Salvioli Mara Novero Laura Miozzi Gian Carlo Tenore Paolo Bagnaresi
|
BMC Genomics
|
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
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2014-03-23
|
Albin Sandelin Kristoffer Vitting-Seerup Johannes Waage Bo Torben Porse
|
|
BMC Bioinformatics
|
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
|
2014-03-23
|
John L. Rinn
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Cole Trapnell Davide Cacchiarelli Jonna Grimsby Prapti Pokharel Shuqiang Li Michael Morse Niall J Lennon Kenneth J Livak Tarjei S Mikkelsen
|
Nature Biotechnology
|
RNA-seq analysis identifies an intricate regulatory network controlling cluster root development in white lupin
|
2014-03-25
|
Oliver Berkowitz James Whelan
|
David Secco Huixia Shou
|
BMC Genomics
|
RNA sequencing reveals upregulation of RUNX1-RUNX1T1 gene signatures in clear cell renal cell carcinoma
|
2014-03-25
|
Jianfeng Xu
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Zuquan Xiong Hongjie Yu Yan Ding Chenchen Feng Hanming Wei Sha Tao Dan Huang Siqun Lilly Zheng Jielin Sun Zujun Fang
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BioMed Research International
|
De novo transcriptome analysis of Hevea brasiliensis tissues by RNA-seq and screening for molecular markers
|
2014-03-26
|
Luiz Gonzaga Paula de Almeida Dominique Garcia Daniel Guariz Pinheiro Antonio Figueira Luiz L Coutinho
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Leonardo Rippel Salgado Daniela Martins Koop Ronan Rivallan Vincent Le Guen Marisa Fabiana Nicolás Viviani Ribeiro Rocha Milena Magalhães Alexandra Lehmkuhl Gerber Júlio Cézar de Mattos Cascardo AnaTereza Ribeiro de Vasconcelos Wilson Araújo Silva
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BMC Genomics
|
De novo transcriptome assembly reveals sex-specific selection acting on evolving neo-sex chromosomes in Drosophila miranda.
|
2014-03-27
|
Doris Bachtrog
|
Vera B Kaiser
|
BMC Genomics
|
RNA-Seq reveals infection-induced gene expression changes in the snail intermediate host of the carcinogenic liver fluke, Opisthorchis viverrini.
|
2014-03-27
|
Thewarach Laha Smarn Tesana
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Sattrachai Prasopdee Javier Sotillo Jutharat Kulsantiwong Matthew J Nolan Alex Loukas Cinzia Cantacessi
|
PLOS Neglected Tropical Diseases
|
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.
|
2014-03-27
|
Hideya Kawaji Masayoshi Itoh Piero Carninci Yoshihide Hayashizaki
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Marina Lizio Mutsumi Kanamori-Katayama Ai Kaiho Hiromi Nishiyori-Sueki Jay W Shin Miki Kojima-Ishiyama Mitsuoki Kawano Mitsuyoshi Murata Noriko Ninomiya-Fukuda Sachi Ishikawa-Kato Sayaka Nagao-Sato Shohei Noma Alistair R R Forrest FANTOM Consortium
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Genome Research
|
Transcriptome analysis of the gill of Takifugu rubripes using Illumina sequencing for discovery of SNPs.
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2014-03-27
|
Shikai Liu
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Jun Cui Hongdi Wang Xuemei Qiu Zhiqiang Jiang Xiuli Wang
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
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RNA-seq dependent transcriptional analysis unveils gene expression profile in the intestine of sea cucumber Apostichopus japonicus during aestivation.
|
2014-03-27
|
Kenneth B. Storey
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Ye Zhao Hongsheng Yang Muyan Chen
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Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
|
HDAC-regulated myomiRs control BAF60 variant exchange and direct the functional phenotype of fibro-adipogenic progenitors in dystrophic muscles.
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2014-03-28
|
Janet Rossant Gianmaria Frigè Lorenzo Giordani Alberto Termanini Chiara Mozzetta Giovanna Borsellino
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Valentina Saccone Silvia Consalvi Iros Barozzi Martina Sandoná Tammy Ryan Agustin Rojas-Muñoz Luca Madaro Pasquale Fasanaro Marco De Bardi Xin Sun Benoit G Bruneau Mark Mercola Saverio Minucci Pier Lorenzo Puri
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Genes & Development
|
Differential meta-analysis of RNA-seq data from multiple studies
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2014-03-29
|
Florence Jaffrézic
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Andrea Rau Guillemette Marot Florence Jaffrézic
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BMC Bioinformatics
|
The Period protein homolog LIN-42 negatively regulates microRNA biogenesis in C. elegans.
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2014-03-31
|
Amy E Pasquinelli Priscilla M Van Wynsberghe
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Emily F Finnegan Thomas Stark Evan P Angelus Kathryn E Homan Gene W Yeo
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Developmental Biology
|
Small regulatory RNAs in Archaea.
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2014-03-31
|
L Randau Jörg Soppa
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Julia Babski Lisa-Katharina Maier Ruth Heyer Katharina Jaschinski Daniela Prasse Dominik Jäger Ruth A Schmitz Anita Marchfelder
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RNA Biology
|
RNA-seq identifies clinically relevant fusion genes in leukemia including a novel MEF2D/CSF1R fusion responsive to imatinib.
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2014-04
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Henrik Lilljebjörn Hans Ehrencrona Thoas Fioretos
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H Ågerstam C Orsmark-Pietras M Rissler L Nilsson J Richter
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Leukemia
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Odorant and gustatory receptors in the tsetse fly Glossina morsitans morsitans
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2014-04
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Daniel K. Masiga Paul O. Mireji Alan Christoffels
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George F O Obiero Steven R G Nyanjom Hugh M Robertson
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PLOS Neglected Tropical Diseases
|
PRADA: pipeline for RNA sequencing data analysis
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2014-04-01
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Gad Getz
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Wandaliz Torres-García Siyuan Zheng Andrey Sivachenko Rahulsimham Vegesna Qianghu Wang Rong Yao Michael F Berger John N Weinstein Roel G W Verhaak
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Bioinformatics
|
RNA sequencing and proteogenomics reveal the importance of leaderless mRNAs in the radiation-tolerant bacterium Deinococcus deserti.
|
2014-04-01
|
Arjan de Groot Laurence Blanchard David Vallenet David Pignol Jean Armengaud
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David Roche Bernard Fernandez Monika Ludanyi Stéphane Cruveiller
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Genome Biology and Evolution
|
Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types.
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2014-04-03
|
Erich Bornberg-Bauer Susanne U Franssen
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Jenny Gu Gidon Winters Ann-Kathrin Huylmans Isabell Wienpahl Maximiliane Sparwel James A Coyer Jeanine L Olsen Thorsten B H Reusch
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Marine Genomics
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LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.
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2014-04-07
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Daniel C. Jeffares Graeme C Smith Charalampos Rallis Jürg Bähler
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Danny A Bitton Charalampos Rallis Graeme C Smith Yuan Y C Chen Sandra Codlin Samuel Marguerat Jürg Bähler
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Genome Research
|
ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells
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2014-04-08
|
Lin Jiang Ola Wallerman Göran Andersson Leif Andersson
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Shady Younis Carl-Johan Rubin Elizabeth R Gilbert Elisabeth Sundström Awaisa Ghazal Xiaolan Zhang Li Wang Tarjei S Mikkelsen
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PLOS ONE
|
Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.
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2014-04-10
|
Gordon G Simpson Nicholas Schurch Christian Cole Sara J Brown Geoffrey J. Barton
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Alexander Sherstnev Junfang Song Céline Duc Kate G Storey W H Irwin McLean
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PLOS ONE
|
Post-translational decrease in respiratory chain proteins in the Polg mutator mouse brain.
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2014-04-10
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David N Hauser Mark R Cookson
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Allissa A Dillman Jinhui Ding Yan Li
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PLOS ONE
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Widespread use of non-productive alternative splice sites in Saccharomyces cerevisiae
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2014-04-10
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Matteo Pellegrini
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Tadashi Kawashima Stephen Douglass Jason Gabunilas Guillaume F Chanfreau
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PLOS Genetics
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Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS.
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2014-04-11
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Juan Pablo Tosar Alfonso Cayota
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Carlos Rovira Hugo Naya
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RNA
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Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq.
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2014-04-11
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Michael E Himmel
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Hui Wei Yan Fu Lauren Magnusson John O Baker Pin-Ching Maness Qi Xu Shihui Yang Andrew Bowersox Igor Bogorad Wei Wang Melvin P Tucker Shi-You Ding
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Frontiers in Microbiology
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Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq
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2014-04-13
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Doug Brownfield Barbara Treutlein
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Angela R Wu Norma F Neff Gary L Mantalas F Hernan Espinoza Tushar J Desai Mark A Krasnow Stephen R Quake
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Nature
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VDR primary targets by genome-wide transcriptional profiling.
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2014-04-13
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Graziano Pesole Matteo Pallocca
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Frauke Goeman Francesca De Nicola Paolo D'Onorio De Meo Berardino Elmi Tiziana Castrignanò Sabrina Strano Giovanni Blandino Maurizio Fanciulli Paola Muti
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The Journal of Steroid Biochemistry and Molecular Biology
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Extensive and coordinated control of allele-specific expression by both transcription and translation in Candida albicans.
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2014-04-14
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Gavin Sherlock Jonathan Weissman
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Dale Muzzey
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Genome Research
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Heat shock alters the expression of schizophrenia and autism candidate genes in an induced pluripotent stem cell model of the human telencephalon
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2014-04-15
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Deyou Zheng
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Mingyan Lin Dejian Zhao Anastasia Hrabovsky Erika Pedrosa Herbert M Lachman
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PLOS ONE
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Comparative genomic and transcriptomic analysis of wangiella dermatitidis, a major cause of phaeohyphomycosis and a model black yeast human pathogen
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2014-04-16
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Christina A Cuomo
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Zehua Chen Diego A Martinez Sharvari Gujja Sean M Sykes Qiandong Zeng Paul J Szaniszlo Zheng Wang
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G3
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Transcriptome profiling to identify genes involved in pathogenicity of Valsa mali on apple tree.
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2014-04-16
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Zhiyuan Yin
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Xiwang Ke Na Song Qingqing Dai Ralf T Voegele Yangyang Liu Haiying Wang Xiaoning Gao Zhensheng Kang Lili Huang
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Fungal Genetics and Biology
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Structure and Function of Steroid Receptor RNA Activator Protein, the Proposed Partner of SRA Noncoding RNA
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2014-04-17
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Thomas Cech
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David B McKay Linghe Xi Kristen K B Barthel
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Journal of Molecular Biology
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Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.
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2014-04-17
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Alexander Idnurm Jason E. Stajich Christina A Cuomo Yuan Chen Gautam Chatterjee Kate L Ormerod Yen-Ping Hsueh James Fraser Tristan Rossignol Kaustuv Sanyal Guilhem Janbon Yong-Sun Bahn Steven Jones Piotr A Mieczkowski Caroline Proux Vikas Yadav Cécile Neuvéglise Joseph Heitman
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Damien Paulet Edmond J Byrnes Nandita Mullapudi Chung-Chau Hon R Blake Billmyre François Brunel Weidong Chen Eve W L Chow Jean-Yves Coppée Anna Floyd-Averette Claude Gaillardin Kimberly J Gerik Jonathan Goldberg Sara Gonzalez-Hilarion Sharvari Gujja Joyce L Hamlin Giuseppe Ianiri Chinnappa D Kodira Lukasz Kozubowski Woei Lam Marco Marra Larry D Mesner Frédérique Moyrand Kirsten Nielsen Jacqueline E Schein Sheng Sun Carolin Wollschlaeger Ian A Wood Qiandong Zeng Carol S Newlon John R Perfect Jennifer K Lodge James W Kronstad Fred S Dietrich
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PLOS Genetics
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IKKα restoration via EZH2 suppression induces nasopharyngeal carcinoma differentiation.
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2014-04-17
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Eric W-F Lam
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Min Yan Yan Zhang Bin He Jin Xiang Zi-feng Wang Fei-meng Zheng Jie Xu Ming-yuan Chen Yu-liang Zhu Hai-jun Wen Xiang-bo Wan Cai-feng Yue Na Yang Wei Zhang Jia-liang Zhang Jing Wang Yang Wang Lian-hong Li Yi-xin Zeng Mien-Chie Hung Quentin Liu
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Nature Communications
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Colorectal cancer cell lines are representative models of the main molecular subtypes of primary cancer.
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2014-04-22
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Diego Arango Walter Bodmer Oliver Sieber Robert N Jorissen Daniel D Buchanan John M Mariadason
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Dmitri Mouradov Clare Sloggett Christopher G Love Shan Li Antony W Burgess Robert L Strausberg Samuel Wormald Liam O'Connor Jennifer L Wilding David Bicknell Ian P M Tomlinson
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Cancer Research
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RNA sequencing shows transcriptomic changes in rectosigmoid mucosa in patients with irritable bowel syndrome-diarrhea: a pilot case-control study.
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2014-04-24
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Michael Camilleri
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Paula Carlson Andres Acosta Irene Busciglio Asha A Nair Simon J Gibbons Gianrico Farrugia Eric W Klee
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American Journal of Physiology - Gastrointestinal and Liver Physiology
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Insights into the trypanosome-host interactions revealed through transcriptomic analysis of parasitized tsetse fly salivary glands.
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2014-04-24
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Michelle B O'Neill Thiago Luiz Alves e Silva Erich L Telleria Serap Aksoy
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Joshua B Benoit Xin Zhao Amy F Savage Sandesh Regmi
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PLOS Neglected Tropical Diseases
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A novel highly divergent protein family identified from a viviparous insect by RNA-seq analysis: a potential target for tsetse fly-specific abortifacients.
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2014-04-24
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Geoffrey Attardo Aaron A Baumann Qirui Zhang Paul O. Mireji Serap Aksoy José M. Ribeiro
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Joshua B Benoit Veronika Michalkova Tyler B Krause Jana Bohova Peter Takáč David L Denlinger
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PLOS Genetics
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A gene expression atlas of early craniofacial development
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2014-04-26
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Phillip Dexheimer
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Eric W Brunskill Andrew S Potter Andrew Distasio Andrew Plassard Bruce J Aronow S Steven Potter
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Developmental Biology
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The cytochrome P450 genes of channel catfish: their involvement in disease defense responses as revealed by meta-analysis of RNA-Seq data sets.
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2014-04-27
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David Robert Nelson Geoff Waldbieser Luyang Sun Shikai Liu Yu Zhang
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Jiaren Zhang Jun Yao Ruijia Wang Yanliang Jiang Jianbin Feng Nannan Liu Geoff Waldbieser Zhanjiang Liu
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Biochimica et Biophysica Acta
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An improved genome release (version Mt4.0) for the model legume Medicago truncatula.
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2014-04-27
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Haibao Tang Vivek Krishnakumar Laurent Gentzbittel Kevin L. Childs
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Shelby Bidwell Benjamin Rosen Agnes Chan Shiguo Zhou Mark Yandell Heidrun Gundlach Klaus F X Mayer David C Schwartz Christopher D Town
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BMC Genomics
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Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival.
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2014-04-29
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Spencer D. Martin Brad H Nelson Robert A Holt
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Scott D Brown Rene L Warren Ewan A Gibb John J Spinelli
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Genome Research
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Microfluidic single-cell whole-transcriptome sequencing.
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2014-04-29
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Liang Zhao Yanyi Huang
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Aaron M Streets Xiannian Zhang Chen Cao Yuhong Pang Xinglong Wu Liang Xiong Lu Yang Yusi Fu Fuchou Tang
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Proceedings of the National Academy of Sciences of the United States of America
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Longer Reads Do Not Significantly Improve RNA-seq Results.
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2014-05-01
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Sagar Chhangawala
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Gabe Rudy Po-Yen Wu Scott Tighe May D. Wang Don A. Baldwin George Grills Christopher E. Mason Jeffrey Rosenfeld
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Journal of Biomolecular Techniques
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From genome to function by studying eQTLs.
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2014-05-04
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Lude Franke
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Harm-Jan Westra
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Biochimica et Biophysica Acta
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Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.
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2014-05-05
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Gregory B. Gloor
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Andrew D Fernandes Jennifer Ns Reid Jean M Macklaim Thomas A McMurrough David R Edgell
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Microbiome
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A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines
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2014-05-05
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Gil Omenn
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Yuanfang Guan Rajasree Menon
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Journal of Proteomics
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Characterization of a genetic mouse model of lung cancer: a promise to identify Non-Small Cell Lung Cancer therapeutic targets and biomarkers.
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2014-05-06
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Matteo Carrara Dario Livio Longo Elena Quaglino Manuela Iezzi Silvio Bicciato Raffaele A. Calogero Federica Cavallo Lorena Landuzzi
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Federica Riccardo Maddalena Arigoni Genny Buson Elisa Zago Alessandra Fiore Simona Nuzzo Patrizia Nanni
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BMC Genomics
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Genome sequencing and comparative genomics of the broad host-range pathogen Rhizoctonia solani AG8.
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2014-05-08
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Jana Sperschneider James K Hane Jonathan P Anderson Karam B. Singh
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Angela H Williams
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PLOS Genetics
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lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs.
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2014-05-09
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Wan Kyu Kim
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Charny Park Namhee Yu Ikjung Choi Sanghyuk Lee
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Bioinformatics
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De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum.
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2014-05-12
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Paul J Kersey Arnaud Kerhornou Sushma Naithani Dan Bolser Gerard Lazo
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Samuel E Fox Matthew Geniza Mamatha Hanumappa Chris Sullivan Justin Preece Vijay K Tiwari Justin Elser Jeffrey M Leonard Abigail Sage Cathy Gresham Fiona McCarthy Pankaj Jaiswal
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PLOS ONE
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Facile functional analysis of insect odorant receptors expressed in the fruit fly: validation with receptors from taxonomically distant and closely related species.
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2014-05-13
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Walter S Leal
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Carlos Ueira-Vieira Deborah A Kimbrell Washington J de Carvalho
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Cellular and Molecular Life Sciences
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Identification of a radiation sensitivity gene expression profile in primary fibroblasts derived from patients who developed radiotherapy-induced fibrosis.
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2014-05-13
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Jason Li
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Helen B Forrester Trevor Leong Michael J McKay Carl N Sprung
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Radiotherapy and Oncology
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Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs
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2014-05-14
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Tiffany Hsu Ronny Kellner Eva H Stukenbrock
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Amitava Bhattacharyya Stephan Poppe Rachel B Brem
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Genome Biology and Evolution
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Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling
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2014-05-16
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Roland Eils Rosario M. Piro
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Stefan Wiesberg Gunnar Schramm Nico Rebel Marcus Oswald Gerhard Reinelt Rainer König
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BMC Systems Biology
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Dual RNA-seq transcriptional analysis of wheat roots colonized by Azospirillum brasilense reveals up-regulation of nutrient acquisition and cell cycle genes.
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2014-05-16
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Glaucio Valdameri Helisson Faoro Lucélia Donatti Leda S Chubatsu
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Doumit Camilios-Neto Paloma Bonato Roseli Wassem Michelle Z Tadra-Sfeir Liziane C C Brusamarello-Santos Vinicius A Weiss Fábio O Pedrosa Emanuel M Souza
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BMC Genomics
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Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data.
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2014-05-19
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Francis M Jiggins
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Andrew Quinn Punita Juneja
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Bioinformatics
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RNA sequencing analysis of the gametophyte transcriptome from the liverwort, Marchantia polymorpha.
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2014-05-19
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Mohan B. Singh Prem L. Bhalla
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Niharika Sharma Chol-Hee Jung
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PLOS ONE
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Production, gene structure and characterization of two orthologs of leptin and a leptin receptor in tilapia.
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2014-05-20
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Tomer Ventura Berta Levavi-Sivan
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Michal Shpilman Lian Hollander-Cohen Arieh Gertler
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General and Comparative Endocrinology
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A dynamic regulatory network explains ParaHox gene control of gut patterning in the sea urchin.
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2014-05-21
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Maria Ina Arnone
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Rossella Annunziata
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Development
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Dual RNA-seq of parasite and host reveals gene expression dynamics during filarial worm-mosquito interactions
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2014-05-22
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George F Mayhew Matthew T Aliota
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Young-Jun Choi Sara M Erickson Bruce M Christensen
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PLOS Neglected Tropical Diseases
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Transcriptome of Atoh7 retinal progenitor cells identifies new Atoh7-dependent regulatory genes for retinal ganglion cell formation.
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2014-05-22
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Xiuqian Mu
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Zhiguang Gao Chai-An Mao Ping Pan William H Klein
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Developmental Neurobiology
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A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia.
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2014-05-22
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Laura Eme Matthew W. Brown Mark van der Giezen Courtney W Stairs Graham Dellaire
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Cornelis Mutsaers Edward Susko Darren M Soanes Andrew J Roger
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Current Biology
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Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling
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2014-05-23
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Bruno M Vieira Octávio S. Paulo Filipa Monteiro Lisete Sousa Mónica Sebastiana Rui Manuel Tavares Andreia Figueiredo
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Teresa Lino-Neto Maria Salomé Pais
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PLOS ONE
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Sequential combination of karyotyping and RNA-sequencing in the search for cancer-specific fusion genes.
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2014-05-23
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Sverre Heim Ioannis Panagopoulos
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Jim Thorsen Ludmila Gorunova Francesca Micci
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International Journal of Biochemistry & Cell Biology
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Selective and flexible depletion of problematic sequences from RNA-seq libraries at the cDNA stage.
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2014-05-26
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Thomas Preiss
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Stuart K Archer Nikolay E Shirokikh
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BMC Genomics
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DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle
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2014-05-26
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Silvère M van der Maarel
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Zizhen Yao Lauren Snider Judit Balog Richard J L F Lemmers Rabi Tawil Stephen J Tapscott
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Human Molecular Genetics
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Time-resolved gene expression profiling during reprogramming of C/EBPα-pulsed B cells into iPS cells
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2014-05-27
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Bruno Di Stefano
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Samuel Collombet Thomas Graf
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Scientific Data
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Transcription of nuclear organellar DNA in a model plant system.
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2014-05-27
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David L. Adelson
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Dong Wang Zhipeng Qu Jian-Kang Zhu Jeremy N Timmis
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Genome Biology and Evolution
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The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis.
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2014-05-29
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Luis Solans Jesús Gonzalo-Asensio Claudia Sala Carlos Martín
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Andrej Benjak Swapna Uplekar Jacques Rougemont Christophe Guilhot Wladimir Malaga Stewart T Cole
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PLOS Pathogens
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SHP2 regulates chondrocyte terminal differentiation, growth plate architecture and skeletal cell fates
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2014-05-29
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Margot Bowen
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Ugur M Ayturk Kyle C Kurek Wentian Yang Matthew L Warman
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PLOS Genetics
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RNA-seq: impact of RNA degradation on transcript quantification.
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2014-05-30
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Irene Gallego Romero
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Athma A Pai Jenny Tung Yoav Gilad
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BMC Biology
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Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato
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2014-06
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Jason Reed
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Ning Liu Shan Wu Jason Van Houten Ying Wang Biao Ding Zhangjun Fei Thomas H Clarke Esther van der Knaap
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Journal of Experimental Botany
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Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation.
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2014-06-01
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Harri Lähdesmäki Zhi Chen Vincent Butty Tarmo Äijö
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Verna Salo Subhash Tripathi Christopher B Burge Riitta Lahesmaa
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Bioinformatics
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Differential RNA-seq: the approach behind and the biological insight gained.
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2014-06-01
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Cynthia Sharma Jörg Vogel
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Current Opinion in Microbiology
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Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.
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2014-06-02
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Charles M. Perou
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Wei Zhao Xiaping He Katherine A Hoadley Joel S Parker David Neil Hayes
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BMC Genomics
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Genome-wide identification of long intergenic noncoding RNA genes and their potential association with domestication in pigs.
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2014-06-02
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David M. Irwin
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Zhong-Yin Zhou Ai-Min Li Adeniyi C Adeola Yan-Hu Liu Hai-Bing Xie Ya-Ping Zhang
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Genome Biology and Evolution
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Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.
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2014-06-03
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Ana Conesa Sonia Tarazona María José Nueda
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Bioinformatics
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The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance.
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2014-06-03
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Remo Sanges David A van Heel Elia Stupka Raquel Marco-Ferreres Ivan Conte Dejan Lazarevic Paola Bovolenta Sandro Banfi
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Stefania Merella Jose Manuel Garcia-Manteiga Chiara Migliore Sabrina Carrella Raffaella Avellino Nathan Paul Davidson Warren Emmett Nicholas Bockett Germana Meroni
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Nucleic Acids Research
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RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri.
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2014-06-06
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Nicholas Thomson
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Marta Vergara-Irigaray Maria C Fookes Christoph M Tang
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BMC Genomics
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Transcriptome sequencing revealed the transcriptional organization at ribosome-mediated attenuation sites in Corynebacterium glutamicum and identified a novel attenuator involved in aromatic amino acid biosynthesis.
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2014-06-06
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Jörn Kalinowski
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Armin Neshat Almut Mentz Christian Rückert
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Journal of Biotechnology
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Comparative transcriptional analysis of asexual and sexual morphs reveals possible mechanisms in reproductive polyphenism of the cotton aphid.
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2014-06-10
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Wei Guo
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Li-Jun Liu Hong-Yuan Zheng Feng Jiang Shu-Tang Zhou
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PLOS ONE
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Variable escape from X-chromosome inactivation: identifying factors that tip the scales towards expression
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2014-06-10 2014-08-01
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Allison M Cotton Carolyn J. Brown
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Samantha B Peeters
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BioEssays
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An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7.
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2014-06-10
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Robert W Jackson Nicola Holden
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Ashleigh Holmes Louise Birse
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Frontiers in Microbiology
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ARH-seq: identification of differential splicing in RNA-seq data
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2014-06-11
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Marie-Laure Yaspo Hans Lehrach Ralf Herwig
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Axel Rasche Matthias Lienhard Marie-Laure Yaspo
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Nucleic Acids Research
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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.
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2014-06-11
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Nir Friedman Aviv Regev Rahul Satija Nir Hacohen Schraga Schwartz Raktima Raychowdhury Alex K. Shalek
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Joe Shuga John J Trombetta Dave Gennert Diana Lu Peilin Chen Rona S Gertner Jellert T Gaublomme Nir Yosef Brian Fowler Suzanne Weaver Jing Wang Xiaohui Wang Ruihua Ding Raktima Raychowdhury Hongkun Park Andrew P May
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Nature
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Comparison of REST cistromes across human cell types reveals common and context-specific functions
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2014-06-12
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Elaine Fuchs Deyou Zheng
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Shira Rockowitz Wen-Hui Lien Erika Pedrosa Gang Wei Mingyan Lin Keji Zhao Herbert M Lachman
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PLOS Computational Biology
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A novel functional role for MMSET in RNA processing based on the link between the REIIBP isoform and its interaction with the SMN complex
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2014-06-12
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Fabio Mirabella Andrew Thompson C Pawlyn Christopher P Wardell Brian A. Walker
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Alexander Murison Lauren I Aronson Sarah J Hanrahan Jacqueline H L Fok Martin F Kaiser Faith E Davies Gareth J Morgan
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PLOS ONE
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Annotation of long non-coding RNAs expressed in collaborative cross founder mice in response to respiratory virus infection reveals a new class of interferon-stimulated transcripts
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2014-06-12
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Ralph S Baric Yoshihiro Kawaoka
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Laurence Josset Nicolas Tchitchek Lisa E Gralinski Martin T Ferris Amie J Eisfeld Richard R Green Matthew J Thomas Jennifer Tisoncik-Go Gary P Schroth Fernando Pardo Manuel de Villena Mark T Heise Xinxia Peng Michael G Katze
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RNA Biology
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A transcription factor network specifying inhibitory versus excitatory neurons in the dorsal spinal cord.
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2014-06-12
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Diogo S. Castro
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Mark D Borromeo David M Meredith Joshua C Chang Kuang-Chi Tung Francois Guillemot Jane E Johnson
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Development
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RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.
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2014-06-13
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Jessica Lasky-Su
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Blanca E Himes Xiaofeng Jiang Peter Wagner Ruoxi Hu Qiyu Wang Barbara Klanderman Reid M Whitaker Qingling Duan Christina Nikolos William Jester Martin Johnson Reynold A Panettieri Kelan G Tantisira Scott T Weiss Quan Lu
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PLOS ONE
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The Aux/IAA gene rum1 involved in seminal and lateral root formation controls vascular patterning in maize (Zea mays L.) primary roots.
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2014-06-13
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Nina Opitz Frank Hochholdinger Cheng-Ting Yeh
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Yanxiang Zhang Anja Paschold Caroline Marcon Sanzhen Liu Huanhuan Tai Josefine Nestler Christa Lanz Patrick S Schnable
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Journal of Experimental Botany
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miR-PREFeR: an accurate, fast and easy-to-use plant miRNA prediction tool using small RNA-Seq data.
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2014-06-14
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Jikai Lei
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Yanni Sun
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Bioinformatics
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An integrative method to normalize RNA-Seq data.
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2014-06-14
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Klopp Christophe
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Cyril Filloux Meersseman Cédric Philippe Romain Forestier Lionel Rocha Dominique Maftah Abderrahman Petit Daniel
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BMC Bioinformatics
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Mapping of HPV transcripts in four human cervical lesions using RNAseq suggests quantitative rearrangements during carcinogenic progression.
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2014-06-14
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Michael Poidinger
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Jinmiao Chen Yuezhen Xue Thimothy Lim Sung Hock Chew Chai Ling Pang Jean-Pierre Abastado Françoise Thierry
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Virology
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A chemical potentiator of copper-accumulation used to investigate the iron-regulons of Saccharomyces cerevisiae.
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2014-06-15
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Ehmke Pohl Nigel Robinson
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Andrew W Foster Samantha J Dainty Carl J Patterson Hannah Blackburn Clare Wilson Corinna R Hess Julian C Rutherford Laura Quaranta Andy Corran
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Molecular Microbiology
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Transcriptomic landscape of prophase I sunflower male meiocytes.
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2014-06-16
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Octavio Martínez
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Nathalia M V Flórez-Zapata M H Reyes-Valdés Fernando Hernandez-Godínez
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Frontiers in Plant Science
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Sugarcane genome sequencing by methylation filtration provides tools for genomic research in the genus Saccharum
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2014-06-17
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W. Richard McCombie Clícia Grativol Felipe Rodrigues da Silva
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Michael Regulski Marcelo Bertalan Adhemar Zerlotini Neto Renato Vicentini Laurent Farinelli Adriana Silva Hemerly Robert A Martienssen Paulo Cavalcanti Gomes Ferreira
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The Plant Journal
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RNA-Seq analysis implicates detoxification pathways in ovine mycotoxin resistance
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2014-06-17
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Jinbi Zhang
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Zengxiang Pan Stephanie Moloney Allan Sheppard
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PLOS ONE
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The Chlamydomonas genome project: a decade on.
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2014-06-17
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David Goodstein Jane Grimwood Crysten E Blaby-Haas Sabeeha Merchant
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Ian K Blaby Nicolas Tourasse Erik F Y Hom David Lopez Munevver Aksoy Arthur Grossman James Umen Susan Dutcher Mary Porter Stephen King George B Witman Mario Stanke Elizabeth H Harris Jane Grimwood Jeremy Schmutz Olivier Vallon Simon Prochnik
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Trends in Plant Science
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Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development
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2014-06-18
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Songnian Hu
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Wei Xu Chengqi Xin Qiang Lin Feng Ding Wei Gong Yuanyuan Zhou Jun Yu Peng Cui
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Genomics Proteomics and Bioinformatics
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Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.
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2014-06-19
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Dominique Rocha Daniel Gautheret
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Coline Billerey Mekki Boussaha Diane Esquerré Emmanuelle Rebours Anis Djari Cédric Meersseman Christophe Klopp
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BMC Genomics
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RNA-Seq for the identification of novel Mediator transcripts in endothelial progenitor cells.
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2014-06-19
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Valerio Costa Concetta Schiano Claudio Napoli Monica Rienzo Amelia Casamassimi
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Margherita Scarpato Vincenzo Grimaldi Alfredo Ciccodicola
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Gene
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Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche
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2014-06-20
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Richard Sandstrom Eric Haugen
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Michael R Foret Douglas A Grow Christopher T Rhodes Astrid E Cardona Clyde F Phelix Yufeng Wang Mitchel S Berger Chin-Hsing Annie Lin
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Scientific Reports
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A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells.
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2014-06-20
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Elena Shklovskaya Barbara Fazekas De St Groth
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David G Hancock Thomas V Guy Reza Falsafi Chris D Fjell William Ritchie Robert E W Hancock
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PLOS ONE
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Genomic characterization of acute leukemias.
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2014-06-20
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Robin Foà
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Sabina Chiaretti Valentina Gianfelici Giulia Ceglie
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Medical Principles and Practice
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RNA-binding protein RBM20 represses splicing to orchestrate cardiac pre-mRNA processing.
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2014-06-24
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Markus Landthaler Nikolaus Rajewsky Marvin Jens Martin Liss Michael H Radke Matthias Heinig Michael Gotthardt Eleonora Adami
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Henrike Maatz Sebastian Schafer Marieluise Kirchner Carola Rintisch Vita Dauksaite Matthias Selbach Paul J R Barton Stuart A Cook Norbert Hubner
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Journal of Clinical Investigation
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Comprehensive analysis of the whole transcriptomes from two different pig breeds using RNA-Seq method.
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2014-06-24
|
Artur Gurgul Maria Oczkowicz Katarzyna Ropka-Molik Katarzyna Piórkowska
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Kacper Zukowski Robert Eckert
|
Animal Genetics
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A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.
|
2014-06-25
|
Richard Emes Joanna Moreton Stephen Dunham
|
|
Frontiers in Genetics
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A comparison of transcriptional patterns and mycological phenotypes following infection of Fusarium graminearum by four mycoviruses
|
2014-06-25
|
Kyunghun Min
|
Kyung-Mi Lee Won Kyong Cho Jisuk Yu Moonil Son Hoseong Choi Yin-Won Lee Kook-Hyung Kim
|
PLOS ONE
|
A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
|
2014-06-27
|
Jia Meng
|
Zhiliang Lu Hui Liu Lin Zhang Shaowu Zhang Yidong Chen Manjeet K Rao Yufei Huang
|
Methods
|
Profile of whole blood gene expression following immune stimulation in a wild passerine
|
2014-06-27
|
Peeter Hõrak Reidar Andreson
|
Richard Meitern Peeter Hõrak
|
BMC Genomics
|
Response of the hepatic transcriptome to aflatoxin B1 in domestic turkey (Meleagris gallopavo).
|
2014-06-30
|
Melissa S Monson
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Robert E Settlage Kevin W McMahon Kristelle M Mendoza Sumit Rawal Hani S El-Nezami Roger A Coulombe Kent M Reed
|
PLOS ONE
|
Building the sugarcane genome for biotechnology and identifying evolutionary trends.
|
2014-06-30
|
Hélène Bergès Monalisa Sampaio Carneiro Claudio Benicio Cardoso-Silva Carlos T Hotta Cushla Jane Metcalfe Glaucia Mendes Souza Changsoo Kim Alessandro Varani Marie-Anne Van Sluys Anete Pereira Souza
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Nathalia de Setta Cláudia Barros Monteiro-Vitorello Guilherme Marcelo Queiroga Cruz Luiz Eduardo Del Bem Renato Vicentini Fábio Tebaldi Silveira Nogueira Roberta Alvares Campos Sideny Lima Nunes Paula Cristina Gasperazzo Turrini Andreia Prata Vieira Edgar Andrés Ochoa Cruz Tatiana Caroline Silveira Corrêa Sonia Vautrin Adilson Silva da Trindade Mariane de Mendonça Vilela Carolina Gimiliani Lembke Paloma Mieko Sato Rodrigo Fandino de Andrade Milton Yutaka Nishiyama Katia Castanho Scortecci Antônio Augusto Franco Garcia Andrew H Paterson Angélique D'Hont Michel Vincentz João Paulo Kitajima
|
BMC Genomics
|
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection
|
2014-07
|
Marvin Whiteley
|
Keith H Turner Jake Everett Urvish Trivedi Kendra P Rumbaugh
|
PLOS Genetics
|
The coding and noncoding architecture of the Caulobacter crescentus genome
|
2014-07
|
Bo Zhou Jared M Schrader Sean Crosson Jonathan Weissman
|
Gene-Wei Li Keren Lasker W Seth Childers Brandon Williams Tao Long Harley H McAdams Lucy Shapiro
|
PLOS Genetics
|
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing
|
2014-07-01
|
Aviv Regev Rahul Satija Alex K. Shalek
|
John J. Trombetta David Gennert Diana Lu
|
Current protocols in molecular biology
|
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.
|
2014-07-01
|
Jingyi Jessica Li Steven E. Brenner
|
Haiyan Huang Peter J Bickel
|
Genome Research
|
SnowyOwl: accurate prediction of fungal genes by using RNA-Seq and homology information to select among ab initio models.
|
2014-07-01
|
Christoph W. Sensen
|
Ian Reid Nicholas O'Toole Omar Zabaneh Reza Nourzadeh Mahmoud Dahdouli Mostafa Abdellateef Paul M K Gordon Jung Soh Gregory Butler Adrian Tsang
|
BMC Bioinformatics
|
IMAGE GUIDED RNA-SEQ REVEALS SUBTYPE-SPECIFIC PATTERNS AT THE INFILTRATIVE MARGINS OF GLIOBLASTOMA.
|
2014-07-01
|
Michael B Sisti
|
Peter Canoll Peter Sims Brian Gil David Pisapia Hani Malone Hannah Goldstein Liang Lei Adam Sonabend Jonathan Yun Jorge Samanamud Jennifer Sims Andrew Teich Sameer Sheth Guy McKhann Jeffrey Bruce
|
Neuro-Oncology
|
Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution.
|
2014-07-01
|
Kasper D. Hansen Jeffrey T. Leek
|
Frazee AC Sabunciyan S Irizarry RA
|
Biostatistics
|
Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes.
|
2014-07-02
|
Melody Baddoo Asuka Nanbo
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Michael J Strong Melody Baddoo Miao Xu Adriane Puetter Zhen Lin
|
Journal of Virology
|
Novel bioinformatics method for identification of genome-wide non-canonical spliced regions using RNA-Seq data.
|
2014-07-03
|
Gil Omenn
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Yongsheng Bai Justin Hassler Ahdad Ziyar Philip Li Zachary Wright Rajasree Menon James D Cavalcoli Randal J Kaufman Maureen A Sartor
|
PLOS ONE
|
Status of duckweed genomics and transcriptomics.
|
2014-07-04
|
Wenqin Wang
|
J Messing
|
Plant Biology
|
Exploring the stability of long intergenic non-coding RNA in K562 cells by comparative studies of RNA-Seq datasets
|
2014-07-05
|
Jing Tu
|
Lei Wang Dequan Zhou Yan Wang Zuhong Lu
|
Biology Direct
|
Large-scale transcriptional response to hypoxia in Aspergillus fumigatus observed using RNAseq identifies a novel hypoxia regulated ncRNA.
|
2014-07-05
|
Suman B Pakala Vinita S Joardar Bridget M Barker Nikhat Zafar
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Liliana Losada Suchitra Pakala Stephanie Mounaud Natalie Fedorova William C Nierman Robert A Cramer
|
Mycopathologia
|
Enhanced whole genome sequence and annotation of Clostridium stercorarium DSM8532T using RNA-seq transcriptomics and high-throughput proteomics.
|
2014-07-07
|
Gerhard G Thallinger Richard Sparling Bernard Henrissat
|
John J Schellenberg Tobin J Verbeke Peter McQueen Oleg V Krokhin Xiangli Zhang Graham Alvare Brian Fristensky John A Wilkins David B Levin
|
BMC Genomics
|
De novo transcriptome sequencing and sequence analysis of the malaria vector Anopheles sinensis (Diptera: Culicidae).
|
2014-07-07
|
Liang Qiao
|
Bin Chen Yu-Juan Zhang Zhengbo He Wanshun Li Fengling Si Yao Tang Qiyi He Zhentian Yan Wenbo Fu Yanfei Che
|
Parasites & Vectors
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Comparative Analysis of Glycogene Expression in Different Mouse Tissues Using RNA-Seq Data
|
2014-07-09
|
Vivekanand Jha Ahmad Firoz Sanjay Kumar Singh
|
Adeel Malik Amjad Ali
|
International Journal of Genomics
|
Occupancy of tissue-specific cis-regulatory modules by Otx2 and TLE/Groucho for embryonic head specification.
|
2014-07-09
|
Yuuri Yasuoka Yoshikazu Haramoto Makoto Asashima
|
Yutaka Suzuki Shuji Takahashi Haruka Someya Norihiro Sudou Ken W Cho Sumio Sugano Masanori Taira
|
Nature Communications
|
Analysis of the transcriptome and immune function of monocytes during IFNα-based therapy in chronic HCV revealed induction of TLR7 responsiveness.
|
2014-07-09
|
Andre Boonstra Wilfred F J van IJcken
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Jun Hou Zwier M A Groothuismink Ludi Koning Robert Roomer Kim Kreefft Bi-Sheng Liu Harry L A Janssen Robert J de Knegt
|
Antiviral Research
|
Apomictic and sexual germline development differ with respect to cell cycle, transcriptional, hormonal and epigenetic regulation.
|
2014-07-10
|
Christian Sailer Ueli Grossniklaus
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Anja Schmidt Marc W Schmid Ulrich C Klostermeier Weihong Qi Daniela Guthörl Manuel Waller Philip Rosenstiel Ueli Grossniklaus
|
PLOS Genetics
|
Expression pattern of immunoglobulin superfamily members in the silkworm, Bombyx mori.
|
2014-07-11
|
Moli Huang
|
Lei He Guangli Cao Renyu Xue Xiaolong Hu Chengliang Gong
|
Gene
|
A memory-efficient algorithm to obtain splicing graphs and de novo expression estimates from de Bruijn graphs of RNA-Seq data
|
2014-07-14
|
Aaron M. Tarone
|
Sing-Hoi Sze
|
BMC Genomics
|
Reference genes for RT-qPCR studies in Corynebacterium pseudotuberculosis identified through analysis of RNA-seq data.
|
2014-07-15
|
Bruno Bastos
|
Daiane M Carvalho Pablo H de Sá Thiago L P Castro Rodrigo D Carvalho Anne Pinto Danilo J P Gil Priscilla Bagano Lilia F M Costa Roberto Meyer Artur Silva Vasco Azevedo Rommel T J Ramos Luis G C Pacheco
|
Antonie van Leeuwenhoek
|
Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot-specific NADPH oxidase.
|
2014-07-15
|
Frank Hochholdinger
|
Josefine Nestler Sanzhen Liu Tsui-Jung Wen Anja Paschold Caroline Marcon Ho Man Tang Delin Li Li Li Robert B Meeley Hajime Sakai Wesley Bruce Patrick S Schnable
|
The Plant Journal
|
Whole transcriptome RNA-seq analysis: tumorigenesis and metastasis of melanoma.
|
2014-07-15
|
Songnian Hu
|
Hua Zhao Yongjun Li Shaobin Wang Yadong Yang Junyun Wang Xiuyan Ruan Yaran Yang Kan Cai Bing Zhang Peng Cui Jiangwei Yan Yongliang Zhao Edward K Wakeland Quanzhen Li Xiangdong Fang
|
Gene
|
SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples
|
2014-07-16
|
Charles M. Perou Liza Makowski Patrick K Kimes
|
Christopher R Cabanski Matthew D Wilkerson Ni Zhao Amy R Johnson Christopher A Maher Yufeng Liu J S Marron D Neil Hayes
|
Nucleic Acids Research
|
Differential gene expression in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation.
|
2014-07-16
|
Kenneth B. Storey
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Ye Zhao Hongsheng Yang Muyan Chen
|
Marine Genomics
|
Polyphosphate accumulation is driven by transcriptome alterations that lead to near-synchronous and near-equivalent uptake of inorganic cations in an arbuscular mycorrhizal fungus.
|
2014-07-16
|
Katsuharu Saito Tatsuhiro Ezawa
|
Yusuke Kikuchi Nowaki Hijikata Kaede Yokoyama Ryo Ohtomo Yoshihiro Handa Masayoshi Kawaguchi
|
New Phytologist
|
Bioinformatic exploration of RIO protein kinases of parasitic and free-living nematodes.
|
2014-07-17
|
Pasi K. Korhonen Neil D. Young Andreas Hofmann Robin B. Gasser Aaron R Jex Paul W. Sternberg
|
Bert Breugelmans Stefano Mangiola Peter R Boag
|
International Journal for Parasitology
|
Developmental heterogeneity of cardiac fibroblasts does not predict pathological proliferation and activation.
|
2014-07-18
|
Kristy Red-Horse
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Shah R Ali Sara Ranjbarvaziri Mahmood Talkhabi Peng Zhao Ali Subat Armin Hojjat Paniz Kamran Antonia M S Müller Katharina S Volz Zhaoyi Tang Kristy Red-Horse Reza Ardehali
|
Circulation Research
|
Gene expression profiling of laser microdissected airway smooth muscle tissue in asthma and atopy.
|
2014-07-19
|
Frank Baas
|
C Y Yick A H Zwinderman P W Kunst K Grünberg T Mauad S Chowdhury E H Bel R Lutter P J Sterk
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Allergy
|
Genome-wide characterization of light-regulated genes in Neurospora crassa.
|
2014-07-21
|
Jeremy Zucker Erin Bredeweg Matthew S. Sachs
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Cheng Wu Fei Yang Kristina M Smith Matthew Peterson Rigzin Dekhang Ying Zhang Chandrashekara Mallappa Xiaoying Zhou Anna Lyubetskaya Jeffrey P Townsend James E Galagan Michael Freitag Jay C Dunlap Deborah Bell-Pedersen
|
G3
|
Sequence, structural and expression divergence of duplicate genes in the bovine genome.
|
2014-07-23
|
Graham Plastow Paul Stothard
|
Xiaoping Liao Hua Bao Yan Meng Stephen Moore
|
PLOS ONE
|
Hierarchical molecular events driven by oocyte-specific factors lead to rapid and extensive reprogramming
|
2014-07-24
|
Charles R Bradshaw Richard P Halley-Stott Vincent Pasque Kei Miyamoto John Gurdon
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Jerome Jullien George E Allen Nigel J Garrett Hiroshi Kimura Keita Ohsumi
|
Molecular Cell
|
A new dataset of spermatogenic vs. oogenic transcriptomes in the nematode Caenorhabditis elegans.
|
2014-07-24
|
Marco A Ortiz Judith Kimble
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Daniel Noble Elena P Sorokin
|
G3
|
Transcriptome Analysis of the Human Striatum in Tourette Syndrome.
|
2014-07-24
|
Gianfilippo Coppola Dean Palejev Flora M. Vaccarino Nenad Sestan
|
Jessica B Lennington Yuko Kataoka-Sasaki Thomas V Fernandez Yifan Li Anita Huttner Mihovil Pletikos Nenad Sestan James F Leckman
|
Biological Psychiatry
|
iRegulon: from a gene list to a gene regulatory network using large motif and track collections.
|
2014-07-24
|
Zeynep Kalender Atak Delphine Potier Stein Aerts Jean-Christophe Marine Bram Van de Sande Gert Hulselmans Marina N Sanchez
|
Rekin's Janky Annelien Verfaillie Hana Imrichová Laura Standaert Valerie Christiaens Koen Herten Dmitry Svetlichnyy Mark Fiers
|
PLOS Computational Biology
|
Characterization of long non-coding RNA transcriptome in clear-cell renal cell carcinoma by next-generation deep sequencing.
|
2014-07-25
|
Olivier Cussenot
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Gabriel G Malouf Jianping Zhang Ying Yuan Eva Compérat Morgan Rouprêt Yunxin Chen Erika J Thompson Nizar M Tannir John N Weinstein Vicente Valero David Khayat Jean-Philippe Spano Xiaoping Su
|
Molecular Oncology
|
RNA-seq of the aging brain in the short-lived fish N. furzeri - conserved pathways and novel genes associated with neurogenesis.
|
2014-07-25
|
Eva Terzibasi Tozzini Francesco Spallotta Mario Baumgart Michela Ori Marco Groth Alessandro Cellerino Carlo Gaetano Matthias Platzer
|
Steffen Priebe Aurora Savino Giovanna Testa Andreas Dix Roberto Ripa Reinhard Guthke
|
Aging Cell
|
Utility of RNA-seq and GPMDB protein observation frequency for improving the sensitivity of protein identification by tandem MS
|
2014-07-28
|
Alexey I Nesvizhskii
|
Avinash K Shanmugam Anastasia K Yocum
|
Journal of Proteome Research
|
Genomes and transcriptomes of partners in plant-fungal-interactions between canola (Brassica napus) and two Leptosphaeria species.
|
2014-07-28
|
Jonathan Grandaubert Angela P Van de Wouw Barbara Jane Howlett
|
Rohan G T Lowe Andrew Cassin Bethany L Clark Thierry Rouxel
|
PLOS ONE
|
Transcriptome analysis reveals the same 17 S-locus F-box genes in two haplotypes of the self-incompatibility locus of Petunia inflata.
|
2014-07-28
|
Joshua P. Der Justin S Williams
|
Claude W dePamphilis Teh-Hui Kao
|
The Plant Cell
|
Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster
|
2014-07-29
|
Vladimir N. Babenko
|
Igor F Zhimulev Tatyana Yu Zykova Fyodor P Goncharov Varvara A Khoroshko Olga V Demakova Valeriy F Semeshin Galina V Pokholkova Lidiya V Boldyreva Darya S Demidova Sergey A Demakov Elena S Belyaeva
|
PLOS ONE
|
Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches.
|
2014-07-30
|
Richard Sandstrom
|
Michael R Foret Christopher T Rhodes Yufeng Wang Mitchel S Berger Chin-Hsing Annie Lin
|
Frontiers in Genetics
|
Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.
|
2014-07-31
|
Zheng Xia Jernej Ule Ravi K. Singh Auinash Kalsotra
|
Christopher S Bland Marissa A Scavuzzo Tomaz Curk Wei Li Thomas A Cooper
|
Molecular Cell
|
Discovery of novel transcripts and gametophytic functions via RNA-seq analysis of maize gametophytic transcriptomes.
|
2014-07-31
|
Scott A. Givan
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Antony M Chettoor Rex A Cole Clayton T Coker Erica Unger-Wallace Zuzana Vejlupkova Erik Vollbrecht John E Fowler Matthew Ms Evans
|
Genome Biology
|
Single-cell RNA-seq: advances and future challenges
|
2014-08 2014-08-01
|
Jörg Vogel Alexander Westermann
|
Antoine-Emmanuel Saliba Stanislaw A. Gorski
|
Nucleic Acids Research
|
Temporally and spatially restricted gene expression profiling
|
2014-08-01
|
Alexandra Tallafuss
|
Philip Washbourne John Postlethwait
|
Current Genomics
|
Characterization of distinct classes of differential gene expression in osteoblast cultures from non-syndromic craniosynostosis bone
|
2014-08-01
|
Rene Olivares-Navarrete
|
Monica L Rojas-Peña Sharon Hyzy Dalia Arafat Zvi Schwartz Barbara D Boyan Joseph Williams Greg Gibson
|
Journal of genomics
|
c-Jun promotes cell migration and drives expression of the motility factor ENPP2 in soft tissue sarcomas
|
2014-08-01
|
Massimo Loda
|
Stefano Sioletic Jeffrey Czaplinski Lan Hu Jonathan A Fletcher Christopher D M Fletcher Andrew J Wagner George D Demetri Ewa T Sicinska Eric L Snyder
|
The Journal of Pathology
|
In vivo mRNA profiling of uropathogenic Escherichia coli from diverse phylogroups reveals common and group-specific gene expression profiles
|
2014-08-05
|
Susanne Häussler Sarah Pohl Denitsa Eckweiler
|
Piotr Bielecki Uthayakumar Muthukumarasamy Agata Bielecka Ansgar Schanz Ute Niemeyer Tonio Oumeraci Nils von Neuhoff Jean-Marc Ghigo
|
mBio
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Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis.
|
2014-08-05
|
Changle Ma
|
Xiaoyan Shen Zenglan Wang Xiaofeng Song Jiajia Xu Chunyun Jiang Yanxiu Zhao Hui Zhang
|
Plant Molecular Biology
|
Reduction of systematic bias in transcriptome data from human peripheral blood mononuclear cells for transportation and biobanking.
|
2014-08-07
|
Hideki Ohmomo
|
Tsuyoshi Hachiya Yu Shiwa Ryohei Furukawa Kanako Ono Shigeki Ito Yoji Ishida Mamoru Satoh Jiro Hitomi Kenji Sobue Atsushi Shimizu
|
PLOS ONE
|
MBASED: allele-specific expression detection in cancer tissues and cell lines.
|
2014-08-07
|
Jinfeng Liu
|
Oleg Mayba Houston N Gilbert Peter M Haverty Suchit Jhunjhunwala Zhaoshi Jiang Colin Watanabe Zemin Zhang
|
Genome Biology
|
Influence of RNA extraction methods and library selection schemes on RNA-seq data.
|
2014-08-11
|
Marie-Laure Yaspo Hans Lehrach
|
Marc Sultan Vyacheslav Amstislavskiy Thomas Risch Moritz Schuette Simon Dökel Meryem Ralser Daniela Balzereit Marie-Laure Yaspo
|
BMC Genomics
|
MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma.
|
2014-08-11
|
Michael B Sisti
|
Brian J Gill David J Pisapia Hani R Malone Hannah Goldstein Liang Lei Adam Sonabend Jonathan Yun Jorge Samanamud Jennifer S Sims Matei Banu Athanassios Dovas Andrew F Teich Sameer A Sheth Guy M McKhann Jeffrey N Bruce Peter A Sims Peter Canoll
|
Proceedings of the National Academy of Sciences of the United States of America
|
SERPINB3/B4 contributes to early inflammation and barrier dysfunction in an experimental murine model of atopic dermatitis.
|
2014-08-11
|
Gurjit Khurana Hershey
|
Umasundari Sivaprasad Kayla G Kinker Mark B Ericksen Mark Lindsey Aaron M Gibson Stacey A Bass Nicolas S Hershey Jingyuan Deng Mario Medvedovic
|
Journal of Investigative Dermatology
|
A comparative study of techniques for differential expression analysis on RNA-Seq data.
|
2014-08-13
|
Naomi R. Wray Zong Hong Zhang Qiong-Yi Zhao Janette Edson Denis C Bauer
|
Dhanisha J Jhaveri Vikki M Marshall Ramesh K Narayanan Gregory J Robinson Andreas E Lundberg Perry F Bartlett
|
PLOS ONE
|
Interferon gene expression signature in rheumatoid arthritis neutrophils correlates with a good response to TNFi therapy.
|
2014-08-13
|
Helen L Wright
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Huw B Thomas Robert J Moots Steven W Edwards
|
Rheumatology
|
Functional expression of dental plaque microbiota.
|
2014-08-14
|
Andrew I. Su Tobias Meißner
|
Scott N Peterson Erik Snesrud Ana C Ong Nicholas J Schork Walter A Bretz
|
Frontiers in cellular and infection microbiology
|
Discovering functional modules by topic modeling RNA-Seq based toxicogenomic data.
|
2014-08-14
|
Binsheng Gong
|
Ke Yu Mikyung Lee Zhichao Liu Joshua Xu Roger Perkins Weida Tong
|
Chemical Research in Toxicology
|
Itch-associated peptides: RNA-Seq and bioinformatic analysis of natriuretic precursor peptide B and gastrin releasing peptide in dorsal root and trigeminal ganglia, and the spinal cord.
|
2014-08-14
|
Danielle Thierry-Mieg Jean Thierry-Mieg
|
Samridhi C Goswami Santosh Mishra Mark A Hoon Andrew J Mannes Michael J Iadarola
|
Molecular Pain
|
De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress.
|
2014-08-14
|
Arghavan Alisoltani
|
Sadegh Mousavi Behrouz Shiran Hossein Fallahi Esameil Ebrahimie Ali Imani Saadollah Houshmand
|
PLOS ONE
|
RNA-Rocket: An RNA-Seq Analysis Resource for Infectious Disease Research
|
2014-08-14
|
Leslie Birgit Vosshall Michael McClelland Cristina Aurrecoechea
|
Andrew S. Warren Brian Brunk Prerak Desai Scott Emrich Gloria I. Giraldo-Calderón Omar Harb Deborah Hix Daniel Lawson Dustin Machi Chunhong Mao Eric Nordberg Maulik Shukla Alice R. Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral
|
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Insights into the epigenomic landscape of the human malaria vector Anopheles gambiae
|
2014-08-15
|
Elena Gómez-Díaz Fabrice Chandre
|
Ana Rivero Victor G Corces
|
Frontiers in Genetics
|
Genetic and pharmacological reactivation of the mammalian inactive X chromosome.
|
2014-08-18
|
Sanchita Bhatnagar
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Xiaochun Zhu Jianhong Ou Ling Lin Lynn Chamberlain Lihua J Zhu Narendra Wajapeyee Michael R Green
|
Proceedings of the National Academy of Sciences of the United States of America
|
H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress.
|
2014-08-18
|
Karl Mechtler
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Anna Sawicka Dominik Hartl Malgorzata Goiser Oliver Pusch Roman R Stocsits Ido M Tamir Christian Seiser
|
Genome Research
|
Dynamic changes in the Streptococcus pneumoniae transcriptome during transition from biofilm formation to invasive disease upon influenza A virus infection.
|
2014-08-18
|
Yong Kong Anders P. Hakansson
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Melinda M Pettigrew Laura R Marks Janneane F Gent Hazeline Roche-Hakansson
|
Infection and Immunity
|
Detecting translational regulation by change point analysis of ribosome profiling data sets
|
2014-08-21
|
Anze Zupanic Daryl P Shanley John C. Mathers
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Catherine Meplan Sushma N Grellscheid Tom B L Kirkwood John E Hesketh
|
RNA
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A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development.
|
2014-08-21
|
Florian Freudenberg Richard S. Nowakowski Cynthia Vied Alexandre A S F Raposo David Feng
|
Yuting Wang
|
Frontiers in Neuroscience
|
Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations
|
2014-08-22
|
Pratik D. Jagtap
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Gloria M Sheynkman James E Johnson Michael R Shortreed Getiria Onsongo Brian L Frey Timothy J Griffin Lloyd M Smith
|
BMC Genomics
|
MicroRNA and mRNA cargo of extracellular vesicles from porcine adipose tissue-derived mesenchymal stem cells.
|
2014-08-23
|
Lilach O. Lerman
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Alfonso Eirin Scott M Riester Xiang-Yang Zhu Hui Tang Jared M Evans Daniel O'Brien Andre J van Wijnen
|
Gene
|
RNA-seq transcriptome profiling reveals that Medicago truncatula nodules acclimate N₂ fixation before emerging P deficiency reaches the nodules.
|
2014-08-23
|
Gabriela Salinas-Riester Claudia Pommerenke
|
Ricardo A Cabeza Rebecca Liese Annika Lingner Ilsabe von Stieglitz Janice Neumann Klaus Dittert Joachim Schulze
|
Journal of Experimental Botany
|
Normalization of RNA-seq data using factor analysis of control genes or samples
|
2014-08-24
|
Davide Risso
|
John Ngai Terence P Speed Sandrine Dudoit
|
Nature Biotechnology
|
The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance
|
2014-08-24
|
Danielle Thierry-Mieg Michele Filosi Roberto Visintainer Florian Caiment Samantha Riccadonna Marco Chierici Lee Lancashire Binsheng Gong Davide Albanese Jean Thierry-Mieg Giuseppe Jurman Jos Kleinjans
|
Charles Wang Pierre R Bushel Joshua Xu Hong Fang Huixiao Hong Jie Shen Zhenqiang Su Joe Meehan Xiaojin Li Lu Yang Haiqing Li Paweł P Łabaj David P Kreil Dalila Megherbi Stan Gaj Joost van Delft Andreas Scherer Viswanath Devanarayan Jian Wang Yong Yang Hui-Rong Qian Marina Bessarabova Yuri Nikolsky Cesare Furlanello Ke K Zhang Jianying Li Jui-Hua Hsieh Daniel L Svoboda James C Fuscoe Youping Deng Leming Shi Richard S Paules Scott S Auerbach Weida Tong
|
Nature Biotechnology
|
RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.
|
2014-08-26
|
Kévin Rue-Albrecht Karsten Hokamp Eamonn Gormley David E. MacHugh Stephen V. Gordon Kate Killick
|
Kirsten E McLoughlin Nicolas C Nalpas John A Browne David A Magee Stephen D E Park Kieran G Meade Cliona O'Farrelly
|
Frontiers in Immunology
|
Deletion of aryl hydrocarbon receptor AHR in mice leads to subretinal accumulation of microglia and RPE atrophy.
|
2014-08-26
|
Anand Swaroop Soo-Young Kim Wai T. Wong Robert N. Fariss Matthew Brooks Emily Chew
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Hyun-Jin Yang Yi-Sheng Chang Jung-Woong Kim Rivka A Rachel Tiziana Cogliati Haohua Qian
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Investigative Ophthalmology & Visual Science
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Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq.
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2014-08-26
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Danielle Thierry-Mieg Jean Thierry-Mieg
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Binsheng Gong Charles Wang Zhenqiang Su Huixiao Hong Leming Shi Scott S Auerbach Weida Tong Joshua Xu
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Scientific Data
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Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq.
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2014-08-26
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Danielle Thierry-Mieg Jean Thierry-Mieg
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Joshua Xu Zhenqiang Su Huixiao Hong David P Kreil Christopher E Mason Weida Tong Leming Shi
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Scientific Data
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RVboost: RNA-seq variants prioritization using a boosting method
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2014-08-27
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Andrew L Feldman
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Chen Wang Jaime I Davila Saurabh Baheti Aditya V Bhagwate Xue Wang Jean-Pierre A Kocher Susan L Slager Anne J Novak James R Cerhan E Aubrey Thompson Yan W Asmann
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Bioinformatics
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RNA-Seq analysis reveals a six-gene SoxR regulon in Streptomyces coelicolor
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2014-08-27
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Joshua Shapiro Nawar Naseer
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Monica Chander
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PLOS ONE
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Identification of sRNAs expressed by the human pathogen Neisseria gonorrhoeae under disparate growth conditions.
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2014-08-28
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Ryan S McClure
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Brian Tjaden Caroline Genco
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Frontiers in Microbiology
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Ionotropic GABA and glycine receptor subunit composition in human pluripotent stem cell-derived excitatory cortical neurones.
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2014-08-28
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Owen Dando Peter C Kind David J Wyllie Giles E. Hardingham Siddharthan Chandran
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Owain T James Matthew R Livesey Jing Qiu Bilada Bilican Ghazal Haghi Rinku Rajan Karen Burr
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The Journal of Physiology
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DNA copy number evolution in Drosophila cell lines
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2014-08-28
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Maurizio Gatti Brenton R. Graveley Teresa M Przytycka
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Hangnoh Lee C Joel McManus Dong-Yeon Cho Matthew Eaton Fioranna Renda Maria Patrizia Somma Lucy Cherbas Gemma May Sara Powell Dayu Zhang Lijun Zhan Alissa Resch Justen Andrews Susan E Celniker Peter Cherbas Brian Oliver David MacAlpine
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Genome Biology
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Identification of differentially expressed genes during development of the zebrafish pineal complex using RNA sequencing.
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2014-08-28
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Q85220273
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Joshua T Gamse
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Developmental Biology
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Assessing the clinical use of clear cell renal cell carcinoma molecular subtypes identified by RNA expression analysis.
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2014-08-28
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Richard W. Joseph Thai Huu Ho
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Jeanette E Eckel-Passow Daniel A Igel Daniel J Serie John C Cheville Alexander S Parker
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Urologic Oncology
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RNA sequencing analysis of the broad-host-range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant
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2014-09
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Lei Li Konrad Förstner Wolfgang R Streit
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Dagmar Krysciak Jessica Grote Mariita Rodriguez Orbegoso Christian Utpatel Christel Schmeisser Hari B Krishnan
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Applied and Environmental Microbiology
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Using heterogeneity of the patient-derived xenograft model to identify the chemoresistant population in ovarian cancer
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2014-09-01
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Britt K. Erickson David A Schneider
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Zachary C Dobbin Ashwini A Katre Adam D Steg Monjri M Shah Ronald D Alvarez Michael G Conner Dongquan Chen Charles N Landen
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Oncotarget
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miR-155 induced transcriptome changes in the MCF-7 breast cancer cell line leads to enhanced mitogen activated protein kinase signaling
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2014-09-01
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Melody Baddoo Erik K Flemington
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Elizabeth C Martin Adrienne E Krebs Hope E Burks Steven Elliott Melody Baddoo Bridgette M Collins-Burow Matthew E Burow
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Genes & Cancer
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Genome-wide interrogation of longitudinal FEV1 in children with asthma
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2014-09-01
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Hae Kyung Im Nancy J Cox
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Kehua Wu Eric R Gamazon Hae Kyung Im Paul Geeleher Steven R White Julian Solway George L Clemmer Scott T Weiss Kelan G Tantisira Mark J Ratain R Stephanie Huang
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American Journal of Respiratory and Critical Care Medicine
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Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.
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2014-09-01
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Gregory E Crawford
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James A Browne Rui Yang Lingyun Song Shih-Hsing Leir Ann Harris
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Molecular Human Reproduction
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The devil in the details of RNA-seq
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2014-09-01
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Anton Kratz Piero Carninci
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Nature Biotechnology
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Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.
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2014-09-02
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Ramon Y Birnbaum Nadav Ahituv
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N Oksenberg G D E Haliburton W L Eckalbar I Oren S Nishizaki K Murphy K S Pollard
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Translational Psychiatry
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RNA-seq reveals aurora kinase-driven mTOR pathway activation in patients with sarcomatoid metastatic renal cell carcinoma.
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2014-09-02
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Tommy Tong Jeremy O Jones
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Sumanta K Pal Miaoling He Huiqing Wu Xueli Liu Clayton Lau Jin-Hui Wang Charles Warden Xiwei Wu Sabina Signoretti Toni K Choueiri Jose A Karam
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Molecular Cancer Research
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Transcriptomic dissection of the rice-Burkholderia glumae interaction.
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2014-09-03
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Teresia J Buza Peng Deng Daniel G. Peterson
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Zenaida V Magbanua Mark Arick Chuan-Yu Hsu Kurt C Showmaker Philippe Chouvarine Shien Lu
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BMC Genomics
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Transcriptional profiles of bovine in vivo pre-implantation development.
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2014-09-04
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Junhong Luo
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Zongliang Jiang Jiangwen Sun Hong Dong Xinbao Zheng Craig Obergfell Yong Tang Jinbo Bi Rachel O'Neill Yijun Ruan Jingbo Chen Xiuchun Cindy Tian
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BMC Genomics
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Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.
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2014-09-04
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Adam G Sowalsky
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Zheng Xia Liguo Wang Hao Zhao Shaoyong Chen Glenn J Bubley Steven P Balk Wei Li
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Molecular Cancer Research
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Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
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2014-09-04
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Elisa Ficarra Lasorella A Iavarone A Raul Rabadan
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Francesco Abate Sakellarios Zairis Andrea Acquaviva Chris H Wiggins Veronique Frattini Giorgio Inghirami
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BMC Systems Biology
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Caught in the act: RNA-Seq provides novel insights into mRNA degradation.
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2014-09-04
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Jörg Stülke
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Jan Gerwig
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Molecular Microbiology
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Transcriptome profiling of spinal muscular atrophy motor neurons derived from mouse embryonic stem cells
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2014-09-05
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Matthew E R Butchbach
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Miho Maeda Ashlee W Harris Brewster F Kingham Casey J Lumpkin Lynn M Opdenaker Suzanne M McCahan Wenlan Wang
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PLOS ONE
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Progressive increase in mtDNA 3243A>G heteroplasmy causes abrupt transcriptional reprogramming.
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2014-09-05
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Paweł Golik
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Martin Picard Jiangwen Zhang Saege Hancock Olga Derbeneva Ryan Golhar Sean O'Hearn Shawn Levy Prasanth Potluri Maria Lvova Antonio Davila Chun Shi Lin Juan Carlos Perin Eric F Rappaport Hakon Hakonarson Ian A Trounce Vincent Procaccio Douglas C Wallace
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Proceedings of the National Academy of Sciences of the United States of America
|
Transcriptome profiling of Vitis amurensis, an extremely cold-tolerant Chinese wild Vitis species, reveals candidate genes and events that potentially connected to cold stress.
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2014-09-05
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Weirong Xu
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Ruimin Li Ningbo Zhang Fuli Ma Yuntong Jiao Zhenping Wang
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Plant Molecular Biology
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Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes.
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2014-09-08
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Yaping Fang
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Le Zhan Hui-Xin Liu Bo Kong Yuqi He Xiao-Bo Zhong Jianwen Fang Yu-Jui Yvonne Wan Grace L Guo
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PLOS ONE
|
The sialotranscriptome of Amblyomma triste, Amblyomma parvum and Amblyomma cajennense ticks, uncovered by 454-based RNA-seq.
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2014-09-08
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Luiz Gustavo Gardinassi José M. Ribeiro Beatriz R Ferreira C L Mafra Matias Pablo Juan Szabó Sandra Regina Maruyama
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Gustavo Rocha Garcia Elen Anatriello Higo Nasser Santanna Moreira Maria Marlene Martins Isabel Kinney Ferreira de Miranda-Santos
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Parasites & Vectors
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RNA-Seq analysis of the multipartite genome of Rhizobium etli CE3 shows different replicon contributions under heat and saline shock.
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2014-09-08
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Q85275267 Santiago Castillo-Ramírez
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Maria Luisa Tabche Alfredo Mendoza-Vargas Miguel A Ramírez-Romero Guillermo Dávila
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BMC Genomics
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Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa.
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2014-09-11
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Søren Molin Rasmus L Marvig
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María Gómez-Lozano Monica V L Tulstrup
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BMC Genomics
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Transcriptome characteristics of filamentous fungi deduced using high-throughput analytical technologies.
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2014-09-11
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Lucía Ramírez
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Martha Lucía Meijueiro Francisco Santoyo Antonio G Pisabarro
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Briefings in functional genomics
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GSAASeqSP: a toolset for gene set association analysis of RNA-Seq data
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2014-09-12
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Terrence S. Furey
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Qing Xiong Sayan Mukherjee
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Scientific Reports
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Transcriptomic analysis identifies gene networks regulated by estrogen receptor α (ERα) and ERβ that control distinct effects of different botanical estrogens
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2014-09-12
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Zeynep Madak-Erdogan
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Ping Gong Jilong Li Jianlin Cheng C Michael Greenlief William Helferich John A Katzenellenbogen Benita S Katzenellenbogen
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Nuclear Receptor Signaling
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TELP, a sensitive and versatile library construction method for next-generation sequencing
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2014-09-15
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Feng Xu
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Xu Peng Jingyi Wu Reinhard Brunmeir Sun-Yee Kim Qiongyi Zhang Chunming Ding Weiping Han Wei Xie
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Nucleic Acids Research
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Onecut1 and Onecut2 redundantly regulate early retinal cell fates during development.
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2014-09-16
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Xiuqian Mu
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Darshan Sapkota Hemabindu Chintala Fuguo Wu Steven J Fliesler Zihua Hu
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Proceedings of the National Academy of Sciences of the United States of America
|
Using normalization to resolve RNA-Seq biases caused by amplification from minimal input.
|
2014-09-16
|
Christiaan V. Henkel Finn-Arne Weltzien
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Eirill Ager-Wick Trude M Haug
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Physiological Genomics
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Understanding gene regulatory mechanisms by integrating ChIP-seq and RNA-seq data: statistical solutions to biological problems.
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2014-09-17
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Claudia Angelini Valerio Costa
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|
Frontiers in cell and developmental biology
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Optimization of extraction of circulating RNAs from plasma--enabling small RNA sequencing
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2014-09-17
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Bettina Haase Benedikt Kirchner Michael W Pfaffl
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Melanie Spornraft Vladimir Benes Irmgard Riedmaier
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PLOS ONE
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SOX9 regulates multiple genes in chondrocytes, including genes encoding ECM proteins, ECM modification enzymes, receptors, and transporters.
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2014-09-17
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Yue Lu
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Chun-do Oh Shoudan Liang Yuko Mori-Akiyama Di Chen Benoit de Crombrugghe Hideyo Yasuda
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PLOS ONE
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Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis.
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2014-09-18
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Francesca Finotello
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Barbara Di Camillo
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Briefings in functional genomics
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Clonal variation in interferon response determines the outcome of oncolytic virotherapy in mouse CT26 colon carcinoma model.
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2014-09-18
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Seppo Ylä-Herttuala Minna Niittykoski
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J J Ruotsalainen M U Kaikkonen M W Martikainen C G Lemay J Cox N S De Silva A Kus T J Falls J-S Diallo F Le Boeuf J C Bell A E Hinkkanen M J Vähä-Koskela
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Gene Therapy
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Nontemplated nucleotide additions distinguish the small RNA composition in cells from exosomes.
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2014-09-18
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Bauke Ylstra Michael Hackenberg Nicoletta Zini Jaap M Middeldorp
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Danijela Koppers-Lalic Irene V Bijnsdorp Monique A J van Eijndhoven Payman Sadek Daud Sie Renee X de Menezes Thomas Würdinger Gerrit A Meijer D Michiel Pegtel
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Cell Reports
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Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli.
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2014-09-18
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Kenneth J McDowall
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Justin E Clarke Louise Kime David Romero A
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Nucleic Acids Research
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A comprehensive transcriptomic analysis of infant and adult mouse ovary.
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2014-09-20
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Songnian Hu
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Linlin Pan Wei Gong Yuanyuan Zhou Xiaonuan Li Jun Yu
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Genomics Proteomics and Bioinformatics
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Rule-based integration of RNA-Seq analyses tools for identification of novel transcripts.
|
2014-09-22
|
Avik Datta
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Harshal Inamdar Sunitha Manjari K Rajendra Joshi
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Journal of Bioinformatics and Computational Biology
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Error estimates for the analysis of differential expression from RNA-seq count data.
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2014-09-23
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Conrad J Burden
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Sumaira E Qureshi Susan R Wilson
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PeerJ
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Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
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2014-09-23
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Robert M. Waterhouse Gareth L. Maslen Daniel Lawson
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Xiaofang Jiang Ashley Peery A Brantley Hall Atashi Sharma Xiao-Guang Chen Aleksey Komissarov Michelle M Riehle Yogesh Shouche Maria V Sharakhova Nazzy Pakpour Peter Arensburger Victoria L M Davidson Karin Eiglmeier Scott Emrich Phillip George Ryan C Kennedy Shrinivasrao P Mane Chioma Oringanje Yumin Qi Robert Settlage Marta Tojo Jose M C Tubio Maria F Unger Bo Wang Kenneth D Vernick Jose M C Ribeiro Anthony A James Kristin Michel Michael A Riehle Shirley Luckhart Igor V Sharakhov Zhijian Tu
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Genome Biology
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Rare occurrence of EGFRvIII deletion in head and neck squamous cell carcinoma.
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2014-09-23
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Arun Khattri Zhixiang Zuo Everett E Vokes
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Johannes Brägelmann Michaela K Keck Mohamed El Dinali Christopher D Brown Thomas Stricker Anish Munagala Ezra E W Cohen Mark W Lingen Kevin P White Tanguy Y Seiwert
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Oral Oncology
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CO2 exposure at pressure impacts metabolism and stress responses in the model sulfate-reducing bacterium Desulfovibrio vulgaris strain Hildenborough.
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2014-09-25
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Matthew J. Marshall
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Michael J Wilkins David W Hoyt Paul A Alderson Andrew E Plymale L Meng Markillie Abby E Tucker Eric D Walter Bryan E Linggi Alice C Dohnalkova Ron C Taylor
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Frontiers in Microbiology
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Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels.
|
2014-09-26
|
Louis Bernatchez Hélène Budzinski
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Lucie Baillon Fabien Pierron Raphaël Coudret Eric Normendeau Antoine Caron Laurent Peluhet Pierre Labadie Gilles Durrieu Jérôme Sarraco Pierre Elie Patrice Couture Magalie Baudrimont
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Ecotoxicology
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Maize and millet transcription factors annotated using comparative genomic and transcriptomic data.
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2014-09-27
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Chun-Ping Yu Wen-Hsiung Li
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Jinn-Jy Lin Yao-Ming Chang Sean Chun-Chang Chen
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BMC Genomics
|
Open-access synthetic spike-in mRNA-seq data for cancer gene fusions.
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2014-09-30
|
Valérie Montel
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Waibhav D Tembe Stephanie J K Pond Christophe Legendre Han-Yu Chuang Winnie S Liang Nancy E Kim Shukmei Wong Timothy K McDaniel David W Craig John D Carpten
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BMC Genomics
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Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.
|
2014-09-30
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Tsuyoshi Tanaka
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Pui Shan Wong Michihiro Tanaka Yoshihiko Sunaga Masayoshi Tanaka Takeaki Taniguchi Tomoko Yoshino Wataru Fujibuchi Sachiyo Aburatani
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PLOS ONE
|
Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.
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2014-09-30
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Martin Kampmann
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Shuo Gu Yue Zhang Lan Jin Yong Huang Feijie Zhang Michael C Bassik Mark A Kay
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Nucleic Acids Research
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RNA-Seq gene profiling--a systematic empirical comparison.
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2014-09-30
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Nuno A. Fonseca Alvis Brazma John C Marioni
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PLOS ONE
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Global transcriptome analysis of Al-induced genes in an Al-accumulating species, common buckwheat (Fagopyrum esculentum Moench).
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2014-09-30
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Naoki Yamaji
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Kengo Yokosho Jian Feng Ma
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Plant and Cell Physiology
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A comparison of sperm RNA-seq methods
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2014-10
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Russ Hauser
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Shihong Mao Edward Sendler Robert J Goodrich Stephen A Krawetz
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Systems Biology in Reproductive Medicine
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Genome-wide discovery of drug-dependent human liver regulatory elements
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2014-10
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Marcelo Rizzatti Luizon Nadav Ahituv
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Robin P Smith Walter L Eckalbar Kari M Morrissey Thomas J Hoffmann Xuefeng Sun Stacy L Jones Shelley Force Aldred Anuradha Ramamoorthy Zeruesenay Desta Yunlong Liu Todd C Skaar Nathan D Trinklein Kathleen M Giacomini
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PLOS Genetics
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Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta.
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2014-10-01
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Reedik Mägi Andres Metspalu Ene Reimann Kristiina Rull Jaak Vilo Lili Milani Andres Salumets Triin Viltrop Maire Peters Sulev Kõks
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Tauno Metsalu Airi Tiirats Balaji Rajashekar Ganesh Acharya Purusotam Basnet Kadri Haller-Kikkatalo
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Epigenetics
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How deep is enough in single-cell RNA-seq?
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2014-10-01
|
Yanyi Huang
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Aaron M Streets
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Nature Biotechnology
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RNA-seq analysis of the rat placentation site reveals maternal obesity-associated changes in placental and offspring thyroid hormone signaling.
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2014-10-05
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Kartik Shankar
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J Saben P Kang Y Zhong K M Thakali H Gomez-Acevedo S J Borengasser A Andres T M Badger
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Placenta
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Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology.
|
2014-10-06
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Stefanie Wehner Ramakanth Madhugiri
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Gopala K Mannala Xiaoxing Qing Trinad Chakraborty Mobarak A Mraheil Torsten Hain Manja Marz
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PLOS ONE
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Role for LSM genes in the regulation of circadian rhythms.
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2014-10-06
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Lauren J. Francey
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Soledad Perez-Santángelo Estefanía Mancini Ruben Gustavo Schlaen Ariel Chernomoretz John B Hogenesch Marcelo J Yanovsky
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Proceedings of the National Academy of Sciences of the United States of America
|
Genome-wide identification and tissue-specific expression analysis of UDP-glycosyltransferases genes confirm their abundance in Cicer arietinum (Chickpea) genome
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2014-10-07
|
Vimal Rawat
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Ranu Sharma C G Suresh
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PLOS ONE
|
Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study.
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2014-10-08
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Jessica C Kissinger Jeremy Debarry Karan Uppal
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Kevin J Lee Weiwei Yin Dalia Arafat Yan Tang ViLinh Tran Monica Cabrera-Mora Stacey Lapp Alberto Moreno Esmeralda Meyer Suman Pakala Vishal Nayak Dean P Jones Mary Galinski Mark P Styczynski Greg Gibson
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Frontiers in cell and developmental biology
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Gene expression plasticity resulting from parental leaf damage in Mimulus guttatus.
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2014-10-08
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Lena Hileman
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Jack M Colicchio Patrick J Monnahan John K Kelly
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New Phytologist
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Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells.
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2014-10-13
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Eduardo Eyras Eneritz Agirre Matías Blaustein Gwendal Dujardin Federico Pelisch Juan Valcárcel Reinhard Georg Lührmann Alberto Kornblihtt
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Mariano Alló Sergey Bessonov Paola Bertucci Luciana Gómez Acuña Valeria Buggiano Nicolás Bellora Babita Singh Ezequiel Petrillo Belén Miñana Berta Pozzi Elías Bechara Dmitry E Agafonov Anabella Srebrow
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Proceedings of the National Academy of Sciences of the United States of America
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trieFinder: an efficient program for annotating Digital Gene Expression (DGE) tags.
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2014-10-13
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Matthew C LaFave Shawn M. Burgess
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Gabriel Renaud Jin Liang Tyra G Wolfsberg
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BMC Bioinformatics
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Characterization of two regulators of the TNF-α signaling pathway in Apostichopus japonicus: LPS-induced TNF-α factor and baculoviral inhibitor of apoptosis repeat-containing 2.
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2014-10-13
|
Chenghua Li
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Xiumei Zhang Pengjuan Zhang Ye Li Chunhua Jin Weiwei Zhang
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Developmental and Comparative Immunology
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RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus
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2014-10-14
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David A Fitzpatrick Gary W Jones Thomas M Keane Sean Doyle
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Grainne O'Keeffe Stephen Hammel Rebecca A Owens
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BMC Genomics
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Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.
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2014-10-15
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James S Blachly
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Karl W Kroll Nima E Mokaram Alexander R Pelletier David E Frankhouser Maximillian S Westphal Paige A Stump Cameron L Stump Ralf Bundschuh Pearlly Yan
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Cancer Informatics
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Rcount: simple and flexible RNA-Seq read counting.
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2014-10-15
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Ueli Grossniklaus
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Marc W Schmid Ueli Grossniklaus
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Bioinformatics
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Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis.
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2014-10-15
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Ross C Hardison Christapher S Morrissey Mitchell J Weiss
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Weisheng Wu Cheryl A Keller Tejaswini Mishra Maxim Pimkin Gerd A Blobel
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Genome Research
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Defining the genome-wide role of CRE1 during carbon catabolite repression in Trichoderma reesei using RNA-Seq analysis.
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2014-10-18
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Rafael Silva-Rocha
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Amanda Cristina Campos Antoniêto Lílian dos Santos Castro Gabriela Felix Persinoti Roberto Nascimento Silva
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Fungal Genetics and Biology
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Transcriptomic portrait of human Mesenchymal Stromal/Stem Cells isolated from bone marrow and placenta.
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2014-10-19
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Javier De Las Rivas Fermin Sanchez-Guijo
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Beatriz Roson-Burgo Consuelo Del Cañizo
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BMC Genomics
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Comparative proteomic and transcriptomic profile of Staphylococcus epidermidis biofilms grown in glucose-enriched medium.
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2014-10-19
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Gerald B Pier Manuel Vilanova Nuno Cerca Rui Vitorino
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Virginia Carvalhais Angela França
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Talanta
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CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors
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2014-10-21
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Nicholas Katsanis Manolis Kellis Stephen J Haggarty Serkan Erdin Michael E. Talkowski Marta Biagioli Christelle Golzio James F. Gusella
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Aarathi Sugathan Ian Blumenthal Poornima Manavalan Ashok Ragavendran Harrison Brand Diane Lucente Judith Miles Steven D Sheridan Alexei Stortchevoi
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Proceedings of the National Academy of Sciences of the United States of America
|
Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut.
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2014-10-21
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Lynn Kimsey
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Matan Shelomi W Cameron Jasper Joel Atallah Brian R Johnson
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BMC Genomics
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Gene expression associated with intersterility in Heterobasidion.
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2014-10-22
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Mårten Lind Malin Elfstrand Magnus Karlsson Jan Stenlid
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M A Van der Nest Å Olson K Dalman M Brandström-Durling B D Wingfield
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Fungal Genetics and Biology
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Gene expression patterns and sequence polymorphisms associated with mosquito resistance to Bacillus thuringiensis israelensis toxins
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2014-10-23
|
Aurélie Bonin Stéphane Reynaud Laurence Despres Jean-Philippe David Guillaume Tetreau
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Renaud Stalinski Margot Paris Vincent Navratil
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BMC Genomics
|
Expression profile of Caenorhabditis elegans mutant for the Werner syndrome gene ortholog reveals the impact of vitamin C on development to increase life span.
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2014-10-27
|
Martin J. Simard
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Alexandra Dallaire Sophie Proulx Michel Lebel
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BMC Genomics
|
Large-scale coding sequence change underlies the evolution of postdevelopmental novelty in honey bees.
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2014-10-28
|
Timothy A Linksvayer
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William Cameron Jasper Timothy A Linksvayer Joel Atallah Daniel Friedman Joanna C Chiu Brian R Johnson
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Molecular Biology and Evolution
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The multidrug resistance 1 gene Abcb1 in brain and placenta: comparative analysis in human and guinea pig
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2014-10-29
|
Gustavo Turecki Matthew Suderman
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Jane J Pappas Sophie Petropoulos Majid Iqbal Vasilis Moisiadis Stephen G Matthews Moshe Szyf
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PLOS ONE
|
In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.
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2014-10-29
|
Roberto Bonasio Michiel Vermeulen
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David B Beck Varun Narendra William J Drury Ryan Casey Pascal W T C Jansen Zuo-Fei Yuan Benjamin A Garcia
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Journal of Proteome Research
|
Transcriptional adaptations during long-term persistence of Staphylococcus aureus in the airways of a cystic fibrosis patient.
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2014-10-29
|
Boyke Bunk Barbara C. Kahl Alexander Mellmann Cathrin Spröer
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Nadine Windmüller Anika Witten Desirée Block
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International Journal of Medical Microbiology
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Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.
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2014-10-31
|
Igor V Grigoriev
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Jennifer M Hurley Arko Dasgupta Jillian M Emerson Xiaoying Zhou Carol S Ringelberg Nicole Knabe Anna M Lipzen Erika A Lindquist Christopher G Daum Kerrie W Barry Kristina M Smith James E Galagan Deborah Bell-Pedersen Michael Freitag Chao Cheng Jennifer J Loros Jay C Dunlap
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Proceedings of the National Academy of Sciences of the United States of America
|
GeneFriends: a human RNA-seq-based gene and transcript co-expression database
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2014-10-31
|
Thomas Craig
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Sipko van Dam João Pedro de Magalhães
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Nucleic Acids Research
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BCOR-CCNB3 fusions are frequent in undifferentiated sarcomas of male children.
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2014-10-31
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Stephen F Sarabia Alexander J. Lazar
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Tricia L Peters Vijetha Kumar Sumanth Polikepahad Frank Y Lin Yu Liang Wei-Lien Wang HarshaVardhan Doddapaneni Hsu Chao Donna M Muzny David A Wheeler M Fatih Okcu Sharon E Plon M John Hicks Dolores López-Terrada D Williams Parsons Angshumoy Roy
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Modern Pathology
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Widespread intron retention in mammals functionally tunes transcriptomes
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2014-11
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Ulrich Braunschweig Thomas Gonatopoulos-Pournatzis Babak Alipanahi Nuno L Barbosa-Morais Manuel Irimia
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Qun Pan Emil N Nachman Brendan Frey Benjamin J Blencowe
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Genome Research
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Several fusion genes identified by whole transcriptome sequencing in a spindle cell sarcoma with rearrangements of chromosome arm 12q and MDM2 amplification
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2014-11
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Sverre Heim Ioannis Panagopoulos
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Bodil Bjerkehagen Ludmila Gorunova Jeanne-Marie Berner Kjetil Boye
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International Journal of Oncology
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Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity.
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2014-11-01
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Carmela Gissi Graziano Pesole Matteo Chiara Anna Maria D'Erchia Ernesto Picardi Anna Atlante
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Gemma Gadaleta Giulio Pavesi Caterina De Virgilio Caterina Manzari Francesca Mastropasqua Gian Marco Prazzoli David Horner Aurelio Reyes Elisabetta Sbisà Apollonia Tullo
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Mitochondrion
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Whole transcriptome analysis for T cell receptor-affinity and IRF4-regulated clonal expansion of T cells
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2014-11-01
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Gordon K Smyth
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Wei Shi Kevin Man Stephen L Nutt Axel Kallies
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Genomics Data
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Increasing gene discovery and coverage using RNA-seq of globin RNA reduced porcine blood samples.
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2014-11-04
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Paul Stothard
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Igseo Choi Hua Bao Arun Kommadath Afshin Hosseini Xu Sun Yan Meng Graham S Plastow Christopher K Tuggle James M Reecy Eric Fritz-Waters Samuel M Abrams Joan K Lunney Le Luo Guan
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BMC Genomics
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DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
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2014-11-05
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Shin Kawano
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Ayako Suzuki Hiroyuki Wakaguri Riu Yamashita Katsuya Tsuchihara Sumio Sugano Yutaka Suzuki Kenta Nakai
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Nucleic Acids Research
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Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq
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2014-11-05
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Alex H Wagner Adam P. DeLuca Arlene Drack Budd A. Tucker Todd E. Scheetz Robert F. Mullins Edwin M. Stone
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S Scott Whitmore Shemin Zeng Terry A Braun
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Experimental Eye Research
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The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.
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2014-11-06
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Xianzhi Lin Feng Li Xinshu Xiao
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Jae Hoon Bahn Qing Zhang Tak-Ming Chan Yong Kim David T W Wong
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Clinical Chemistry
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Biochemical and molecular changes associated with heteroxylan biosynthesis in Neolamarckia cadamba (Rubiaceae) during xylogenesis
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2014-11-07
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Antony Bacic
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Xianhai Zhao Kunxi Ouyang Siming Gan Wei Zeng Lili Song Shuai Zhao Juncheng Li Monika S Doblin Xiao-Yang Chen Alan Marchant Xiaomei Deng Ai-Min Wu
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Frontiers in Plant Science
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Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state
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2014-11-07
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Christopher J. Lengner Rudolf Jaenisch
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Yarden Katz Feifei Li Nicole J Lambert Ethan S Sokol Wai-Leong Tam Albert W Cheng Edoardo M Airoldi Piyush B Gupta Zhengquan Yu Christopher B Burge
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eLife
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Nasonia vitripennis venom causes targeted gene expression changes in its fly host.
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2014-11-10
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Aisha L Siebert
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Ellen O Martinson David Wheeler Jeremy Wright Mrinalini John H Werren
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Molecular Ecology
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COXPRESdb in 2015: coexpression database for animal species by DNA-microarray and RNAseq-based expression data with multiple quality assessment systems.
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2014-11-11
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Yasunobu Okamura Shu Tadaka
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Yuichi Aoki Takeshi Obayashi Satoshi Ito Takafumi Narise Kengo Kinoshita
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Nucleic Acids Research
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Suppression of the FOXM1 transcriptional programme via novel small molecule inhibition
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2014-11-12
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Christopher Lowe Michael V Gormally Ajit Jadhav
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Thomas S Dexheimer Giovanni Marsico Deborah A Sanders Dijana Matak-Vinković Sam Michael Ganesha Rai David J Maloney Anton Simeonov Shankar Balasubramanian
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Nature Communications
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The putative Leishmania telomerase RNA (LeishTER) undergoes trans-splicing and contains a conserved template sequence
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2014-11-12
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Marcelo Santos da Silva
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Elton J R Vasconcelos Vinícius S Nunes Marcela Segatto Peter J Myler Maria Isabel N Cano
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PLOS ONE
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Investigating the molecular underpinnings underlying morphology and changes in carbon partitioning during tension wood formation in Eucalyptus.
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2014-11-12
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Shawn D Mansfield
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Eshchar Mizrachi Victoria J Maloney Janine Silberbauer Charles A Hefer Dave K Berger Alexander A Myburg
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New Phytologist
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Functional diversity of carbohydrate-active enzymes enabling a bacterium to ferment plant biomass.
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2014-11-13
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Jean Weissenbach Andrew C Tolonen Adriana Alberti
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Magali Boutard Tristan Cerisy Pierre-Yves Nogue Marcel Salanoubat
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PLOS Genetics
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RNA-seq analysis of Quercus pubescens Leaves: de novo transcriptome assembly, annotation and functional markers development.
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2014-11-13
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Alessio Fini Federico Sebastiani Cecilia Brunetti Massimiliano Tattini
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Sara Torre Silvia Fineschi Francesco Ferrini
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PLOS ONE
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De-regulation of gene expression and alternative splicing affects distinct cellular pathways in the aging hippocampus.
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2014-11-13
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Stefan Bonn Roman Stilling
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Eva Benito Michael Gertig Jonas Barth Vincenzo Capece Susanne Burkhardt Andre Fischer
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Frontiers in Cellular Neuroscience
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Transcriptomic and physiological insights into the robustness of long filamentous cells of Methanosaeta harundinacea, prevalent in upflow anaerobic sludge blanket granules.
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2014-11-14
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Songnian Hu
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Liguang Zhou Haiying Yu Guomin Ai Bo Zhang Xiuzhu Dong
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Applied and Environmental Microbiology
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Detection theory in identification of RNA-DNA sequence differences using RNA-sequencing.
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2014-11-14
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Gregory R Grant
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Jonathan M Toung Nicholas Lahens John B Hogenesch
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PLOS ONE
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Construction and assessment of individualized proteogenomic databases for large-scale analysis of nonsynonymous single nucleotide variants.
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2014-11-17
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Boris Macek
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Karsten Krug Sasa Popic Alejandro Carpy Christoph Taumer
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Proteomics
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Genome-wide analysis of the omega-3 fatty acid desaturase gene family in Gossypium
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2014-11-18
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Daniel Ilut
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Olga P Yurchenko Sunjung Park Jay J Inmon Jon C Millhollon Zach Liechty Justin T Page Matthew A Jenks Kent D Chapman Joshua A Udall Michael A Gore John M Dyer
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BMC Plant Biology
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Omics profiles used to evaluate the gene expression of Exiguobacterium antarcticum B7 during cold adaptation.
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2014-11-18
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Vivian H. Pellizari Adriano M C Pimenta
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Hivana P M B Dall'Agnol Rafael A Baraúna Pablo H C G de Sá Rommel T J Ramos Felipe Nóbrega Catarina I P Nunes Diego A das Graças Adriana R Carneiro Daniel M Santos Marta S P Carepo Vasco Azevedo Maria P C Schneider Artur Silva
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BMC Genomics
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IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.
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2014-11-18
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Pedro Miura Piero Sanfilippo Eric C Lai
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Sol Shenker
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RNA
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Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling
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2014-11-19
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Mathias Uhlén Linn Fagerberg
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Per-Henrik D Edqvist Björn M Hallström Angelika Danielsson Karolina Edlund Fredrik Pontén
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Journal of Histochemistry & Cytochemistry
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Aberrant expression of miR-218 and miR-204 in human mesial temporal lobe epilepsy and hippocampal sclerosis-convergence on axonal guidance.
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2014-11-19
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Anne Yael Nossent Kees Fluiter A Sabers Lisbeth Birk Møller Asli Silahtaroglu Rikke S Møller Niels Tommerup Eleonora Aronica
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Sanne S Kaalund Morten T Venø Mads Bak Henning Laursen Flemming Madsen Helle Broholm Bjørn Quistorff Peter Uldall Sakari Kauppinen Jørgen Kjems Zeynep Tümer
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Epilepsia
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ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts
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2014-11-20
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Alfonso Valencia Alessandro Gorohovski Milana Frenkel-Morgenstern
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Dunja Vucenovic Lorena Maestre
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Nucleic Acids Research
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DB-AT: a 2015 update to the Full-parasites database brings a multitude of new transcriptomic data for apicomplexan parasites.
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2014-11-20
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Tabea G Kischka Marcin Jąkalski Ikuo Igarashi Xuenan Xuan Yoshifumi Nishikawa
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Hiroyuki Wakaguri Shin-ichiro Kawazu Makoto Matsubayashi Fumiya Kawahara Naotoshi Tsuji Shinuo Cao Fujiko Sunaga Kazuhiro Okubo Josef Tuda Arthur E Mongan Yuki Eshita Ryuichiro Maeda Wojciech Makałowski Yutaka Suzuki Junya Yamagishi
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Nucleic Acids Research
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The TCF C-clamp DNA binding domain expands the Wnt transcriptome via alternative target recognition.
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2014-11-20
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Pierre Baldi
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Nate P Hoverter Michael D Zeller Miriam M McQuade Angela Garibaldi Anke Busch Elizabeth M Selwan Klemens J Hertel Marian L Waterman
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Nucleic Acids Research
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The mechanisms of genome-wide target gene regulation by TCF7L2 in liver cells
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2014-11-20
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Ralph A DeFronzo
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Luke Norton Xi Chen Marcel Fourcaudot Nikhil K Acharya Sami Heikkinen
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Nucleic Acids Research
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Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing.
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2014-11-24
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Sten Linnarsson Peter Lönnerberg Jens Hjerling-Leffler Patrik Ernfors
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Dmitry Usoskin Alessandro Furlan Saiful Islam Hind Abdo Daohua Lou Jesper Haeggström Olga Kharchenko Peter V Kharchenko
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Nature Neuroscience
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Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells.
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2014-11-25
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Rhodri Ceredig
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Peter Keane Cathal Seoighe
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Bioinformatics
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Identification of Salt-Stress-Induced Genes from the RNA-Seq Data of Reaumuria trigyna Using Differential-Display Reverse Transcription PCR.
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2014-11-26
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Shu-Biao Wu
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Zhen-Hua Dang Qi Qi Hui-Rong Zhang Hao-Yu Li Ying-Chun Wang
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International Journal of Genomics
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Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast
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2014-11-28
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Jürg Bähler María Rodríguez-López Francesc X. Marsellach Christopher T. Workman
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Mathieu Clément-Ziza Sandra Codlin Manos A Papadakis Susanne Reinhardt Stuart Martin Samuel Marguerat Alexander Schmidt Eunhye Lee Jürg Bähler Andreas Beyer
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Molecular Systems Biology
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The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
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2014-12
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Kerstin Lindblad-Toh Jessica Alföldi Federica Di Palma Marcia Lara Thibaut Hourlier Adam C. Siepel Christophe Dessimoz Jason Turner-Maier David Brawand Kevin Gori Bronwen Aken John F Engelhardt Yoshihiro Kawaoka
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Xinxia Peng Amie J Eisfeld Scott R Tyler Jennifer Tisoncik-Go G Lynn Law Nives Skunca Masato Hatta David J Gasper Sara M Kelly Jean Chang Matthew J Thomas Jeremy Johnson Aaron M Berlin Pamela Russell Ross Swofford Jason Turner-Maier Sarah Young Steve Searle Xingshen Sun Yaling Yi M Suresh Terrence M Tumpey Samantha M Wisely Bruce W Birren Robert E Palermo Michael G Katze
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Nature Biotechnology
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Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis
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2014-12-01
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Melinda K Duncan Shawn W Polson
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Abby L Manthey Anne M Terrell Salil A Lachke
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Genomics Data
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Transcriptome profiling of Set5 and Set1 methyltransferases: Tools for visualization of gene expression.
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2014-12-01
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Devin A King Ashby Morrison
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Glòria Mas Martín Pablo E Garcia-Nieto
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Genomics Data
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Genotet: An Interactive Web-based Visual Exploration Framework to Support Validation of Gene Regulatory Networks.
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2014-12-01
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Christoph Hafemeister
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Bowen Yu Harish Doraiswamy Xi Chen Emily Miraldi Mario Luis Arrieta-Ortiz Christoph Hafemeister Aviv Madar Richard Bonneau Cláudio T Silva
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IEEE Transactions on Visualization and Computer Graphics
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Identifying direct targets of transcription factor Rfx2 that coordinate ciliogenesis and cell movement
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2014-12-01
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Taejoon Kwon
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Mei-I Chung Rakhi Gupta Julie C Baker John B Wallingford
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Genomics Data
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Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software.
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2014-12-01
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Laura Treu Stefano Campanaro
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Alessandro Sardu
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BMC Genomics
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Early transcriptional changes in the reef-building coral Acropora aspera in response to thermal and nutrient stress.
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2014-12-02
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Nedeljka N. Rosic Chon-Kit Kenneth Chan Sophie Dove David Edwards Ove Hoegh-Guldberg
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Paulina Kaniewska Edmund Yew Siang Ling
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BMC Genomics
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An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era
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2014-12-03
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Lee Lancashire
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Zhenqiang Su Hong Fang Huixiao Hong Leming Shi Wenqian Zhang Wenwei Zhang Yanyan Zhang Zirui Dong Marina Bessarabova Xi Yang Baitang Ning Binsheng Gong Joe Meehan Joshua Xu Weigong Ge Roger Perkins Matthias Fischer Weida Tong
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Genome Biology
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Impact of the genetic background on the composition of the chicken plasma MiRNome in response to a stress
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2014-12-04
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Marie-Laure Endale Ahanda
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Tatiana Zerjal Sophie Dhorne-Pollet Andrea Rau Amanda Cooksey Elisabetta Giuffra
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PLOS ONE
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QuASAR: quantitative allele-specific analysis of reads.
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2014-12-04
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Xiaoquan Wen Francesca Luca Roger Pique-Regi
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Chris T Harvey Gregory A Moyerbrailean Gordon O Davis
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Bioinformatics
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rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data
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2014-12-05 2014-12-23
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Zhi-xiang Lu Michael D. Henry
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Shihao Shen Juw Won Park Lan Lin Ying Nian Wu Qing Zhou Yi Xing Michael D. Henry
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Proceedings of the National Academy of Sciences of the United States of America
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RNA-seq analysis of oil palm under cold stress reveals a different C-repeat binding factor (CBF) mediated gene expression pattern in Elaeis guineensis compared to other species.
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2014-12-05
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Yaodong Yang Annaliese S Mason
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Xintao Lei Yong Xiao Wei Xia Zilong Ma Ming Peng
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PLOS ONE
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SNPlice: variants that modulate Intron retention from RNA-sequencing data.
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2014-12-06
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Kamran Kowsari
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Prakriti Mudvari Mercedeh Movassagh Ali Seyfi Maria Kokkinaki Nathan J Edwards Nady Golestaneh Anelia Horvath
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Bioinformatics
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Direct and indirect consequences on gene expression of a thyroid hormone receptor alpha 1 mutation restricted to Sertoli cells.
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2014-12-08
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Gabriel Livera
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Fabrice Chatonnet Betty Fumel Sophie FouchÉCourt Frédéric Flamant
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Molecular Reproduction and Development
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Dynamic changes in the cardiac methylome during postnatal development.
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2014-12-09
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Mark Ziemann James E Hudson Enzo R Porrello Assam El-osta
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Choon Boon Sim Antony Kaspi K N Harikrishnan Jenny Ooi Ishant Khurana Lisa Chang
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FASEB Journal
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MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification.
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2014-12-10
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Edward R. Dougherty
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Jason M Knight Ivan Ivanov
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BMC Bioinformatics
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An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator.
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2014-12-10
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Thomas Bleazard Thomas Preiss Nicole Cloonan Andras Nagy Sean M. Grimmond
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Dong-Sung Lee Jong-Yeon Shin Peter D Tonge Mira C Puri Seungbok Lee Hansoo Park Won-Chul Lee Samer M I Hussein Ji-Young Yun Jihye Kim Mira Li David Wood Jennifer L Clancy Rowland Mosbergen Jae-Hyuk Yi Kap-Seok Yang Hyungtae Kim Hwanseok Rhee Christine A Wells Ian M Rogers Jeong-Sun Seo
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Nature Communications
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RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature.
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2014-12-10
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Carl J Schmidt
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Derrick J Coble Damarius Fleming Michael E Persia Chris M Ashwell Max F Rothschild Susan J Lamont
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BMC Genomics
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High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies
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2014-12-11
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Aviv Regev Nir Hacohen Raktima Raychowdhury Nir Friedman
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Michal Rabani Raktima Raychowdhury Marko Jovanovic Michael Rooney Deborah J Stumpo Andrea Pauli Alexander F Schier Perry J Blackshear Ido Amit
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Cell
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UPF2, a nonsense-mediated mRNA decay factor, is required for prepubertal Sertoli cell development and male fertility by ensuring fidelity of the transcriptome.
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2014-12-11
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Wei Yan Shuiqiao Yuan Jianqiang Bao Bo Torben Porse
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Chong Tang
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Development
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Whole exome sequencing of a single osteosarcoma case--integrative analysis with whole transcriptome RNA-seq data.
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2014-12-11
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Sulev Kõks
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Ene Reimann Xuan Dung Ho Katre Maasalu Aare Märtson
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Human genomics
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The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data
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2014-12-16
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Richard Weinshilboum Kevin J Thompson Xiaojia Tang Krishna R Kalari
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Saurabh Baheti Khader Shameer Quin Wills Nifang Niu Ilona N Holcomb Stephane C Boutet Ramesh Ramakrishnan Jennifer M Kachergus Jean-Pierre A Kocher Liewei Wang E Aubrey Thompson
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Nucleic Acids Research
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Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems.
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2014-12-16
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Julie Dickerson
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Ruolin Liu Ann E Loraine
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BMC Bioinformatics
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Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms
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2014-12-16
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Youping Deng
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Jack Y Yang A Dunker Jun S Liu Xiang Qin Hamid R Arabnia William Yang Andrzej Niemierko Zhongxue Chen Zuojie Luo Liangjiang Wang Yunlong Liu Dong Xu Weida Tong Mary Yang
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BMC Bioinformatics
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Identification of genes and pathways involved in kidney renal clear cell carcinoma
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2014-12-16
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Youping Deng
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William Yang Kenji Yoshigoe Xiang Qin Jun S Liu Jack Y Yang Andrzej Niemierko Yunlong Liu A Dunker Zhongxue Chen Liangjiang Wang Dong Xu Hamid R Arabnia Weida Tong Mary Yang
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BMC Bioinformatics
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Regulation of the KNOX-GA gene module induces heterophyllic alteration in North American lake cress.
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2014-12-16
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Hitoshi Sakakibara Seisuke Kimura
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Hokuto Nakayama Naomi Nakayama Sumer Seiki Mikiko Kojima Neelima Sinha
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The Plant Cell
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Recurrent PRDM10 gene fusions in undifferentiated pleomorphic sarcoma.
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2014-12-16
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Fredrik Mertens
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Jakob Hofvander Johnbosco Tayebwa Jenny Nilsson Linda Magnusson Otte Brosjö Olle Larsson Fredrik Vult von Steyern Nils Mandahl Christopher D M Fletcher
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Clinical Cancer Research
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Evaluation and validation of a robust single cell RNA-amplification protocol through transcriptional profiling of enriched lung cancer initiating cells.
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2014-12-17
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Luca Roz Giulia Bertolini Louise Carter Massimo Moro Crispin J. Miller Fiona Blackhall Caroline Dive
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Dominic G Rothwell Yaoyong Li Mahmood Ayub Catriona Tate Gillian Newton Yvonne Hey Suzanne Faulkner Stuart Pepper Ged Brady
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BMC Genomics
|
Identification of a candidate prognostic gene signature by transcriptome analysis of matched pre- and post-treatment prostatic biopsies from patients with advanced prostate cancer.
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2014-12-18
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Chris Ponting Andreas Heger Jacqueline Stockley Ian Sudbery Hing Y Leung Prabhakar Rajan
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Janis T Fleming Ann Hedley Gabriela Kalna David Sims Craig N Robson Rhona M McMenemin Ian D Pedley
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BMC Cancer
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Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.
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2014-12-18
|
Delphine Potier Kristofer Davie Stein Aerts Gert Hulselmans
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Marina Naval Sanchez Lotte Haagen Vân Anh Huynh-Thu Duygu Koldere Arzu Celik Pierre Geurts Valerie Christiaens
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Cell Reports
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RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis.
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2014-12-19
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Paolo Ronza Ana Paula Losada Peter W Harrison Belén G Pardo Ariadna Sitjà-Bobadilla Paulino Martínez
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Diego Robledo Roberto Bermúdez María José Redondo María Isabel Quiroga
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BMC Genomics
|
Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature.
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2014-12-19
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Maite Huarte Alejandro Athie Francesco P Marchese
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Yolanda Sánchez Victor Segura Oskar Marín-Béjar Jovanna González Luis Bujanda Shuling Guo Ander Matheu
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Nature Communications
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plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants.
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2014-12-23
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Peter F. Stadler David Langenberger
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Deblina Patra Mario Fasold Gerhard Steger Ivo Grosse
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Frontiers in Plant Science
|
A note on an exon-based strategy to identify differentially expressed genes in RNA-seq experiments.
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2014-12-26
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Laura L. Elo
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Asta Laiho
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PLOS ONE
|
RNA-seq profiling of small numbers of Drosophila neurons.
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2014-12-26
|
Michael Rosbash E Nagoshi Xiao Chen
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Katharine Abruzzi Abby Zadina
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Methods in Enzymology
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Considerations for RNA-seq analysis of circadian rhythms.
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2014-12-26
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Gregory R Grant
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Jiajia Li John B Hogenesch Michael E Hughes
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Methods in Enzymology
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Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data.
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2014-12-29
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Silvia Fustinoni Giorgio Dieci Davide Carnevali Matteo Pellegrini Anastasia Conti
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Nucleic Acids Research
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Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data.
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2014-12-31
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Ratan Chopra
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Gloria Burow Andrew Farmer Joann Mudge Charles E Simpson Mark D Burow
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PLOS ONE
|
Subgroup-elimination transcriptomics identifies signaling proteins that define subclasses of TRPV1-positive neurons and a novel paracrine circuit.
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2014-12-31
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Tim Hucho
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Jörg Isensee Carsten Wenzel Rene Buschow Robert Weissmann Andreas W Kuss
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PLOS ONE
|
Β-catenin-dependent control of positional information along the AP body axis in planarians involves a teashirt family member.
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2014-12-31
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Gilbert Weidinger
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Hanna Reuter Martin März Matthias C Vogg David Eccles Laura Grífol-Boldú Daniel Wehner Suthira Owlarn Teresa Adell Kerstin Bartscherer
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Cell Reports
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Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties
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2015
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Eshita Mutt Pritha Ghosh Oommen K Mathew
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Atul K Upadhyay Anita R Chacko A Gandhimathi K Harini Agnel P Joseph Adwait G Joshi Snehal D Karpe Swati Kaushik Nagesh Kuravadi Chandana S Lingu J Mahita Ramya Malarini Sony Malhotra Manoharan Malini Mahantesha Naika Sathyanarayanan Nitish Shaik Naseer Pasha Upadhyayula S Raghavender Anantharamanan Rajamani S Shilpa Prashant N Shingate Heikham Russiachand Singh Anshul Sukhwal Margaret S Sunitha Manojkumar Sumathi S Ramaswamy Malali Gowda Ramanathan Sowdhamini
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BMC Plant Biology
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ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelines
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2015
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Fabian Amman Florian Eggenhofer
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Michael T Wolfinger Jörg Fallmann
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F1000Research
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Ixodes scapularis and Ixodes ricinus tick cell lines respond to infection with tick-borne encephalitis virus: transcriptomic and proteomic analysis
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2015
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Margarita Villar José de la Fuente John Fazakerley Mick Watson Hana Tykalová Lesley Bell-Sakyi
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Sabine Weisheit Marina Popara Julia Loecherbach Daniel Růžek Libor Grubhoffer
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Parasites & Vectors
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Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis
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2015
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Daniel Spies Constance Ciaudo
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Computational and Structural Biotechnology Journal
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Remodeling of the Nuclear Envelope and Lamina during Bovine Preimplantation Development and Its Functional Implications
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2015
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Valeri Zakhartchenko Eckhard Wolf Volker J Schmid
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Jens Popken Alexander Graf Stefan Krebs Helmut Blum Axel Strauss Tuna Guengoer Thomas Cremer
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PLOS ONE
|
Genes expressed in grapevine leaves reveal latent wood infection by the fungal pathogen Neofusicoccum parvum
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2015
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Andrew J McElrone Grant Cramer
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Stefan Czemmel Erin R Galarneau Renaud Travadon Kendra Baumgartner
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PLOS ONE
|
Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research
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2015
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Tetsuya Sakurai
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Yoshikazu Mikami Atsushi Fukushima Takao Kuwada-Kusunose Taiichi Kitano Yusuke Komiyama Takashi Iwase Kazuo Komiyama
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PLOS ONE
|
Transcriptomic Characterization of Innate and Acquired Immune Responses in Red-Legged Partridges (Alectoris rufa): A Resource for Immunoecology and Robustness Selection
|
2015
|
Natalia Sevane
|
Javier Cañon Ignacio Gil Susana Dunner
|
PLOS ONE
|
Size of the Ovulatory Follicle Dictates Spatial Differences in the Oviductal Transcriptome in Cattle
|
2015
|
Fernando S Mesquita Luiz L Coutinho
|
Angela María Gonella-Diaza Sónia Cristina da Silva Andrade Mariana Sponchiado Guilherme Pugliesi Veerle Van Hoeck Ricardo de Francisco Strefezzi Gustavo R Gasparin Mario Binelli
|
PLOS ONE
|
Comparative Analysis of Muscle Transcriptome between Pig Genotypes Identifies Genes and Regulatory Mechanisms Associated to Growth, Fatness and Metabolism
|
2015
|
Rita Benítez Ana Isabel Rey Cristina Ovilo
|
Miriam Ayuso Almudena Fernández Yolanda Núñez Beatriz Isabel Carmen Barragán Ana Isabel Fernández Juan F Medrano Ángela Cánovas Antonio González-Bulnes Clemente López-Bote
|
PLOS ONE
|
From Insect to Man: Photorhabdus Sheds Light on the Emergence of Human Pathogenicity
|
2015
|
Helge Bode Nicholas J Tobias Michael L. Beeton Richard ffrench-Constant
|
Geraldine Mulley Paul Wilkinson Isabella Vlisidou Nina Ockendon-Powell Alexia Hapeshi Friederike I Nollmann Jean van den Elsen Nicholas R Waterfield
|
PLOS ONE
|
Decreased SMAD4 expression is associated with induction of epithelial-to-mesenchymal transition and cetuximab resistance in head and neck squamous cell carcinoma.
|
2015
|
Ruchira Ranaweera Elana J. Fertig
|
Haixia Cheng Hiroyuki Ozawa Hiromitsu Hatakeyama Jason D Howard Jimena Perez Michael Considine Manjusha Thakar Gabriel Krigsfeld Christine H Chung
|
Cancer Biology and Therapy
|
A cell-based systems biology assessment of human blood to monitor immune responses after influenza vaccination
|
2015
|
Nripesh Prasad Parimal Samir Sebastian Joyce Shawn Levy Q52577914
|
Kristen L Hoek Leigh M Howard Xinnan Niu Allison Galassie Qi Liu Tara M Allos Kyle A Floyd Yan Guo Yu Shyr Andrew J Link
|
PLOS ONE
|
Activin-A and Bmp4 levels modulate cell type specification during CHIR-induced cardiomyogenesis
|
2015
|
Karl Stamm
|
Min-Su Kim Audrey Horst Steven Blinka Donna Mahnke James Schuman Rebekah Gundry Aoy Tomita-Mitchell John Lough
|
PLOS ONE
|
mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer
|
2015
|
Manuel Nietert Gabriela Salinas-Riester Silvia von der Heyde
|
Steve Wagner Alexander Czerny Fabian Ludewig Dorit Arlt Tim Beißbarth
|
PLOS ONE
|
The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway
|
2015
|
Amber L. Mosley
|
Melanie J Fox Hongyu Gao Whitney R Smith-Kinnaman Yunlong Liu
|
PLOS Genetics
|
A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family
|
2015
|
Diane Mather Rachel A Burton Brian Steffenson Kanwarpal S Dhugga Robbie Waugh
|
Kelly Houston Beata Sznajder Antoni J Rafalski Jillian Taylor Geoffrey B Fincher
|
PLOS ONE
|
Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems
|
2015
|
Abdimajid Osman Patrick Provost Adam Ameur
|
Walter E Hitzler
|
PLOS ONE
|
Asparagus Spears as a Model to Study Heteroxylan Biosynthesis during Secondary Wall Development
|
2015
|
Kelsey L. Picard Wei Zeng Edwin R. Lampugnani Antony Bacic
|
Lili Song Aimin Wu Roshan Cheetamun Cherie Beahan Andrew Cassin Andrew Lonsdale Monika S Doblin
|
PLOS ONE
|
Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax
|
2015
|
Matthew Berriman Mandy Sanders Sophie Goyard Andrew P Jackson Dong Xia Paola Minoprio
|
Bernardo J Foth Jonathan M Wastling
|
PLOS Neglected Tropical Diseases
|
Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages
|
2015
|
John Monahan
|
Anupama Reddy Joseph D Growney Nick S Wilson Caroline M Emery Jennifer A Johnson Rebecca Ward Kelli A Monaco Joshua Korn Mark D Stump Felipa A Mapa Christopher J Wilson Janine Steiger Jebediah Ledell Richard J Rickles Vic E Myer Seth A Ettenberg Robert Schlegel William R Sellers Heather A Huet Joseph Lehár
|
PLOS ONE
|
RNA-Seq Analysis of Human Trigeminal and Dorsal Root Ganglia with a Focus on Chemoreceptors
|
2015
|
Janine Altmüller Hanns Hatt Günter Gisselmann
|
Caroline Flegel Nicole Schöbel Christian Becker Andrea Tannapfel Günter Gisselmann
|
PLOS ONE
|
Whole Body Melanoma Transcriptome Response in Medaka
|
2015
|
Manfred Schartl
|
Yingjia Shen Katja Maurus Ron Walter Chad Tomlinson Richard K Wilson John Postlethwait Wesley C Warren
|
PLOS ONE
|
OperomeDB: A Database of Condition-Specific Transcription Units in Prokaryotic Genomes
|
2015
|
Sarath Chandra Janga
|
Kashish Chetal Sarath Chandra Janga
|
BioMed Research International
|
Genome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009
|
2015
|
Annick Wilmotte
|
Magdalena Calusinska Christopher Hamilton Pieter Monsieurs Gregory Mathy Natalie Leys Fabrice Franck Bernard Joris Philippe Thonart Serge Hiligsmann
|
Biotechnology for Biofuels
|
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data
|
2015
|
Detlef Weigel Korbinian Schneeberger Vimal Rawat
|
Ahmed Abdelsamad Björn Pietzenuk Danelle K Seymour Daniel Koenig Ales Pecinka
|
PLOS ONE
|
Using RNA-Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean
|
2015
|
Hon-Ming Lam
|
Aldrin Kay-Yuen Yim Johanna Wing-Hang Wong Yee-Shan Ku Hao Qin Ting-Fung Chan
|
PLOS ONE
|
274: Next generation sequencing (RNA-seq) of the human decidual and placental villous transcriptomes in intra-amniotic infection (IAI) induced preterm birth (PTB)
|
2015-01
|
Antonis Rokas
|
William Ackerman Irina Buhimschi Haley Eidem David Rinker Kara Rood Guomao Zhao Taryn Summerfield Mark Landon Catalin Buhimschi
|
American Journal of Obstetrics and Gynecology
|
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli
|
2015-01-01
|
Thorsten Bischler Alexander Herbig Cynthia Sharma Konrad Förstner
|
Maureen K Thomason Sara K Eisenbart Aixia Zhang Kay Nieselt Gisela Storz
|
Journal of Bacteriology
|
A pan-cancer analysis of prognostic genes.
|
2015-01-01
|
Stefan Bekiranov Wei-Min Chen Anindya Dutta
|
Jordan Anaya Brian Reon Stefan Bekiranov
|
PeerJ
|
The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells
|
2015-01-01
|
Anthony T. Papenfuss Chen-Fang Weng Louise Y. Cheng
|
Francesca Froldi Milan Szuperak Wei Shi
|
Genes & Development
|
Quantifying entire transcriptomes by aligned RNA-seq data.
|
2015-01-01
|
Raffaele A. Calogero
|
Francesca Zolezzi
|
Methods in Molecular Biology
|
Exploring the RNA editing potential of RNA-Seq data by ExpEdit.
|
2015-01-01
|
Graziano Pesole Anna Maria D'Erchia Ernesto Picardi
|
Mattia D'Antonio Tiziana Castrignanò
|
Methods in Molecular Biology
|
Integrated whole transcriptome and DNA methylation analysis identifies gene networks specific to late-onset Alzheimer's disease.
|
2015-01-01
|
Margaret A. Pericak-Vance
|
Crystal E Humphries Martin A Kohli Lubov Nathanson Patrice Whitehead Gary Beecham Eden Martin Deborah C Mash John Gilbert
|
Journal of Alzheimer's Disease
|
Translating Ribosome Affinity Purification (TRAP) followed by RNA sequencing technology (TRAP-SEQ) for quantitative assessment of plant translatomes.
|
2015-01-01
|
María Eugenia Zanetti
|
Mauricio A Reynoso Piyada Juntawong Marcos Lancia Flavio A Blanco Julia Bailey-Serres
|
Methods in Molecular Biology
|
Nuclear transcriptome profiling of induced pluripotent stem cells and embryonic stem cells identify non-coding loci resistant to reprogramming
|
2015-01-01
|
Piero Carninci
|
Alexandre Fort Daisuke Yamada Kosuke Hashimoto Haruhiko Koseki
|
Cell Cycle
|
Plasticity of DNA methylation in a nerve injury model of pain.
|
2015-01-01
|
Julie M. Cunningham
|
Meike Gölzenleuchter Rahul Kanwar Manal Zaibak Fadi Al Saiegh Theresa Hartung Jana Klukas Regenia L Smalley Maria E Figueroa Gary P Schroth Terry M Therneau Michaela S Banck Andreas S Beutler
|
Epigenetics
|
Interferon regulatory factor 1 and histone H4 acetylation in systemic lupus erythematosus.
|
2015-01-01
|
Michelle A. Petri
|
Yiu Tak Leung Lihua Shi Kelly Maurer Li Song Zhe Zhang Kathleen E Sullivan
|
Epigenetics
|
Identification of secretaglobin Scgb2a1 as a target for developmental reprogramming by BPA in the rat prostate
|
2015-01-01
|
Kurunthachalam Kannan
|
Rebecca Lee Yean Wong Quan Wang Lindsey S Treviño Maarten C Bosland Jing Chen Mario Medvedovic Gail S Prins Shuk-Mei Ho Cheryl Lyn Walker
|
Epigenetics
|
Characterization of the Olfactory Receptors Expressed in Human Spermatozoa
|
2015-01-01
|
Hanns Hatt Günter Gisselmann
|
Caroline Flegel Felix Vogel Adrian Hofreuter Benjamin S P Schreiner Sandra Osthold Sophie Veitinger Christian Becker Norbert H Brockmeyer Michael Muschol Gunther Wennemuth Janine Altmüller Günter Gisselmann
|
Frontiers in molecular biosciences
|
MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.
|
2015-01-01
|
Kenneth Bryan Daniel G. Bradley David J. Lynn David E. MacHugh Stephen V. Gordon
|
Peter Vegh David A Magee Nicolas C Nalpas Matthew S McCabe John A Browne Kevin M Conlon
|
Tuberculosis
|
Noncoding regions of C. elegans mRNA undergo selective adenosine to inosine deamination and contain a small number of editing sites per transcript.
|
2015-01-01
|
Michael C Washburn
|
Emily C Wheeler Francois Major Douglas B Rusch Heather A Hundley
|
RNA Biology
|
Investigating CRISPR RNA Biogenesis and Function Using RNA-seq.
|
2015-01-01
|
Jörg Vogel Cynthia Sharma Gaurav Dugar Nadja Heidrich
|
|
Methods in Molecular Biology
|
Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
|
2015-01-01
|
Oliver Stegle Cyriac Kandoth Nikolaus Schultz
|
Kjong-Van Lehmann André Kahles William Lee Gunnar Rätsch
|
Pacific Symposium on Biocomputing
|
Analysis of alternative splicing events in custom gene datasets by AStalavista.
|
2015-01-01
|
Sylvain Foissac Michael Sammeth
|
|
Methods in Molecular Biology
|
Computer-assisted annotation of small RNA transcriptomes.
|
2015-01-01
|
Grant W Hennig Wei Yan
|
Nicole Ortogero Dickson Luong
|
Methods in Molecular Biology
|
First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics.
|
2015-01-02
|
Bisong Yue
|
Lianming Du Wujiao Li Zhenxin Fan Fujun Shen Mingyu Yang Zili Wang Zuoyi Jian Rong Hou Xiuyue Zhang
|
Molecular Ecology Resources
|
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data.
|
2015-01-05
|
Åslaug Helland Lynnette Fernandez-Cuesta Joachim H Clement Martin Peifer Stefan Haas Gavin Wright Peter Nürnberg Steinar Solberg Martin Vingron Elisabeth Brambilla
|
Ruping Sun Roopika Menon Julie George Susanne Lorenz Leonardo A Meza-Zepeda Dennis Plenker Johannes M Heuckmann Frauke Leenders Thomas Zander Ilona Dahmen Mirjam Koker Jakob Schöttle Roland T Ullrich Christian Becker Henrik Seidel Diana Böhm Friederike Göke Sascha Ansén Prudence A Russell Zoe Wainer Benjamin Solomon Iver Petersen Jörg Sänger Odd-Terje Brustugun Marius Lund-Iversen Reinhard Buettner Jürgen Wolf Sven Perner Roman K Thomas
|
Genome Biology
|
Characterization of human cyclin-dependent kinase 12 (CDK12) and CDK13 complexes in C-terminal domain phosphorylation, gene transcription, and RNA processing
|
2015-01-05
|
Laurence Florens Michael P. Washburn
|
Kaiwei Liang Xin Gao Joshua M Gilmore Edwin Smith Ali Shilatifard
|
Molecular and Cellular Biology
|
rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples.
|
2015-01-05
|
Wolfgang Kaisers
|
Wolfgang Kaisers Heiner Schaal Holger Schwender
|
Bioinformatics
|
iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
|
2015-01-06
|
Susanne Mandrup Bjørk Ditlev Larsen Søren Fisker Schmidt
|
Jesper Grud Skat Madsen Anne Loft Ronni Nielsen
|
Nucleic Acids Research
|
Astrovirus VA1/HMO-C: an increasingly recognized neurotropic pathogen in immunocompromised patients
|
2015-01-07
|
Vincent Plagnol Divya Shah Sofia Morfopoulou Julianne R Brown Judith Breuer Waseem Qasim
|
Jonathan Hubb Warren A Emmett Winnie Ip Tony Brooks Simon M L Paine Glenn Anderson Alex Virasami C Y William Tong Duncan A Clark Thomas S Jacques Mike Hubank
|
Clinical Infectious Diseases
|
RNA-Rocket: an RNA-Seq analysis resource for infectious disease research
|
2015-01-07
|
Andrew Warren Omar S. Harb Daniel Lawson Leslie Birgit Vosshall Michael McClelland Cristina Aurrecoechea
|
Brian Brunk Prerak Desai Scott Emrich Gloria I Giraldo-Calderón Deborah Hix Dustin Machi Chunhong Mao Eric Nordberg Maulik Shukla Alice R Wattam Rebecca Will Hyun Seung Yoo Bruno Sobral
|
Bioinformatics
|
Systems biology with high-throughput sequencing reveals genetic mechanisms underlying the metabolic syndrome in the Lyon hypertensive rat.
|
2015-01-08
|
Man Chun John Ma Anne E Kwitek
|
Jinkai Wang Amanda K Mennie Janette M Pettus Yang Xu Lan Lin Matthew G Traxler Jessica Jakoubek Santosh S Atanur Timothy J Aitman Yi Xing
|
Circulation: Cardiovascular Genetics
|
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.
|
2015-01-12
|
Xiaoliang Sunney Xie
|
Huiyi Chen Katsuyuki Shiroguchi Hao Ge
|
Molecular Systems Biology
|
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq.
|
2015-01-13
|
Oliver Kurzai Reinhard Guthke
|
Jörg Linde Seána Duggan Michael Weber Fabian Horn Patricia Sieber Daniela Hellwig Konstantin Riege Manja Marz Ronny Martin
|
Nucleic Acids Research
|
Deep sequencing of the murine olfactory receptor neuron transcriptome.
|
2015-01-15
|
Hanns Hatt Günter Gisselmann Christian H. Wetzel Eva M. Neuhaus
|
Ninthujah Kanageswaran Marilen Demond Maximilian Nagel Benjamin S P Schreiner Sabrina Baumgart Paul Scholz Janine Altmüller Christian Becker Julia F Doerner Heike Conrad Sonja Oberland Günter Gisselmann
|
PLOS ONE
|
Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.
|
2015-01-15
|
Kemal Avican Mikael Huss
|
Anna Fahlgren Ann Kathrin Heroven Michael Beckstette Petra Dersch Maria Fällman
|
PLOS Pathogens
|
Blocking miRNA Biogenesis in Adult Forebrain Neurons Enhances Seizure Susceptibility, Fear Memory, and Food Intake by Increasing Neuronal Responsiveness.
|
2015-01-16
|
Angel Barco
|
Anna Fiorenza Jose P Lopez-Atalaya Victor Rovira Marilyn Scandaglia Emilio Geijo-Barrientos
|
Cerebral Cortex
|
Partial dosage compensation in Strepsiptera, a sister group of beetles.
|
2015-01-18
|
Doris Bachtrog
|
Shivani Mahajan
|
Genome Biology and Evolution
|
Integrated modeling of protein-coding genes in the Manduca sexta genome using RNA-Seq data from the biochemical model insect.
|
2015-01-20
|
Xiaolong Cao Haobo Jiang
|
|
Insect Biochemistry and Molecular Biology
|
Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.
|
2015-01-20
|
Marco Mangone
|
Stephen M Blazie Cody Babb Henry Wilky Alan Rawls Jin G Park
|
BMC Biology
|
Combining RNA and protein profiling data with network interactions identifies genes associated with spermatogenesis in mouse and human.
|
2015-01-21
|
Bernard Jégou Fatima Smagulova Soazik P Jamin Fabrice G Petit Emmanuelle Becker Frédéric Chalmel Michael Primig
|
Christine Kervarrec Chunxiang Hao Bernard Jégou
|
Biology of Reproduction
|
Claudin multigene family in channel catfish and their expression profiles in response to bacterial infection and hypoxia as revealed by meta-analysis of RNA-Seq datasets.
|
2015-01-21
|
Luyang Sun Shikai Liu
|
Lisui Bao Yun Li Jianbin Feng Zhanjiang Liu
|
Comparative Biochemistry and Physiology. Part D: Genomics and Proteomics
|
Quantitative visualization of alternative exon expression from RNA-seq data.
|
2015-01-22
|
Schraga Schwartz Jill P. Mesirov Helga Thorvaldsdóttir
|
Yarden Katz Eric T Wang Jacob Silterra Bang Wong Helga Thorvaldsdóttir James T Robinson Edoardo M Airoldi Christopher B Burge
|
Bioinformatics
|
RNA-Seq reveals a role for NFAT-signaling in human retinal microvascular endothelial cells treated with TNFα.
|
2015-01-24
|
Colin A Bretz
|
Sara R Savage John S Penn
|
PLOS ONE
|
Blocking yersiniabactin import attenuates extraintestinal pathogenic Escherichia coli in cystitis and pyelonephritis and represents a novel target to prevent urinary tract infection.
|
2015-01-26
|
Harry L T Mobley
|
Ariel R Brumbaugh Sara N Smith Sargurunathan Subashchandrabose Stephanie D Himpsl Tracy H Hazen David A Rasko
|
Infection and Immunity
|
The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4.
|
2015-01-26
|
Sergio Abrignani Massimiliano Pagani
|
Valeria Ranzani Grazisa Rossetti Ilaria Panzeri Alberto Arrigoni Raoul Jp Bonnal Serena Curti Paola Gruarin Elena Provasi Elisa Sugliano Maurizio Marconi Raffaele De Francesco Jens Geginat Beatrice Bodega
|
Nature Immunology
|
Next-Generation Sequencing Reveals Low-Dose Effects of Cationic Dendrimers in Primary Human Bronchial Epithelial Cells
|
2015-01-27
|
Pekka Kohonen Hanna L. Karlsson Bengt Fadeel Neus Feliu Yuning Zhang
|
Neus Feliu Jie Ji Lena Palmberg Andreas Nyström
|
ACS Nano
|
Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
|
2015-01-27
|
Stephanie McKay
|
Benjamin B Green David E Kerr
|
BMC Genomics
|
Computational and analytical challenges in single-cell transcriptomics.
|
2015-01-28
|
Sarah Teichmann John C Marioni Oliver Stegle
|
|
Nature Reviews Genetics
|
The transcriptional stress response of Candida albicans to weak organic acids.
|
2015-01-29
|
Norman Pavelka Michael Poidinger
|
Fabien Cottier Alrina Shin Min Tan Jinmiao Chen Josephine Lum Francesca Zolezzi
|
G3
|
The avian transcriptome response to malaria infection
|
2015-01-29
|
Olof Hellgren Gediminas Valkiūnas Elin Videvall Vaidas Palinauskas
|
Charlie K Cornwallis
|
Molecular Biology and Evolution
|
Saccharomyces cerevisiae transcriptional reprograming due to bacterial contamination during industrial scale bioethanol production.
|
2015-01-30
|
Melline F Noronha Luciana S Mofatto Juan Lucas Argueso Piotr A Mieczkowski
|
Osmar V Carvalho-Netto Marcelo F Carazzolle Paulo J P L Teixeira Luige A L Calderón Gonçalo A G Pereira
|
Microbial Cell Factories
|
RNA-seq SSRs and small RNA-seq SSRs: new approaches in cancer biomarker discovery.
|
2015-01-30
|
Arghavan Alisoltani
|
Arghavan Alisoltani Hossein Fallahi Behrouz Shiran Anousheh Alisoltani Esmaeil Ebrahimie
|
Gene
|
RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance.
|
2015-01-31
|
Jérôme Gouzy
|
Arnaud Duhoux Sébastien Carrère Ludovic Bonin Christophe Délye
|
Plant Molecular Biology
|
Sensitive and highly resolved identification of RNA-protein interaction sites in PAR-CLIP data.
|
2015-02-01
|
Federico Comoglio
|
Cem Sievers Renato Paro
|
BMC Bioinformatics
|
Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle.
|
2015-02-01
|
Trudee Fair Niamh Forde John R. Roche
|
P A McGettigan J A Browne S D Carrington M A Crowe B J Loftus A Lohan P Lonergan K Pluta S Mamo A Murphy S W Walsh C J Creevey B Earley S Keady D A Kenny D Matthews M McCabe D Morris A O'Loughlin S Waters M G Diskin A C O Evans
|
Reproduction, Fertility and Development
|
The role of TP53 in miRNA loading onto AGO2 and in remodelling the miRNA-mRNA interaction network.
|
2015-02-01
|
Teresa Colombo Valerio Fulci
|
Jonathan Krell Justin Stebbing Adam Enver Frampton Claudia Carissimi Victoria Harding Alexander De Giorgio Giuseppe Macino Leandro Castellano
|
The Lancet
|
Whole-epigenome analysis in multiple myeloma reveals DNA hypermethylation of B cell-specific enhancers.
|
2015-02-02
|
Laura Clarke Paul Flicek Xabier Agirre Michael I Robson Marien Pascual Avik Datta Renée Beekman David Richardson Giancarlo Castellano Juan R Rodriguez-Madoz José I Martín-Subero Norma C. Gutiérrez José M García-Verdugo Elias Campo Simon Heath Felipe Prosper Eric C Schirmer Reiner Siebert
|
Marta Kulis Victor Segura Anke Bergmann Anna Esteve Angelika Merkel Emanuele Raineri Lidia Agueda Julie Blanc Nuria Russiñol Ana C Queirós Edurne San José-Enériz Fang Fang Elisabeth Guruceaga Joost H A Martens Marta Gut Maria J Calasanz Jesús F San Miguel Ari Melnick Hendrik G Stunnenberg Ivo G Gut
|
Genome Research
|
Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling.
|
2015-02-02
|
Jens Nielsen Mathias Uhlén
|
Pouyan Ghaffari Adil Mardinoglu Anna Asplund Saeed Shoaie Caroline Kampf
|
Scientific Reports
|
The genomic landscape of phaeochromocytoma.
|
2015-02-02
|
Stephen B. Fox Richard W. Tothill Rodney J. Hicks Aidan Flynn Jason Li Grant McArthur Roderick J Clifton-Bligh
|
Diana Benn Bruce Robinson Alison H Trainer Paul James Annette Hogg Kelly Waldeck Joshy George Anthony J Gill
|
The Journal of Pathology
|
Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.
|
2015-02-04
|
Karsten Hokamp David E. MacHugh Kate Killick
|
Maura E Casey Kieran G Meade Nicolas C Nalpas Maria Taraktsoglou John A Browne Stephen D E Park Eamonn Gormley David A Magee
|
Frontiers in Immunology
|
Comparison of larval and adult Drosophila astrocytes reveals stage-specific gene expression profiles
|
2015-02-04
|
Yanmei Huang
|
Fanny S Ng F Rob Jackson
|
G3
|
Integrating transcriptomics and proteomics to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism in gastric cancer cells.
|
2015-02-05
|
Chia-Lang Hsu Hsuan-Cheng Huang Hsueh-Fen Juan
|
Li-Ling Lin Chieh-Ren Hsia
|
BMC Genomics
|
Computational prediction of molecular pathogen-host interactions based on dual transcriptome data.
|
2015-02-06
|
Reinhard Guthke
|
Sylvie Schulze Sebastian G Henkel Dominik Driesch Jörg Linde
|
Frontiers in Microbiology
|
Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease
|
2015-02-07
|
Anand Swaroop Rinki Ratnapriya
|
Hyun-Jin Yang Tiziana Cogliati Jung-Woong Kim
|
Progress in Retinal and Eye Research
|
Regulatory small RNAs from the 3' regions of bacterial mRNAs.
|
2015-02-09
|
Jörg Vogel Masatoshi Miyakoshi Yanjie Chao
|
|
Current Opinion in Microbiology
|
Deep transcriptome sequencing provides new insights into the structural and functional organization of the wheat genome.
|
2015-02-10
|
Catherine Feuillet Etienne Paux Frédéric Choulet Adriana Alberti
|
Lise Pingault Natasha Glover Patrick Wincker
|
Genome Biology
|
Rapid changes in gene expression direct rapid shifts in intestinal form and function in the Burmese python after feeding.
|
2015-02-10
|
David D. Pollock
|
Audra L Andrew Daren C Card Robert P Ruggiero Drew R Schield Richard H Adams Stephen M Secor Todd A Castoe
|
Physiological Genomics
|
Bridger: a new framework for de novo transcriptome assembly using RNA-seq data.
|
2015-02-11
|
Cody Ashby
|
Zheng Chang Guojun Li Juntao Liu Yu Zhang Deli Liu Carole L Cramer Xiuzhen Huang
|
Genome Biology
|
Distinct Transcriptomic Features are Associated with Transitional and Mature B-Cell Populations in the Mouse Spleen.
|
2015-02-11
|
Daria Salyakina Jean-Christophe Renauld
|
Eden Kleiman Magali De Heusch Kristen L Hoek Joan M Llanes Iris Castro Jacqueline A Wright Emily S Clark Derek M Dykxhoorn Enrico Capobianco Akiko Takeda Wasif N Khan
|
Frontiers in Immunology
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Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues.
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2015-02-12
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Je Hyuk Lee George M. Church
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Evan R Daugharthy Jonathan Scheiman Reza Kalhor Thomas C Ferrante Richard Terry Brian M Turczyk Joyce L Yang Ho Suk Lee John Aach Kun Zhang
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Nature Protocols
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The herbicide linuron inhibits cholesterol biosynthesis and induces cellular stress responses in brown trout.
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2015-02-12
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Eduarda M. Santos Tamsyn M Uren Webster
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Mandy H Perry
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Environmental Science & Technology
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The evolutionary panorama of organ-specifically expressed or repressed orthologous genes in nine vertebrate species.
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2015-02-13
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Zhan Zhou
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Libing Shen Gangbiao Liu Yangyun Zou Zhixi Su Xun Gu
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PLOS ONE
|
Asexual expansion of Toxoplasma gondii merozoites is distinct from tachyzoites and entails expression of non-overlapping gene families to attach, invade, and replicate within feline enterocytes.
|
2015-02-13
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Peter Deplazes
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Adrian B Hehl Walter U Basso Christoph Lippuner Chandra Ramakrishnan Michal Okoniewski Robert A Walker Michael E Grigg Nicholas C Smith
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BMC Genomics
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SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.
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2015-02-14
|
Gaurav Sablok
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Xiaoyong Sun Fenghua Zuo Yuanbin Ru Jiqiang Guo Xiaoyan Yan
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Computer Methods and Programs in Biomedicine
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Transcriptome analysis of thermophilic methylotrophic Bacillus methanolicus MGA3 using RNA-sequencing provides detailed insights into its previously uncharted transcriptional landscape
|
2015-02-14
|
Jörn Kalinowski
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Marta Irla Armin Neshat Trygve Brautaset Christian Rückert Volker F Wendisch
|
BMC Genomics
|
Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli.
|
2015-02-14
|
Vânia Pobre Cecília Maria Arraiano
|
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BMC Genomics
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Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation
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2015-02-17
|
Cynthia Sharma Kai Papenfort Bonnie Bassler Konrad Förstner
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Jian-Ping Cong
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Proceedings of the National Academy of Sciences of the United States of America
|
DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.
|
2015-02-17
|
Ann-Christine Syvänen Christofer L. Bäcklin Ann Nordgren Jonas Abrahamsson Trond Flægstad Kjeld Schmiegelow Rolf Larsson
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Jessica Nordlund Vasilios Zachariadis Lucia Cavelier Johan Dahlberg Ingegerd Öfverholm Gisela Barbany Elin Övernäs Mats M Heyman Ólafur G Jónsson Jukka Kanerva Josefine Palle Mats G Gustafsson Gudmar Lönnerholm Erik Forestier
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Clinical epigenetics
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Aging-like changes in the transcriptome of irradiated microglia
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2015-02-17
|
Matthew D Li Steven A. Sloan
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Terry C Burns Sunny Kumar Alexander A Morgan Theo D Palmer
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Glia
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Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis).
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2015-02-17
|
Barry J Pogson
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Junxiang Zhang Hui Yuan Zhangjun Fei Lugang Zhang Li Li
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Planta
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StringTie enables improved reconstruction of a transcriptome from RNA-seq reads
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2015-02-18
|
Steven Salzberg Mihaela Pertea
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Geo M Pertea Corina M Antonescu Tsung-Cheng Chang Joshua T Mendell
|
Nature Biotechnology
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RNA Seq analysis of the Eimeria tenella gametocyte transcriptome reveals clues about the molecular basis for sexual reproduction and oocyst biogenesis
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2015-02-18
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Peter Deplazes
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Robert A Walker Philippa A Sharman Catherine M Miller Christoph Lippuner Michal Okoniewski Ramon M Eichenberger Chandra Ramakrishnan Fabien Brossier Adrian B Hehl Nicholas C Smith
|
BMC Genomics
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Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
|
2015-02-19
|
Sten Linnarsson Peter Lönnerberg Jens Hjerling-Leffler Gioele La Manno Hermany Munguba Charlotte Rolny Gonçalo Castelo-Branco Christer Betsholtz
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Amit Zeisel Ana B Muñoz-Manchado Simone Codeluppi Anna Juréus Sueli Marques Liqun He
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Science
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Flexible expressed region analysis for RNA-seq with derfinder
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2015-02-19
|
Michael I Love Leonardo Collado-Torres Jeffrey T. Leek Ben Langmead Abhinav Nellore
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Alyssa C Frazee Christopher Wilks Rafael A Irizarry Andrew E Jaffe
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The lncRNA DRAIC/PCAT29 Locus Constitutes a Tumor-Suppressive Nexus.
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2015-02-20
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Anindya Dutta Jordan Anaya
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Kouhei Sakurai Brian J Reon
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Molecular Cancer Research
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Inferring bona fide transfrags in RNA-Seq derived-transcriptome assemblies of non-model organisms.
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2015-02-21
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Peter van Heusden Uljana Hesse Alan Christoffels
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Stanley Kimbung Mbandi
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BMC Bioinformatics
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A phylogenetic backbone for Bivalvia: an RNA-seq approach
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2015-02-22
|
Casey W. Dunn Sónia C S Andrade Rüdiger Bieler Gonzalo Giribet John D. Taylor
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Vanessa L González Timothy M Collins Paula M Mikkelsen
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Proceedings of the Royal Society B
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A transcriptome derived female-specific marker from the invasive Western mosquitofish (Gambusia affinis).
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2015-02-23
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Manfred Schartl Shinichi Nakagawa
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Dunja K Lamatsch Sofia Adolfsson Alistair M Senior Guntram Christiansen Maria Pichler Yuichi Ozaki Linnea Smeds
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PLOS ONE
|
Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.
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2015-02-23
|
John Mattick Peter M Clark Aristeidis G Telonis Yohei Kirino Michelle Lally Karen E Knudsen Isidore Rigoutsos George A. Calin Michael J. Keating
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Eric Londin Phillipe Loher Kevin Quann Yi Jing Eleftheria Hatzimichael Shozo Honda Bharat Ramratnam Clay E S Comstock Leonard Gomella George L Spaeth Lisa Hark L Jay Katz Agnieszka Witkiewicz Abdolmohamad Rostami Sergio A Jimenez Michael A Hollingsworth Jen Jen Yeh Chad A Shaw Steven E McKenzie Paul Bray Peter T Nelson Simona Zupo Katrien Van Roosbroeck Charles Yeo Masaya Jimbo Joseph Cozzitorto Jonathan R Brody Kathleen Delgrosso Paolo Fortina
|
Proceedings of the National Academy of Sciences of the United States of America
|
Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome.
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2015-02-23
|
Vivek Krishnakumar
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Xingtan Zhang Benjamin D Rosen Haibao Tang Christopher D Town
|
PLOS ONE
|
RNA-seq analysis of the response of the halophyte, Mesembryanthemum crystallinum (ice plant) to high salinity.
|
2015-02-23
|
Hironaka Tsukagoshi Sumie Ishiguro
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Takamasa Suzuki Kouki Nishikawa Sakae Agarie Tetsuya Higashiyama
|
PLOS ONE
|
Overlapping and unique signatures in the proteomic and transcriptomic responses of the nematode Caenorhabditis elegans toward pathogenic Bacillus thuringiensis.
|
2015-02-23
|
Andreas Tholey
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Wentao Yang Katja Dierking Daniela Esser Matthias Leippe Philip Rosenstiel Hinrich Schulenburg
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Developmental and Comparative Immunology
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Guidance for RNA-seq co-expression network construction and analysis: safety in numbers.
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2015-02-24
|
Jesse Gillis
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S Ballouz W Verleyen
|
Bioinformatics
|
RNAseq reveals weed-induced PIF3-like as a candidate target to manipulate weed stress response in soybean.
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2015-02-25
|
Brian Scheffler Ronald Pierik
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David P Horvath Stephanie A Hansen Janet P Moriles-Miller Changhui Yan David E Clay Sharon A Clay
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New Phytologist
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RNA-Seq: Improving Our Understanding of Retinal Biology and Disease.
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2015-02-26
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Eric A Pierce
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Michael H Farkas Elizabeth D Au Maria E Sousa
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Cold Spring Harbor Perspectives in Medicine
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Exon Skipping Is Correlated with Exon Circularization.
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2015-02-26
|
Steven Kelly Argyris Papantonis
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Chris Greenman Peter R Cook
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Journal of Molecular Biology
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The landscape of long noncoding RNAs in the human transcriptome
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2015-03
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John R. Prensner
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Matthew K Iyer Yashar S Niknafs Rohit Malik Udit Singhal Anirban Sahu Yasuyuki Hosono Terrence R Barrette Joseph R Evans Shuang Zhao Anton Poliakov Xuhong Cao Saravana M Dhanasekaran Yi-Mi Wu Dan R Robinson David G Beer Felix Y Feng Hariharan K Iyer Arul M Chinnaiyan
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Nature Genetics
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Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines
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2015-03
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James Taylor
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Jeremy Goecks Bassel F El-Rayes Shishir K Maithel H Jean Khoury Michael R Rossi
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Cancer Medicine
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Simultaneous generation of many RNA-seq libraries in a single reaction
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2015-03-02
|
Georgia Giannoukos Jenny Chen Alper Kucukural
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Alexander A Shishkin Dawn Ciulla Michele Busby Christine Surka Roby P Bhattacharyya Robert F Rudy Milesh M Patel Nathaniel Novod Deborah T Hung Andreas Gnirke Manuel Garber Mitchell Guttman Jonathan Livny
|
Nature Methods
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Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators.
|
2015-03-03
|
Steven A. Sloan
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Qinghong Yan Sebastien M Weyn-Vanhentenryck Jie Wu Ye Zhang Kenian Chen Jia Qian Wu Ben A Barres Chaolin Zhang
|
Proceedings of the National Academy of Sciences of the United States of America
|
Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits
|
2015-03-03
|
Shiri Freilich
|
Shery Lev Itay Gonda Eli Reuveni Vitaly Portnoy Elad Oren Marc Lohse Navot Galpaz Einat Bar Galil Tzuri Guy Wissotsky Ayala Meir Joseph Burger Yaakov Tadmor Arthur Schaffer Zhangjun Fei James Giovannoni Efraim Lewinsohn Nurit Katzir
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BMC Plant Biology
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Discovery of putative small non-coding RNAs from the obligate intracellular bacterium Wolbachia pipientis.
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2015-03-04
|
Jean Popovici Jonathan M Keith
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Megan Woolfit Manjula Algama Elizabeth A McGraw
|
PLOS ONE
|
Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma.
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2015-03-05
|
Gregg B Morin
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Ewan A Gibb René L Warren Gavin W Wilson Scott D Brown Gordon A Robertson Robert A Holt
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Genome Medicine
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PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function.
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2015-03-09
|
Wilfried Ellmeier Rengul Cetin-Atalay
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Nazli Keskin Emre Deniz Jitka Eryilmaz Manolya Un Tugce Batur Tulin Ersahin Shinya Sakaguchi Batu Erman
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Molecular and Cellular Biology
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Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing.
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2015-03-09
|
Lars K. Nielsen Anton J. Enright John Mattick Marcel E. Dinger Kim-Anh Lê Cao Tommaso Leonardi Giovanni Bussotti Michael B. Clark Joanna Crawford Gethin Thomas
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Tim R Mercer Katelin R Haynes Marion E Brunck Kim-Anh Lê Cao Wendy Y Chen Ryan J Taft
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Nature Methods
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Conditional-ready mouse embryonic stem cell derived macrophages enable the study of essential genes in macrophage function
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2015-03-10
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Oliver Billker
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A T Y Yeung C Hale J Xia P H Tate D Goulding J A Keane S Mukhopadhyay L Forrester W C Skarnes R E W Hancock G Dougan
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Scientific Reports
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DNA methylation dynamics at imprinted genes during bovine pre-implantation embryo development.
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2015-03-10
|
Niamh Forde Alan M O'Doherty Trudee Fair
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David A Magee Lynee C O'Shea Marijke E Beltman Solomon Mamo
|
BMC Developmental Biology
|
Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation
|
2015-03-12
|
Andreas Hejnol Gonzalo Giribet
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Christopher E Laumer
|
eLife
|
Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum
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2015-03-12
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Qin Ma
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Wen-Chi Chou Shihui Yang Sha Cao Dawn M Klingeman Steven D Brown Ying Xu
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Nucleic Acids Research
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RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection.
|
2015-03-14
|
Jun Wang
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Rama Rao Ya Bing Zhu Tahereh Alinejad Suma Tiruvayipati Kwai Lin Thong Subha Bhassu
|
Gut Pathogens
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Modifying effects of vitamin E on chlorpyrifos toxicity in atlantic salmon
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2015-03-16
|
Pål A. Olsvik
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Marc H G Berntssen Liv Søfteland
|
PLOS ONE
|
Cyclic GMP balance is critical for malaria parasite transmission from the mosquito to the mammalian host
|
2015-03-17
|
Sebastian A. Mikolajczak
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Viswanathan Lakshmanan Matthew E Fishbaugher Bob Morrison Michael Baldwin Michael Macarulay Ashley M Vaughan Stefan H I Kappe
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mBio
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Transcriptomic profiling of linolenic acid-responsive genes in ROS signaling from RNA-seq data in Arabidopsis.
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2015-03-17
|
Juan C Begara-Morales Francisco J. Corpas
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Capilla Mata-Pérez Beatriz Sánchez-Calvo Francisco Luque Jaime Jiménez-Ruiz María N Padilla Jesús Fierro-Risco Raquel Valderrama Ana Fernández-Ocaña Juan B Barroso
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Frontiers in Plant Science
|
Neuronal identity genes regulated by super-enhancers are preferentially down-regulated in the striatum of Huntington's disease mice.
|
2015-03-17
|
Irwin Davidson Christian Neri
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Mayada Achour Stéphanie Le Gras Céline Keime Frédéric Parmentier François-Xavier Lejeune Anne-Laurence Boutillier Karine Merienne
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Human Molecular Genetics
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Goodness-of-fit tests and model diagnostics for negative binomial regression of RNA sequencing data
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2015-03-18
|
Gu Mi
|
Yanming Di Daniel W Schafer
|
PLOS ONE
|
Escape from X inactivation varies in mouse tissues.
|
2015-03-18
|
Jay Shendure
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Joel B Berletch Wenxiu Ma Fan Yang William S Noble Christine M Disteche Xinxian Deng
|
PLOS Genetics
|
Immunoglobulin transcript sequence and somatic hypermutation computation from unselected RNA-seq reads in chronic lymphocytic leukemia.
|
2015-03-18
|
Albert de la Chapelle John C Byrd
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James S Blachly Amy S Ruppert Weiqiang Zhao Susan Long Joseph Flynn Ian Flinn Jeffrey Jones Kami Maddocks Leslie Andritsos Emanuela M Ghia Laura Z Rassenti Thomas J Kipps
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Proceedings of the National Academy of Sciences of the United States of America
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A comparative study of RNA-seq analysis strategies.
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2015-03-18
|
Ernest Turro Alexandra M. Lewin
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Jürgen Jänes Fengyuan Hu
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Briefings in Bioinformatics
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Gene expression dosage regulation in an allopolyploid fish
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2015-03-19
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Maria Manuela Coelho Manfred Schartl
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I Matos M P Machado
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PLOS ONE
|
The transcriptome of equine peripheral blood mononuclear cells.
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2015-03-19
|
Alicja Pacholewska
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Michaela Drögemüller Jolanta Klukowska-Rötzler Simone Lanz Eman Hamza Emmanouil T Dermitzakis Eliane Marti Vincent Gerber Tosso Leeb Vidhya Jagannathan
|
PLOS ONE
|
Preclinical activity of combined HDAC and KDM1A inhibition in glioblastoma.
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2015-03-19
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Michelle Craig Barton
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Melissa M Singh Blake Johnson Avinashnarayan Venkatarayan Elsa R Flores Jianping Zhang Xiaoping Su Frederick Lang Joya Chandra
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Neuro-Oncology
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GLI2 inhibition abrogates human leukemia stem cell dormancy.
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2015-03-21
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John McPherson Tannishtha Reya
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Anil Sadarangani Gabriel Pineda Kathleen M Lennon Hye-Jung Chun Alice Shih Annelie E Schairer Angela C Court Daniel J Goff Sacha L Prashad Ifat Geron Russell Wall Richard A Moore Minya Pu Lei Bao Amy Jackson-Fisher Michael Munchhof Todd VanArsdale Sheldon R Morris Mark D Minden Karen Messer Hanna K A Mikkola Marco A Marra Thomas J Hudson Catriona H M Jamieson
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Journal of Translational Medicine
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Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR.
|
2015-03-23
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Ludwig Christian Hinske Anamaria Aranha Camargo Lucila Ohno-Machado
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Pedro A F Galante Elisabeth Limbeck Patrick Möhnle Raphael B Parmigiani Simone Kreth
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PLOS ONE
|
SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing.
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2015-03-23
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Annemieke Aartsma-Rus Peter A.C. 't Hoen Jeroen Laros
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Irina Pulyakhina Isabella Gazzoli Nisha Verwey Johan T den Dunnen
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Nucleic Acids Research
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A cytochrome P450, OsDSS1, is involved in growth and drought stress responses in rice (Oryza sativa L.).
|
2015-03-24
|
Hideo Matsumura
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Muluneh Tamiru Jerwin R Undan Hiroki Takagi Akira Abe Kakoto Yoshida Jesusa Q Undan Satoshi Natsume Aiko Uemura Hiromasa Saitoh Naoya Urasaki Takao Yokota Ryohei Terauchi
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Plant Molecular Biology
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The RNAi machinery controls distinct responses to environmental signals in the basal fungus Mucor circinelloides.
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2015-03-25
|
Victoriano Garre Simon Moxon
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Francisco E Nicolás Ana Vila María D Cascales Santiago Torres-Martínez Rosa M Ruiz-Vázquez
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BMC Genomics
|
Discovery of molecular markers to discriminate corneal endothelial cells in the human body.
|
2015-03-25
|
Masahito Yoshihara Hideya Kawaji Masayoshi Itoh Kohji Nishida Yoshihide Hayashizaki
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Hiroko Ohmiya Susumu Hara Satoshi Kawasaki FANTOM consortium Motokazu Tsujikawa
|
PLOS ONE
|
Correction: Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.
|
2015-03-25
|
PLOS Pathogens Staff
|
|
PLOS Pathogens
|
Low-cost, low-input RNA-seq protocols perform nearly as well as high-input protocols.
|
2015-03-26
|
Michael Eisen Peter A Combs
|
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PeerJ
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SplAdder: Identification, quantification and testing of alternative splicing events from RNA-Seq data
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2015-03-26
|
Gunnar Rätsch
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Andre Kahles Cheng Soon Ong Yi Zhong
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Assessing allele-specific expression across multiple tissues from RNA-seq read data
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2015-03-27
|
Tuuli Lappalainen Matti Pirinen Mark McCarthy Peter Donnelly
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Noah A Zaitlen GTEx Consortium Emmanouil T Dermitzakis Manuel A Rivas
|
Bioinformatics
|
Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels
|
2015-03-27
|
Cisca Wijmenga Daria V. Zhernakova Kristin Abbott Patrick Deelen Jingyuan Fu Marc Jan Bonder Morris A Swertz
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Mark de Haan Marijke van der Sijde Juha Karjalainen K Joeri van der Velde Richard J Sinke Lude Franke
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Genome Medicine
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Folate receptor-α (FOLR1) expression and function in triple negative tumors
|
2015-03-27
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Krishna R Kalari Karla V Ballman Zhifu Sun
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Brian M Necela Jennifer A Crozier Cathy A Andorfer Laura Lewis-Tuffin Jennifer M Kachergus Xochiquetzal J Geiger Daniel J Serie Alvaro Moreno-Aspitia Daniel J O'Shannessy Julia D Maltzman Ann E McCullough Barbara A Pockaj Heather E Cunliffe E Aubrey Thompson Edith A Perez
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PLOS ONE
|
Functional characterization of BC039389-GATM and KLK4-KRSP1 chimeric read-through transcripts which are up-regulated in renal cell cancer
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2015-03-27
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Mark Rubin
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Dorothee Pflueger Christiane Mittmann Silvia Dehler Holger Moch Peter Schraml
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BMC Genomics
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BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis.
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2015-03-28
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Yang Pan
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Quan Wan Hayley Dingerdissen Yu Fan Naila Gulzar Tsung-Jung Wu Cheng Yan Haichen Zhang Raja Mazumder
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Database
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The Listeria monocytogenes strain 10403S BioCyc database.
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2015-03-28
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Teresa M Bergholz Kathryn J Boor Martin Wiedmann
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Renato H Orsi
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Database
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Linear mRNA amplification approach for RNAseq from limited amount of RNA.
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2015-03-28
|
Maria A Nagai Dirce Carraro Helena Brentani Renata Pasqualini
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Elisa Napolitano Ferreira Gustavo de Campos Molina Renato David Puga Antônio Hugo José Froes Marques Campos Gustavo Cardoso Guimarães Diana Noronha Nunes Wadih Arap Emmanuel Dias-Neto Ricardo R Brentani
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Gene
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UV irradiation responses in Giardia intestinalis.
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2015-03-28
|
Karin Troell Staffan G Svärd
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Elin Einarsson
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Experimental Parasitology
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Long intervening non-coding RNA 00320 is human brain-specific and highly expressed in the cortical white matter.
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2015-03-29
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Glenda Halliday Eleonora Aronica
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James D Mills Jieqiong Chen Woojin S Kim Paul D Waters Avanita S Prabowo Michael Janitz
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Neurogenetics
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Assessing the consistency of public human tissue RNA-seq data sets.
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2015-03-30
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David Gomez-Cabrero Mikael Huss
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Frida Danielsson Tojo James
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Briefings in Bioinformatics
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The Solanum commersonii Genome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives
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2015-04
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Toni Gabaldón Riccardo Aiese Cigliano Walter Sanseverino Salvador Capella-Gutierrez Riccardo Aversano James M Bradeen Alessandra Dal Molin
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Felice Contaldi Maria Raffaella Ercolano Valentina Grosso Massimo Iorizzo Filippo Tatino Luciano Xumerle Carla Avanzato Alberto Ferrarini Massimo Delledonne Luigi Frusciante Domenico Carputo
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The Plant Cell
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Methyl-CpG Binding Protein 2 Regulates Microglia and Macrophage Gene Expression in Response to Inflammatory Stimuli.
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2015-04-01
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Jonathan Kipnis Tajie H. Harris Stephen D Turner Steffen Jung Igor Smirnov
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James C Cronk Noël C Derecki Emily Ji Yang Xu Aaron E Lampano Wendy Baker Geoffrey T Norris Ioana Marin Nathan Coddington Yochai Wolf Alan Aderem Alexander L Klibanov Vladimir Litvak
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Immunity
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p53 Enables metabolic fitness and self-renewal of nephron progenitor cells
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2015-04-01
|
Melody Baddoo Yumei Feng
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Yuwen Li Jiao Liu Wencheng Li Aaron Brown Melody Baddoo Marilyn Li Thomas Carroll Leif Oxburgh Zubaida Saifudeen
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Development
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A pooled shRNA screen for regulators of primary mammary stem and progenitor cells identifies roles for Asap1 and Prox1.
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2015-04-03
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Ross A. Dickins Matthew E Ritchie Geoffrey J. Lindeman Gordon K Smyth
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Julie M Sheridan Sarah A Best Kun Jiang Tamara J Beck François Vaillant Kevin Liu Jane E Visvader
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BMC Cancer
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EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments.
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2015-04-05
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Christina Kendziorski
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Ning Leng Yuan Li Brian E McIntosh Bao Kim Nguyen Bret Duffin Shulan Tian James A Thomson Colin N Dewey Ron Stewart
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Bioinformatics
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Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1.
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2015-04-06
|
Stephen L. Nutt Ellen V. Rothenberg
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Ameya Champhekar Sagar S Damle George Freedman Sebastian Carotta
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Genes & Development
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Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.
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2015-04-06
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Alexias Safi Gregory E Crawford
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Christopher L Frank Fang Liu Ranjula Wijayatunge Lingyun Song Matthew T Biegler Marty G Yang Christopher M Vockley Charles A Gersbach Anne E West
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Nature Neuroscience
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The level of residual dispersion variation and the power of differential expression tests for RNA-Seq data
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2015-04-07
|
Gu Mi
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Yanming Di
|
PLOS ONE
|
The immune signaling pathways of Manduca sexta
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2015-04-07
|
Haobo Jiang
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Xiaolong Cao Yan He Yingxia Hu Yang Wang Yun-Ru Chen Bart Bryant Rollie J Clem Lawrence M Schwartz Gary Blissard
|
Insect Biochemistry and Molecular Biology
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Characterization of the transcriptome of nascent hair cells and identification of direct targets of the Atoh1 transcription factor
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2015-04-08
|
Andrew K. Groves Huda Zoghbi
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Tiantian Cai Hsin-I Jen Hyojin Kang Tiemo J Klisch
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Journal of Neuroscience
|
Genome-wide analysis of the family 1 glycosyltransferases in cotton.
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2015-04-08
|
Juan Huang
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Juan Huang Chaoyou Pang Shuli Fan Meizhen Song Jiwen Yu Hengling Wei Qifeng Ma Libei Li Chi Zhang Shuxun Yu
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Molecular Genetics and Genomics
|
Purification and Transcriptomic Analysis of Mouse Fetal Leydig Cells Reveals Candidate Genes for Specification of Gonadal Steroidogenic Cells.
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2015-04-08
|
Alicia Oshlack Josephine Bowles Kathryn S McClelland Vincent R Harley Peter Koopman
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Katrina Bell Christian Larney Andrew H Sinclair
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Biology of Reproduction
|
New basal cell carcinoma susceptibility loci.
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2015-04-09
|
Laufey Tryggvadottir Unnur Þorsteinsdóttir Hrefna Johannsdottir Anne Tjønneland Gudmar Thorleifsson Thorunn Rafnar Y Gilaberte Hreinn Stefansson Eduardo Nagore Rajiv Kumar Ulla Vogel Kim Overvad Augustine Kong Peter Rudnai Patrick Sulem Daniel F Gudbjartsson Kári Stefánsson
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Simon N Stacey Hannes Helgason Sigurjon A Gudjonsson Florian Zink Asgeir Sigurdsson Birte Kehr Julius Gudmundsson Bardur Sigurgeirsson Kristrun R Benediktsdottir Kristin Thorisdottir Rafn Ragnarsson Victoria Fuentelsaz Cristina Corredera Matilde Grasa Dolores Planelles Onofre Sanmartin Eugene Gurzau Kvetoslava Koppova Bjørn A Nexø Jon G Jonasson Anna M Kristinsdottir Gisli Masson Olafur T Magnusson Bjarni V Halldorsson José I Mayordomo Jon H Olafsson
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Nature Communications
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New signaling pathways govern the host response to C. albicans infection in various niches.
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2015-04-09
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Jacques Ravel Jennifer Schwartz Amol C Shetty Claire M. Fraser
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Yaoping Liu L Latey Bradford Wenjie Xu Qyunh T Phan Priti Kumari Anup Mahurkar Aaron P Mitchell Scott G Filler Vincent M Bruno
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Genome Research
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Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.
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2015-04-09
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Bernhard Payer David Colognori Ruslan I Sadreyev
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Stefan F Pinter Brian J Beliveau Eda Yildirim Chao-Ting Wu Jeannie T Lee
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Genetics
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Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.
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2015-04-10
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Reinhard Ertl Fritz Sedlazeck Regina Hofmann-Lehmann
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Milica Krunic Benedikt Hagen Arndt von Haeseler Dieter Klein
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BMC Veterinary Research
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High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
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2015-04-13
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Kaia Achim Daria Gavriouchkina Luis R. Saraiva John C Marioni
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Jean-Baptiste Pettit Tomas Larsson Detlev Arendt
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Nature Biotechnology
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Spatial reconstruction of single-cell gene expression data.
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2015-04-13
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Aviv Regev Rahul Satija Jeffrey A Farrell
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David Gennert Alexander F Schier
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Nature Biotechnology
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Identification of non-coding RNAs associated with telomeres using a combination of enChIP and RNA sequencing
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2015-04-13
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Hodaka Fujii Daisuke Okuzaki
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Toshitsugu Fujita Miyuki Yuno Rieko Ohki
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PLOS ONE
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Asymmetric transcript discovery by RNA-seq in C. elegans blastomeres identifies neg-1, a gene important for anterior morphogenesis.
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2015-04-13
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Erin Osborne Bob Goldstein
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Jay C Zhang Adam D Werts Jason D Lieb
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PLOS Genetics
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Leaps and lulls in the developmental transcriptome of Dictyostelium discoideum.
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2015-04-13
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Gad Shaulsky
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Rafael David Rosengarten Balaji Santhanam Danny Fuller Mariko Katoh-Kurasawa William F Loomis Blaz Zupan
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BMC Genomics
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ChIP-Seq and RNA-Seq analyses identify components of the Wnt and Fgf signaling pathways as Prep1 target genes in mouse embryonic stem cells.
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2015-04-13
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Miguel Torres Hans-Jörg Warnatz Marie-Laure Yaspo
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Audrey Laurent Manuela Calabrese Marie-Laure Yaspo Vsevolod Tkachuk Francesco Blasi Dmitry Penkov
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PLOS ONE
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A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii.
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2015-04-13
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Giel G van Dooren Stuart A Ralph
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Lee M Yeoh Christopher D Goodman Nathan E Hall Geoffrey I McFadden
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Nucleic Acids Research
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RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress.
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2015-04-13
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Ahmed Bahieldin
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Ahmed Atef Jamal S M Sabir Nour O Gadalla Sherif Edris Ahmed M Alzohairy Nezar A Radhwan Mohammed N Baeshen Ahmed M Ramadan Hala F Eissa Sabah M Hassan Nabih A Baeshen Osama Abuzinadah Magdy A Al-Kordy Fotouh M El-Domyati Robert K Jansen
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Comptes Rendus Biologies
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Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching
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2015-04-14
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Yonggui Fu Jie Li
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Rui Li Leiming You Anlong Xu Shengfeng Huang
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PLOS ONE
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NMD3 regulates both mRNA and rRNA nuclear export in African trypanosomes via an XPOI-linked pathway.
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2015-04-14
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Paul Capewell Isabel Roditi Alasdair Ivens
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Melanie Bühlmann Pegine Walrad Eva Rico Arunasalam Naguleswaran Keith R Matthews
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Nucleic Acids Research
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Identification of candidate mimicry proteins involved in parasite-driven phenotypic changes
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2015-04-15
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Nadia Aubin-Horth Mahesh Panchal Iain Barber
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Francois Olivier Hebert Luke Phelps Irene Samonte Stephan Grambauer Martin Kalbe Christian R Landry
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Parasites & Vectors
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Antagonistic regulation of mRNA expression and splicing by CELF and MBNL proteins.
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2015-04-16
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Amanda J Ward Jimena Giudice
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Eric T Wang Jennifer M Cherone Thomas T Wang Daniel J Treacy Nicole J Lambert Peter Freese Tanvi Saxena Thomas A Cooper Christopher B Burge
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Genome Research
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Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast
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2015-04-16
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Jürg Bähler
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Danny A Bitton Sophie R Atkinson Charalampos Rallis Graeme C Smith David A Ellis Yuan Y C Chen Michal Malecki Sandra Codlin Jean-François Lemay Cristina Cotobal François Bachand Samuel Marguerat Juan Mata Jürg Bähler
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Genome Research
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SF3B1 association with chromatin determines splicing outcomes.
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2015-04-16
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Arnab Datta
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Nir Kfir Galit Lev-Maor Ohad Glaich Adi Alajem Siu K Sze Eran Meshorer Gil Ast
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Cell Reports
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First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1.
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2015-04-16
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Ruth Schmitz-Streit Dörte Becher
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Daniela Prasse Jens Thomsen Rebecca De Santis Jan Muntel
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Biochimie
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PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization.
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2015-04-17
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Sean M. Grimmond Nicola J Waddell Anil K Madugundu
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Shivashankar H Nagaraj Scott Wood Alun Jones Ramya A Mandyam Katia Nones John V Pearson
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Journal of Proteome Research
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ContextMap 2: fast and accurate context-based RNA-seq mapping
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2015-04-17
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Ralf Zimmer
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Thomas Bonfert Evelyn Kirner Gergely Csaba Caroline C Friedel
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BMC Bioinformatics
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High throughput profiling of the cotton bollworm Helicoverpa armigera immunotranscriptome during the fungal and bacterial infections
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2015-04-18
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Haobo Jiang
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Guang-Hua Xiong Long-Sheng Xing Zhe Lin Tusar T Saha Chengshu Wang Zhen Zou
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BMC Genomics
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Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection.
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2015-04-18
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Mark Ziemann
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Naghmeh Nejat David M Cahill Ganesan Vadamalai James Rookes Neda Naderali
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Molecular Genetics and Genomics
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Transcriptome analysis reveals the host response to Schmallenberg virus in bovine cells and antagonistic effects of the NSs protein
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2015-04-19
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Alain Kohl
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Anne-Lie Blomström Quan Gu Gerald Barry Gavin Wilkie Jessica K Skelton Margaret Baird Melanie McFarlane Esther Schnettler Richard M Elliott Massimo Palmarini
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BMC Genomics
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A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.
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2015-04-21
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David Murphy
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Kory R Johnson C C T Hindmarch Yasmmyn D Salinas YiJun Shi Michael Greenwood See Ziau Hoe Harold Gainer
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PLOS ONE
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Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells.
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2015-04-21
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Robert Tjian Claudia Cattoglio
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Elisa T Zhang Ivan Grubisic Kunitoshi Chiba Yick W Fong
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Proceedings of the National Academy of Sciences of the United States of America
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edgeRun: an R package for sensitive, functionally relevant differential expression discovery using an unconditional exact test.
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2015-04-21
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Winston Hide Rory Kirchner
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Emmanuel Dimont Jiantao Shi
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Bioinformatics
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From Gigabyte to Kilobyte: A Bioinformatics Protocol for Mining Large RNA-Seq Transcriptomics Data.
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2015-04-22
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Thomas P Mawhinney
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Jilong Li Jie Hou Lin Sun Jordan Maximillian Wilkins Yuan Lu Chad E Niederhuth Benjamin Ryan Merideth Valeri V Mossine C Michael Greenlief John C Walker William R Folk Mark Hannink Dennis B Lubahn James A Birchler Jianlin Cheng
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PLOS ONE
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Hepatitis D Virus Infection of Mice Expressing Human Sodium Taurocholate Co-transporting Polypeptide
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2015-04-22
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Wenhui Li Jianhua Sui
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Wenhui He Bijie Ren Fengfeng Mao Zhiyi Jing Yunfei Li Yang Liu Bo Peng Huan Yan Yonghe Qi Yinyan Sun Ju-Tao Guo Fengchao Wang
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PLOS Pathogens
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Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis).
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2015-04-22
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Chao Zheng
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Lei Zhao Yu Wang Jiazhi Shen Yinfei Zhang Sisi Jia Yusheng Li Zhaotang Ding
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PLOS ONE
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Functional analysis and transcriptomic profiling of iPSC-derived macrophages and their application in modeling Mendelian disease.
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2015-04-22
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Muredach P. Reilly
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Hanrui Zhang Chenyi Xue Rhia Shah Kate Bermingham Christine C Hinkle Wenjun Li Amrith Rodrigues Jennifer Tabita-Martinez John S Millar Marina Cuchel Evanthia E Pashos Ying Liu Ruilan Yan Wenli Yang Sager J Gosai Daniel VanDorn Stella T Chou Brian D Gregory Edward E Morrisey Mingyao Li Daniel J Rader
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Circulation Research
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Individual genome sequencing identified a novel enhancer element in exon 7 of the CSFR1 gene by shift of expressed allele ratios.
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2015-04-22
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Ekaterina E Khrameeva S Zhenilo
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S Tsygankova N Zhigalova A Mazur E Prokhortchouk
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Gene
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ZNF804A Transcriptional Networks in Differentiating Neurons Derived from Induced Pluripotent Stem Cells of Human Origin
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2015-04-23
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Deyou Zheng
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Jian Chen Mingyan Lin Anastasia Hrabovsky Erika Pedrosa Jason Dean Swati Jain Herbert M Lachman
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PLOS ONE
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De Novo Reconstruction of Adipose Tissue Transcriptomes Reveals Long Non-coding RNA Regulators of Brown Adipocyte Development.
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2015-04-23
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Nikolai Slavov Harvey Lodish
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Juan R Alvarez-Dominguez Zhiqiang Bai Dan Xu Bingbing Yuan Kinyui Alice Lo Myeong Jin Yoon Yen Ching Lim Marko Knoll Shuai Chen Chen Peng Lei Sun
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Cell Metabolism
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Imprinted expression in cystic embryoid bodies shows an embryonic and not an extra-embryonic pattern
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2015-04-24
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Christoph Bock Sylvia Knapp Josef M Penninger Tomasz Kuliński Paul Datlinger
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M Rita T Casari Philipp M Guenzl Daniel Wenzel Daniel Andergassen Anastasiya Hladik Matthias Farlik H-Christian Theussl Denise P Barlow Quanah J Hudson
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Developmental Biology
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PtaRHE1, a Populus tremula × Populus alba RING-H2 protein of the ATL family, has a regulatory role in secondary phloem fibre development.
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2015-04-25
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Wout Boerjan Annegret Kohler
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Fabien Baldacci-Cresp Jihad Moussawi Jean-Charles Leplé Rebecca Van Acker Julie Candiracci Laure Twyffels Antanas V Spokevicius Gerd Bossinger Françoise Laurans Nicole Brunel Marjorie Vermeersch Mondher El Jaziri Marie Baucher
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The Plant Journal
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Tet3 regulates synaptic transmission and homeostatic plasticity via DNA oxidation and repair
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2015-04-27
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Guo-Li Ming Hongjun Song Daniel Geschwind
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Huimei Yu Yijing Su Jaehoon Shin Chun Zhong Junjie U Guo Yi-Lan Weng Fuying Gao Giovanni Coppola
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Nature Neuroscience
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High-performance probes for light and electron microscopy
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2015-04-27
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Gerald M. Rubin Megan E Williams Erik B. Bloss Brian P. English
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Sarada Viswanathan Timothy J Stasevich Colenso M Speer Aljoscha Nern Barret D Pfeiffer Bryan M Hooks Wei-Ping Li Teresa Tian Gilbert L Henry John J Macklin Ronak Patel Charles R Gerfen Xiaowei Zhuang Yalin Wang Loren L Looger
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Nature Methods
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Polyester: simulating RNA-seq datasets with differential transcript expression.
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2015-04-28
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Jeffrey T. Leek Andrew E Jaffe Ben Langmead
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Alyssa C Frazee
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Bioinformatics
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New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription.
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2015-04-29
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Melody Baddoo Michael J Strong Tina O'Grady Erik K Flemington
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Subing Cao Walter Moss Monica Concha Xia Wang Yi Yu Melody Baddoo Kun Zhang Claire Fewell Zhen Lin Yan Dong
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Journal of Virology
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Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.
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2015-04-29
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Gordon K Smyth
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Ruijie Liu Aliaksei Z Holik Shian Su Natasha Jansz Kelan Chen Huei San Leong Marnie E Blewitt Marie-Liesse Asselin-Labat Matthew E Ritchie
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Nucleic Acids Research
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Oviduct-Embryo Interactions in Cattle: Two-Way Traffic or a One-Way Street?
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2015-04-29
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Niamh Forde Thomas E. Spencer Alfonso Gutierrez-Adan Gregory W Burns V Maillo Peadar Ó Gaora D Rizos
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Urban Besenfelder Vitezslav Havlicek Patrick Lonergan
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Biology of Reproduction
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Coronary Artery Disease Associated Transcription Factor TCF21 Regulates Smooth Muscle Precursor Cells That Contribute to the Fibrous Cap
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2015-05
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Thomas Quertermous Sylvia T Nurnberg Ivan Carcamo-Oribe Michelle D Tallquist Lars Maegdefessel Ulf Hedin
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Karen Cheng Azad Raiesdana Ramendra Kundu Clint L Miller Juyong B Kim Komal Arora Yiqin Xiong Nikhil Tellakula Vivek Nanda Nikitha Murthy William A Boisvert Ljubica Perisic Silvia Aldi Milos Pjanic Gary K Owens
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PLOS Genetics
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Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo.
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2015-05-01
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Sean D McGrath Malachi Griffith Timothy A. Graubert Catrina Fronick
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Cara Lunn Shirai James N Ley Brian S White Sanghyun Kim Justin Tibbitts Jin Shao Matthew Ndonwi Brian Wadugu Eric J Duncavage Theresa Okeyo-Owuor Tuoen Liu Vincent Magrini Robert S Fulton Michelle O'Laughlin Matthew J Walter
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Cancer Cell
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Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer.
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2015-05-01
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Saurabh Gupta
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Pushpinder Bawa Sajna Zackaria Mohit Verma R Srivatsan Bibha Chaudhary Subhashini Srinivasan
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PLOS ONE
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Perturbations of heart development and function in cardiomyocytes from human embryonic stem cells with trisomy 21.
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2015-05-01
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Stylianos Antonarakis Outi Hovatta Laura Sartiani Marisa Jaconi Biljana Dumevska
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Alexis Bosman Audrey Letourneau Martina Del Lungo Flavio Ronzoni Rostyslav Kuziakiv Virpi Tohonen Marco Zucchelli Federico Santoni Michel Guipponi Outi Hovatta
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Stem Cells
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Telomere dysfunction drives aberrant hematopoietic differentiation and myelodysplastic syndrome.
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2015-05-01
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Marianna D'Anca Matteo Marchesini Paola Storti Simona Colla Marcos Estecio Nicola Giuliani Lynda Chin Hagop Kantarjian Guillermo Garcia-Manero
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Derrick Sek Tong Ong Yamini Ogoti Nipun A Mistry Karen Clise-Dwyer Sonny A Ang Andrea Viale Kathryn Ruisaard Irene Ganan Gomez Christopher A Bristow David C Weksberg Yan Wing Ho Baoli Hu Giannicola Genovese Piergiorgio Pettazzoni Asha S Multani Shan Jiang Sujun Hua Michael C Ryan Alessandro Carugo Luigi Nezi Yue Wei Hui Yang Li Zhang Sarah Gaddis Ting Gong James W Horner Timothy P Heffernan Philip Jones Laurence J N Cooper Han Liang Y Alan Wang Carlos Bueso-Ramos Ronald A DePinho
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Cancer Cell
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regionReport: Interactive reports for region-level and feature-level genomic analyses.
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2015-05-01
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Leonardo Collado-Torres Andrew E Jaffe Jeffrey T. Leek
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F1000Research
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A bioinformatics approach to distinguish plant parasite and host transcriptomes in interface tissue by classifying RNA-Seq reads.
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2015-05-03
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Tomoaki Sakamoto
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Daisuke Ikeue Christian Schudoma Wenna Zhang Yoshiyuki Ogata Tetsuya Kurata Takeshi Furuhashi Friedrich Kragler Koh Aoki
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Plant Methods
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Bariatric Surgery Induces Disruption in Inflammatory Signaling Pathways Mediated by Immune Cells in Adipose Tissue: A RNA-Seq Study
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2015-05-04
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Yuna Blum Karine Clément
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Christine Poitou Claire Perret François Mathieu Vinh Truong Hervé Durand Rohia Alili Nadjim Chelghoum Véronique Pelloux Judith Aron-Wisnewsky Adriana Torcivia Jean-Luc Bouillot Brian W Parks Ewa Ninio Laurence Tiret
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PLOS ONE
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The Transcriptome and Terpene Profile of Eucalyptus grandis Reveals Mechanisms of Defense Against the Insect Pest, Leptocybe invasa.
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2015-05-05
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Bernard Slippers
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Caryn N Oates Carsten Külheim Alexander A Myburg Sanushka Naidoo
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Plant and Cell Physiology
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Identification of genes involved in the phosphate metabolism in Cryptococcus neoformans.
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2015-05-05
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Yu Kanesaki
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Akio Toh-e Misako Ohkusu Hao-Man Li Kiminori Shimizu Azusa Takahashi-Nakaguchi Toru Gonoi Susumu Kawamoto Hirofumi Yoshikawa Masafumi Nishizawa
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Fungal Genetics and Biology
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MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse
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2015-05-07
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Gil Omenn
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Hong-Dong Li Yuanfang Guan
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Database
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Principles of long noncoding RNA evolution derived from direct comparison of transcriptomes in 17 species.
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2015-05-07
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Igor Ulitsky
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Hadas Hezroni David Koppstein Matthew G Schwartz Alexandra Avrutin David P Bartel
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Cell Reports
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Rail-RNA: Scalable analysis of RNA-seq splicing and coverage
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2015-05-07
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Jeffrey T. Leek Ben Langmead Abhinav Nellore
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Leonardo Collado-Torres Andrew E Jaffe José Alquicira-Hernández Jacob Pritt James Morton
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Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.
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2015-05-08
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Gustavo Rodriguez-Esteban Emili Salo Josep F. Abril
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Alejandro González-Sastre José Ignacio Rojo-Laguna
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BMC Genomics
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Combining GWAS and RNA-Seq Approaches for Detection of the Causal Mutation for Hereditary Junctional Epidermolysis Bullosa in Sheep.
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2015-05-08
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Gwenola Tosser-Klopp Julio Benavides Gwenola Tosser-Klopp Juan J Arranz Valentín Pérez
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Aroa Suárez-Vega Beatriz Gutiérrez-Gil Christophe Klopp Stephen J Keennel
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PLOS ONE
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Gene expression associated with white syndromes in a reef building coral, Acropora hyacinthus.
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2015-05-09
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Mikhail Matz
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Rachel M Wright Galina V Aglyamova Eli Meyer
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BMC Genomics
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Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data.
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2015-05-12
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Angelika N Christ Nicole Cloonan Sean M. Grimmond
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David L A Wood Katia Nones Anita Steptoe Ivon Harliwong Felicity Newell Timothy J C Bruxner David Miller
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PLOS ONE
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Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability.
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2015-05-12
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Antti Honkela
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Karolis Uziela Antti Honkela
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PLOS ONE
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Contrasting host-pathogen interactions and genome evolution in two generalist and specialist microsporidian pathogens of mosquitoes.
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2015-05-13
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Christina A Cuomo Hiten D. Madhani James J. Becnel
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Christopher A Desjardins Neil D Sanscrainte Jonathan M Goldberg David Heiman Sarah Young Qiandong Zeng
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Nature Communications
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Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data.
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2015-05-14
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Frank Emmert-Streib
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Ricardo de Matos Simoes Sabine Dalleau Kate E Williamson
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BMC Systems Biology
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GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development.
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2015-05-17
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Tin-Lap Lee
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Alfred Chun-Shui Luk Huayan Gao Sizhe Xiao Jinyue Liao Daxi Wang Jiajie Tu Owen M Rennert Wai-Yee Chan
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Database
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Splice variants and regulatory networks associated with host resistance to the intestinal worm Cooperia oncophora in cattle.
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2015-05-18
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Steven G Schroeder Weizhong Li Cong-Jun Li
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Robert W Li Sitao Wu
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Veterinary Parasitology
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Ratios of Four STAT3 Splice Variants in Human Eosinophils and Diffuse Large B Cell Lymphoma Cells
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2015-05-18
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Stephane Esnault
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Keren B Turton Douglas S Annis Lixin Rui Deane F Mosher
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PLOS ONE
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Genome-wide analysis links NFATC2 with asparaginase hypersensitivity.
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2015-05-18
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Seth Karol Laura B Ramsey Charles G. Mullighan Ching-Hon Pui Stephen P Hunger
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Christian A Fernandez Colton Smith Wenjian Yang Chunxu Qu Eric Larsen W Paul Bowman Chengcheng Liu Tamara Chang Mignon L Loh Elizabeth A Raetz Naomi J Winick William L Carroll Sima Jeha William E Evans Meenakshi Devidas Mary V Relling
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Blood
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Chlamydomonas reinhardtii cells adjust the metabolism to maintain viability in response to atrazine stress.
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2015-05-19
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Marta Esperanza Marta Seoane Concepción Herrero Carmen Rioboo Ángeles Cid
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Aquatic Toxicology
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Effect of ovarian hormones on the healthy equine uterus: a global gene expression analysis.
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2015-05-20
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Neil D. Young Natali Krekeler
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Christina D Marth Lisa Y Glenton Drew M Noden Glenn F Browning
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Reproduction, Fertility and Development
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Diffusion maps for high-dimensional single-cell analysis of differentiation data.
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2015-05-21
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Q85197310 Florian Buettner Fabian J. Theis
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Laleh Haghverdi
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Bioinformatics
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Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations
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2015-05-21
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Chris Ponting Caroline Oedekoven Fernando J Calero-Nieto Florian Buettner Iain C Macaulay David Kent Fabian J. Theis Anthony R Green Berthold Göttgens Carlos Caldas
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Nicola K Wilson Mona Shehata Manuel Sánchez Castillo Evangelia Diamanti Reiner Schulte Thierry Voet John Stingl
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Cell Stem Cell
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Effects of Tris(1,3-dichloro-2-propyl) Phosphate (TDCPP) in Tetrahymena Thermophila: Targeting the Ribosome.
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2015-05-21
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John P Giesy
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Jing Li Liqin Yu Guangyu Li Chunsheng Liu
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Scientific Reports
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Alzheimer disease (AD) specific transcription, DNA methylation and splicing in twenty AD associated loci
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2015-05-21
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Margaret A. Pericak-Vance
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Crystal Humphries Martin A Kohli Patrice Whitehead Deborah C Mash John Gilbert
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Molecular and Cellular Neuroscience
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TRUFA: A User-Friendly Web Server for de novo RNA-seq Analysis Using Cluster Computing.
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2015-05-24
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Julio Rozas Rafael Zardoya
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Etienne Kornobis Luis Cabellos Fernando Aguilar Cristina Frías-López Jesús Marco
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Evolutionary Bioinformatics
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RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.
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2015-05-25
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Masayoshi Kawaguchi
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Yoshihiro Handa Hiroyo Nishide Naoya Takeda Yutaka Suzuki Katsuharu Saito
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Plant and Cell Physiology
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A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala) Based on RNA-Seq Data
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2015-05-26
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Shaokui Yi
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Xiaoke Duan Xianwu Guo Weimin Wang
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International Journal of Molecular Sciences
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Systematic transcriptome analysis reveals tumor-specific isoforms for ovarian cancer diagnosis and therapy
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2015-05-26
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Christopher DeBoever Frazer KA
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Christian L Barrett Kristen Jepsen Cheryl C Saenz Dennis A Carson
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Proceedings of the National Academy of Sciences of the United States of America
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nagnag: Identification and quantification of NAGNAG alternative splicing using RNA-Seq data.
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2015-05-27
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Gaurav Sablok
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Xiaoyan Yan Gang Feng Jiaxin Ma Hongwei Zhao Xiaoyong Sun
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FEBS Letters
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Cellular microRNA miR-26a suppresses replication of porcine reproductive and respiratory syndrome virus by activating innate antiviral immunity.
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2015-05-27
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Yuhai Bi
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Xiaojuan Jia Jing Li Qing Xie Hanchun Yang Wenjun Liu
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Scientific Reports
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Towards Elucidating Carnosic Acid Biosynthesis in Lamiaceae: Functional Characterization of the Three First Steps of the Pathway in Salvia fruticosa and Rosmarinus officinalis
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2015-05-28
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Q85232174 Irini Pateraki Fani Chatzopoulou Albert Ferrer Alain Tissier Sotirios Kampranis Angelos K Kanellis
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Dimitra Papaefthimiou Kathleen Brückner Ric C H de Vos Constantinos A Tsoleridis Dimitra Katsarou Antigoni Papanikolaou Eleni Dimitriadou Stefanos Kostas David Manzano Ulschan Scheler Antonios M Makris
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PLOS ONE
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Identification of regulatory network hubs that control lipid metabolism in Chlamydomonas reinhardtii
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2015-05-28
|
Leslie M. Hicks
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Mahmoud Gargouri Jeong-Jin Park F Omar Holguin Min-Jeong Kim Hongxia Wang Rahul R Deshpande Yair Shachar-Hill David R Gang
|
Journal of Experimental Botany
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Tracking global gene expression responses in T cell differentiation.
|
2015-05-28
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Vincent Piras Kumar Selvarajoo
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Oriane Simeoni Masaru Tomita
|
Gene
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Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
|
2015-05-29
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Alexias Safi Gregory E Crawford
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Lauren R Polstein Pablo Perez-Pinera D Dewran Kocak Christopher M Vockley Peggy Bledsoe Lingyun Song Timothy E Reddy Charles A Gersbach
|
Genome Research
|
Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae
|
2015-05-30
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Isabelle Rosinski-Chupin Patrick Trieu-Cuot Philippe Bouloc Marie-Agnès Dillies Marie-Frédérique Lartigue
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Elisabeth Sauvage Odile Sismeiro Adrien Villain Violette Da Cunha Marie-Elise Caliot Philippe Glaser
|
BMC Genomics
|
Functionally defined therapeutic targets in diffuse intrinsic pontine glioma
|
2015-06
|
Wenchao Sun Jacques Grill Michelle Monje Javad Nazarian Maryam Fouladi Cynthia Hawkins
|
Catherine S Grasso Yujie Tang Nathalene Truffaux Noah E Berlow Lining Liu Marie-Anne Debily Michael J Quist Lara E Davis Elaine C Huang Pamelyn J Woo Anitha Ponnuswami Spenser Chen Tessa B Johung Mari Kogiso Yuchen Du Lin Qi Yulun Huang Marianne Hütt-Cabezas Katherine E Warren Ludivine Le Dret Paul S Meltzer Hua Mao Martha Quezado Dannis G van Vuurden Jinu Abraham Matthew N Svalina Nicholas Wang Marta M Alonso Eric H Raabe Esther Hulleman Paul T Spellman Xiao-Nan Li Charles Keller Ranadip Pal
|
Nature Medicine
|
3USS: a web server for detecting alternative 3'UTRs from RNA-seq experiments
|
2015-06-01
|
Anna Tramontano
|
Loredana Le Pera Mariagiovanna Mazzapioda
|
Bioinformatics
|
FourCSeq: analysis of 4C sequencing data.
|
2015-06-01
|
Yad Ghavi-Helm Wolfgang Huber Simon Anders Eileen E. M. Furlong
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Felix A Klein Tibor Pakozdi
|
Bioinformatics
|
FunPat: function-based pattern analysis on RNA-seq time series data.
|
2015-06-01
|
Francesca Finotello Tiziana Sanavia
|
Barbara Di Camillo
|
BMC Genomics
|
Condensin-driven remodelling of X chromosome topology during dosage compensation.
|
2015-06-01
|
Rachel Patton McCord
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Emily Crane Qian Bian Bryan R Lajoie Bayly S Wheeler Edward J Ralston Satoru Uzawa Job Dekker Barbara J Meyer
|
Nature
|
Dynamics of GATA1 binding and expression response in a GATA1-induced erythroid differentiation system
|
2015-06-01
|
Ross C Hardison Christapher S Morrissey Mitchell J Weiss
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Deepti Jain Tejaswini Mishra Belinda M Giardine Cheryl A Keller Susan Magargee Christine M Dorman Maria Long
|
Genomics Data
|
RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application.
|
2015-06-01
|
Matteo Pallocca Anna Maria D'Erchia Ernesto Picardi Raffaele A. Calogero
|
Mattia D'Antonio Paolo D'Onorio De Meo Tiziana Castrignanò Graziano Pesole
|
BMC Genomics
|
Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.
|
2015-06-01
|
Gane Ka-Shu Wong Megan M Augustin
|
Dan R Ruzicka Ashutosh K Shukla Jörg M Augustin Courtney M Starks Mark O'Neil-Johnson Michael R McKain Bradley S Evans Matt D Barrett Ann Smithson Michael K Deyholos Patrick P Edger J Chris Pires James H Leebens-Mack David A Mann Toni M Kutchan
|
The Plant Journal
|
Detecting disease genes of non-small lung cancer based on consistently differential interactions.
|
2015-06-01
|
Xiaoping Liu Tao Zeng
|
Qianqian Shi William Wang Luonan Chen
|
Cancer and Metastasis Reviews
|
Immune cell profiling to guide therapeutic decisions in rheumatic diseases
|
2015-06-02
|
Deepak A Rao Soumya Raychaudhuri
|
Joerg Ermann Nikola C Teslovich Michael B Brenner
|
Nature Reviews Rheumatology
|
RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice.
|
2015-06-03
|
Carsten T Kuenne Mario Looso Thomas Braun
|
Stefan Guenther Ting Zhang Marcus Krueger Yonggang Zhou Johnny Kim
|
Genomics Data
|
CD24(+) cells fuel rapid tumor growth and display high metastatic capacity
|
2015-06-04
|
Derek LeRoith
|
Ran Rostoker Sagi Abelson Inna Genkin Sarit Ben-Shmuel Ravi Sachidanandam Eyal J Scheinman Keren Bitton-Worms Zila Shen Orr Avishay Caspi Maty Tzukerman
|
Breast Cancer Research
|
Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton.
|
2015-06-05
|
Ling Min Longfu Zhu Daojun Yuan Xianlong Zhang
|
Yuanlong Wu Zancheng Wu Li Yang Xiyan Yang Xiaoping Guo
|
Scientific Reports
|
The generation of macrophages with anti-inflammatory activity in the absence of STAT6 signaling.
|
2015-06-05
|
Najib El-sayed
|
Bryan D Fleming Prabha Chandrasekaran Laura A L Dillon Elizabeth Dalby Rahul Suresh Arup Sarkar David M Mosser
|
Journal of Leukocyte Biology
|
Scalable microfluidics for single-cell RNA printing and sequencing.
|
2015-06-06
|
Dana Pe'er Peter A Sims
|
Sayantan Bose Zhenmao Wan Ambrose Carr Abbas H Rizvi Gregory Vieira Dana Pe'er
|
Genome Biology
|
Flagellin Is Required for Host Cell Invasion and Normal Salmonella Pathogenicity Island 1 Expression by Salmonella enterica Serovar Paratyphi A
|
2015-06-08
|
Michael McClelland
|
Dana Elhadad Prerak Desai Galia Rahav Ohad Gal-Mor
|
Infection and Immunity
|
Infiltration of chitin by protein coacervates defines the squid beak mechanical gradient.
|
2015-06-08
|
Ali Miserez
|
YerPeng Tan Shawn Hoon Paul A Guerette Wei Wei Ali Ghadban Cai Hao J Herbert Waite
|
Nature Chemical Biology
|
hnRNP U protein is required for normal pre-mRNA splicing and postnatal heart development and function
|
2015-06-09
|
Rhonda Bassel-Duby Tom Maniatis Junqiang Ye Lindsey J. Macpherson
|
Nadine Beetz Sean O'Keeffe Juan Carlos Tapia Weisheng V. Chen Eric N. Olson
|
Proceedings of the National Academy of Sciences of the United States of America
|
From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response
|
2015-06-10
|
Barbara Blasi Hakim Tafer
|
Donatella Tesei Katja Sterflinger
|
PLOS ONE
|
Molecular characterization of two novel molecular chaperones in bacterial-challenged Apostichopus japonicus.
|
2015-06-10
|
Chenghua Li
|
Haihong Wang Yina Shao Weiwei Zhang Zhimeng Lv Chunhua Jin
|
Gene
|
RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
|
2015-06-12
|
Sean C Daugherty
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Tracy H Hazen Amol Shetty Anup A Mahurkar Owen White James B Kaper David A Rasko
|
Frontiers in Microbiology
|
The Impact of Normalization Methods on RNA-Seq Data Analysis.
|
2015-06-15
|
Marek Figlerowicz
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J Zyprych-Walczak A Szabelska L Handschuh K Górczak K Klamecka I Siatkowski
|
BioMed Research International
|
Combined Targeted DNA Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using UNCseq and NGScopy, and RNA Sequencing Using UNCqeR for the Detection of Genetic Aberrations in NSCLC.
|
2015-06-15
|
Norman Sharpless Nirali M Patel Vonn Walter
|
Xiaobei Zhao Anyou Wang David A Eberhard Michele C Hayward Ashley H Salazar Heejoon Jo Matthew G Soloway Matthew D Wilkerson Joel S Parker Xiaoying Yin Guosheng Zhang Marni B Siegel Gary B Rosson H Shelton Earp Margaret L Gulley Karen E Weck D Neil Hayes Stergios J Moschos
|
PLOS ONE
|
Suppressing Sorbitol Synthesis Substantially Alters the Global Expression Profile of Stress Response Genes in Apple (Malus domestica) Leaves.
|
2015-06-15
|
Yi Zheng Abhaya Dandekar
|
Ting Wu Yi Wang Zhangjun Fei Kenong Xu Zhenhai Han Lailiang Cheng
|
Plant and Cell Physiology
|
Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori.
|
2015-06-16
|
Cynthia Sharma
|
Thorsten Bischler Hock Siew Tan Kay Nieselt
|
Methods
|
RNASequel: accurate and repeat tolerant realignment of RNA-seq reads.
|
2015-06-16
|
Lincoln Stein
|
Gavin W Wilson
|
Nucleic Acids Research
|
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut.
|
2015-06-17
|
Abhaya Dandekar
|
Sandeep Chakraborty Monica Britton Jill Wegrzyn Timothy Butterfield Pedro José Martínez-García Russell L Reagan Basuthkar J Rao Charles A Leslie Mallikarjuna Aradhaya David Neale Keith Woeste
|
F1000Research
|
RNA-seq analysis of an apical meristem time series reveals a critical point in Arabidopsis thaliana flower initiation
|
2015-06-18
|
Anna V Klepikova Sergey E. Dmitriev
|
Maria D Logacheva Aleksey A Penin
|
BMC Genomics
|
RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications.
|
2015-06-18
|
Gane Ka-Shu Wong Udo Gowik
|
Ming-Ju Amy Lyu Steve Kelly Sarah Covshoff Julia Mallmann Peter Westhoff Julian M Hibberd Matt Stata Rowan F Sage Haorong Lu Xiaofeng Wei Xin-Guang Zhu
|
BMC Evolutionary Biology
|
Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens
|
2015-06-19
|
Dario Cantu
|
Abraham Morales-Cruz Katherine C H Amrine Barbara Blanco-Ulate Daniel P Lawrence Renaud Travadon Philippe E Rolshausen Kendra Baumgartner
|
BMC Genomics
|
PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome.
|
2015-06-19
|
Thomas Preiss Traude H. Beilharz David Powell Ana Traven Torsten Seemann
|
Paul F Harrison Jennifer L Clancy Peter R Boag
|
RNA
|
Benchmarking Transcriptome Quantification Methods for Duplicated Genes in Xenopus laevis.
|
2015-06-19
|
Taejoon Kwon
|
|
Cytogenetics and Genome Research
|
RNA-Seq analysis of resistant and susceptible potato varieties during the early stages of potato virus Y infection.
|
2015-06-20
|
Jeff H. Chang
|
Aymeric Goyer Launa Hamlin James M Crosslin Alex Buchanan
|
BMC Genomics
|
Marrying microfluidics and microwells for parallel, high-throughput single-cell genomics.
|
2015-06-20
|
Alex K. Shalek
|
Marc H Wadsworth Travis K Hughes
|
Genome Biology
|
Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data.
|
2015-06-22
|
Bonnie Berger
|
Sean Simmons Jian Peng Jadwiga Bienkowska
|
Journal of Computational Biology
|
ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli.
|
2015-06-22
|
Eve Syrkin Wurtele Dan Nettleton
|
Fengwei Jiang Chunxia An Yinli Bao Xuefeng Zhao Robert L Jernigan Andrew Lithio Ling Li Lisa K Nolan Chengping Lu Ganwu Li
|
Infection and Immunity
|
RNA Seq profiling reveals a novel expression pattern of TGF-β target genes in human blood eosinophils.
|
2015-06-22
|
Stephane Esnault
|
Zhong-Jian Shen Jie Hu Igor Dozmorov James S Malter
|
Immunology Letters
|
RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L.
|
2015-06-23
|
Yuan Chen Liuyang Wang
|
Zhili Zhou Huancheng Ma Kevin Lin Youjie Zhao Zhi Xiong Bin Tian
|
Evolutionary Bioinformatics
|
An integrated RNA-Seq and network study reveals a complex regulation process of rice embryo during seed germination.
|
2015-06-23
|
Songnian Hu
|
Ting Wei Zilong He XinYu Tan Xue Liu Xiao Yuan Yingfeng Luo
|
Biochemical and Biophysical Research Communications
|
Systematically evaluating interfaces for RNA-seq analysis from a life scientist perspective.
|
2015-06-23
|
Alicia Poplawski Federico Marini
|
Moritz Hess Tanja Zeller Johanna Mazur Harald Binder
|
Briefings in Bioinformatics
|
How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq.
|
2015-06-24
|
Luis Fernando García-Ortega Octavio Martínez
|
|
PLOS ONE
|
Gene expression analysis of skin grafts and cultured keratinocytes using synthetic RNA normalization reveals insights into differentiation and growth control.
|
2015-06-25
|
Juha Kere Eeva-Mari Jouhilahti Sten Linnarsson Peter Lönnerberg Tiina Skoog Shintaro Katayama Esko Kankuri
|
H Annika Siitonen Kristo Nuutila Mari H Tervaniemi Jyrki Vuola Anna Johnsson Outi Elomaa
|
BMC Genomics
|
Comparison of RNA-seq and microarray-based models for clinical endpoint prediction.
|
2015-06-25
|
Benedikt Brors Danielle Thierry-Mieg Falk Hertwig Weihong Xu Marco Chierici Lee Lancashire Richard G Grundy Heng Luo Davide Albanese Martin Peifer Jean Thierry-Mieg Jun Wang Zhiyu Peng Jo Vandesompele
|
Wenqian Zhang Ying Yu Wenwei Zhang Jian Wang Cesare Furlanello Viswanath Devanarayan Jie Cheng Youping Deng Barbara Hero Huixiao Hong Meiwen Jia Li Li Simon M Lin Yuri Nikolsky André Oberthuer Tao Qing Zhenqiang Su Ruth Volland Charles Wang May D Wang Junmei Ai Shahab Asgharzadeh Smadar Avigad Wenjun Bao Marina Bessarabova Murray H Brilliant Tzu-Ming Chu Jibin Zhang Min Max He Scott Hebbring Howard L Kaufman Samir Lababidi Yan Li Xin X Lu Xiwen Ma Baitang Ning Rosa Noguera John H Phan Frederik Roels Carolina Rosswog Susan Shao Jie Shen Jessica Theissen Gian Paolo Tonini Po-Yen Wu Wenzhong Xiao Joshua Xu Jiekun Xuan Yong Yang Zhan Ye Zirui Dong Ke K Zhang Ye Yin Chen Zhao Yuanting Zheng Russell D Wolfinger Tieliu Shi Linda H Malkas Frank Berthold Weida Tong Leming Shi Matthias Fischer
|
Genome Biology
|
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
|
2015-06-25
|
Eduardo Eyras Allan B. James Yamile Marquez Maria Kalyna Hugh G. Nimmo Andrea Barta
|
Runxuan Zhang Cristiane P G Calixto Nikoleta A Tzioutziou Craig G Simpson Wenbin Guo Rob Patro John W S Brown
|
New Phytologist
|
Correction: A RNA-Seq Analysis of the Rat Supraoptic Nucleus Transcriptome: Effects of Salt Loading on Gene Expression.
|
2015-06-25
|
David Murphy
|
Kory R Johnson C C T Hindmarch Yasmmyn D Salinas YiJun Shi Michael Greenwood See Ziau Hoe Harold Gainer
|
PLOS ONE
|
Intratumoral morphologic and molecular heterogeneity of rhabdoid renal cell carcinoma: challenges for personalized therapy.
|
2015-06-26
|
Lalit Patel
|
Rajesh R Singh Paari Murugan Horatiu Voicu Suk-Young Yoo Tadeusz Majewski Meenakshi Mehrotra Khalida Wani Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Chad J Creighton L Jeffrey Medeiros Russell R Broaddus Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak Rajyalakshmi Luthra Kanishka Sircar
|
Modern Pathology
|
Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.
|
2015-06-27
|
Hideya Kawaji Mathias Uhlén Nancy Y Yu Linn Fagerberg Piero Carninci Yoshihide Hayashizaki
|
Björn M Hallström Fredrik Ponten Alistair R R Forrest Fantom Consortium Carsten O Daub
|
Nucleic Acids Research
|
Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers.
|
2015-06-29
|
Yohei Kirino
|
Shozo Honda Phillipe Loher Megumi Shigematsu Juan P Palazzo Ryusuke Suzuki Issei Imoto Isidore Rigoutsos
|
Proceedings of the National Academy of Sciences of the United States of America
|
Gene fusion detection in formalin-fixed paraffin-embedded benign fibrous histiocytomas using fluorescence in situ hybridization and RNA sequencing.
|
2015-06-29
|
David Gisselsson Fredrik Mertens
|
Charles Walther Jakob Hofvander Jenny Nilsson Linda Magnusson Henryk A Domanski Johnbosco Tayebwa Leona A Doyle Christopher D M Fletcher
|
Laboratory Investigation
|
A nested parallel experiment demonstrates differences in intensity-dependence between RNA-seq and microarrays.
|
2015-06-30
|
John D. Storey
|
David G Robinson Jean Y Wang
|
Nucleic Acids Research
|
Phylogenetic analysis and expression profiling of the pattern recognition receptors: Insights into molecular recognition of invading pathogens in Manduca sexta
|
2015-07
|
Xiaolong Cao Haobo Jiang
|
Xiufeng Zhang Yan He Ramesh T Gunaratna Yun-ru Chen Gary Blissard Michael R Kanost
|
Insect Biochemistry and Molecular Biology
|
Isoform-level brain expression profiling of the spermidine/spermine N1-Acetyltransferase1 (SAT1) gene in major depression and suicide
|
2015-07
|
Victoria Arango Peter L Nagy
|
Spiro P Pantazatos Stuart J Andrews Jane Dunning-Broadbent Jiuhong Pang Yung-Yu Huang J John Mann
|
Neurobiology of Disease
|
The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster
|
2015-07
|
Giada Ferrari Fergal M Waldron Jewelna Osei-Poku Elizabeth H Bayne Ben Longdon Amy H Buck Darren J. Obbard
|
Claire L Webster Shaun Robertson Daisy Crowson Juan F Quintana Jean-Michel Brouqui Brian P Lazzaro Penelope R Haddrill
|
PLOS Biology
|
Computational assignment of cell-cycle stage from single-cell transcriptome data.
|
2015-07-01
|
Sarah Teichmann Valentina Proserpio Kedar N Natarajan Antonio Scialdone Florian Buettner Luis R. Saraiva Oliver Stegle John C Marioni
|
|
Methods
|
The 3'-5' exoribonuclease Dis3 regulates the expression of specific microRNAs in Drosophila wing imaginal discs.
|
2015-07-01
|
Christopher Jones Sandra Cristina Viegas Cecília Maria Arraiano
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Benjamin P Towler Patricia Apura Joseph A Waldron Sarah K Smalley Sarah F Newbury
|
RNA Biology
|
Gene and miRNA expression changes in squamous cell carcinoma of larynx and hypopharynx.
|
2015-07-01
|
Prachi Jain
|
Jayalakshmi Nair Udita Chandola Vinayak Palve N R Harsha Vardhan Ram Bhupal Reddy Vikram D Kekatpure Amritha Suresh Moni Abraham Kuriakose Binay Panda
|
Genes & Cancer
|
Positional RNA-Seq identifies candidate genes for phenotypic engineering of sexual traits.
|
2015-07-03
|
Peter Ladurner Eugene Berezikov
|
Roberto Arbore Kiyono Sekii Christian Beisel Lukas Schärer
|
Frontiers in Zoology
|
Quantitative and functional interrogation of parent-of-origin allelic expression biases in the brain.
|
2015-07-03
|
Catherine Dulac
|
Julio D Perez Nimrod D Rubinstein Daniel E Fernandez Stephen W Santoro Leigh A Needleman Olivia Ho-Shing John J Choi Mariela Zirlinger Shau-Kwaun Chen Jun S Liu
|
eLife
|
"Pocket-sized RNA-Seq": A Method to Capture New Mature microRNA Produced from a Genomic Region of Interest.
|
2015-07-03
|
Florent Hube
|
Claire Francastel
|
Non-coding RNA
|
Age-Related Gene Expression Differences in Monocytes from Human Neonates, Young Adults, and Older Adults.
|
2015-07-06
|
Tobias Kollmann
|
Michelle M Lissner Brandon J Thomas Kathleen Wee Ann-Jay Tong Stephen T Smale
|
PLOS ONE
|
Transcriptomic Responses of the Heart and Brain to Anoxia in the Western Painted Turtle.
|
2015-07-06
|
Cyriac Kandoth
|
Sarah W Keenan Craig A Hill Leslie T Buck Daniel E Warren
|
PLOS ONE
|
Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans
|
2015-07-06
|
Denis Dupuy Eric Cornes J Cerón
|
Montserrat Porta-De-La-Riva David Aristizábal-Corrales Ana María Brokate-Llanos Francisco Javier García-Rodríguez Iris Ertl Mònica Díaz Laura Fontrodona Kadri Reis Robert Johnsen David Baillie Manuel J Muñoz Mihail Sarov
|
RNA
|
Transcriptomic profiling of gene expression and RNA processing during Leishmania major differentiation.
|
2015-07-06
|
Najib El-sayed
|
Laura A L Dillon Kwame Okrah V Keith Hughitt Rahul Suresh Yuan Li Maria Cecilia Fernandes A Trey Belew Hector Corrada Bravo David M Mosser
|
Nucleic Acids Research
|
Biphasic components of sarcomatoid clear cell renal cell carcinomas are molecularly similar to each other, but distinct from, non-sarcomatoid renal carcinomas
|
2015-07-07
|
Lalit Patel
|
Kanishka Sircar Suk-Young Yoo Tadeusz Majewski Khalida Wani Horatiu Voicu Wandaliz Torres-Garcia Roel G W Verhaak Nizar Tannir Jose A Karam Eric Jonasch Christopher G Wood Pheroze Tamboli Keith A Baggerly Kenneth D Aldape Bogdan Czerniak
|
The journal of pathology. Clinical research
|
Transcriptional landscape of trans-kingdom communication between Candida albicans and Streptococcus gordonii.
|
2015-07-07
|
Sophie Shaw Howard F. Jenkinson Angela H Nobbs
|
L C Dutton K H Paszkiewicz R J Silverman P R Splatt R J Lamont M Ramsdale
|
Molecular Oral Microbiology
|
Tungsten-induced carcinogenesis in human bronchial epithelial cells.
|
2015-07-08
|
Steven Shen Maria Antonietta Zoroddu Massimiliano Peana
|
Freda Laulicht Jason Brocato Laura Cartularo Joshua Vaughan Feng Wu Thomas Kluz Hong Sun Betul Akgol Oksuz Serenella Medici Max Costa
|
Toxicology and Applied Pharmacology
|
Impact of feed additives on surface mucosal health and columnaris susceptibility in channel catfish fingerlings, Ictalurus punctatus.
|
2015-07-08
|
Eric Peatman Wilawan Thongda
|
Honggang Zhao Chao Li Benjamin H Beck Ran Zhang Wilawan Thongda D Allen Davis
|
Fish and Shellfish Immunology
|
Revealing Missing Human Protein Isoforms Based on Ab Initio Prediction, RNA-seq and Proteomics
|
2015-07-09
|
Parvathy Venugopal Bergithe E Oftedal Zhiqiang Hu Chaochun Wei David L. Adelson Hamish S. Scott
|
Guangrong Qin Guangyong Zheng Xixia Chu Lu Xie Milena Babic Christopher N Hahn Bing Zhang Xiaojing Wang Nan Li
|
Scientific Reports
|
Evolutionary Divergence of Gene and Protein Expression in the Brains of Humans and Chimpanzees.
|
2015-07-10
|
Chet C. Sherwood
|
Amy L Bauernfeind Erik J Soderblom Meredith E Turner M Arthur Moseley John J Ely Patrick R Hof Gregory A Wray Courtney C Babbitt
|
Genome Biology and Evolution
|
Drosophila anti-nematode and antibacterial immune regulators revealed by RNA-Seq
|
2015-07-11
|
Upasana Shokal Julio Cesar Castillo Todd Creasy
|
Priti Kumari Amol Shetty Luke J Tallon Ioannis Eleftherianos
|
BMC Genomics
|
Differential and coherent processing patterns from small RNAs
|
2015-07-13
|
Jan Gorodkin Sachin Pundhir
|
|
Scientific Reports
|
Microbes & neurodevelopment--Absence of microbiota during early life increases activity-related transcriptional pathways in the amygdala.
|
2015-07-13
|
Roman Stilling Feargal J Ryan Marcus J Claesson Gerard Clarke Timothy G. Dinan John F. Cryan
|
Alan E Hoban Fergus Shanahan
|
Brain, Behavior, and Immunity
|
Opposing roles of STAT1 and STAT3 in IL-21 function in CD4+ T cells
|
2015-07-13
|
Majid Kazemian
|
Chi-Keung Wan Allison B Andraski Rosanne Spolski Peng Li Jangsuk Oh Leigh Samsel Phillip A Swanson Dorian B McGavern Elizabeth P Sampaio Alexandra F Freeman Joshua D Milner Steven M Holland Warren J Leonard
|
Proceedings of the National Academy of Sciences of the United States of America
|
Physiology and immunology of mucosal barriers in catfish (Ictalurus spp.)
|
2015-07-15
|
Eric Peatman
|
Miles Lange Honggang Zhao Benjamin H Beck
|
Tissue Barriers
|
Leveraging transcript quantification for fast computation of alternative splicing profiles.
|
2015-07-15
|
Eduardo Eyras
|
Gael P Alamancos Amadís Pagès Juan L Trincado Nicolás Bellora
|
RNA
|
Correction: De novo Transcriptome Analysis of Portunus trituberculatus Ovary and Testis by RNA-Seq: Identification of Genes Involved in Gonadal Development.
|
2015-07-15
|
PLOS ONE staff
|
|
PLOS ONE
|
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package
|
2015-07-16
|
María José Nueda Antonio Di Pietro
|
Sonia Tarazona Pedro Furió-Tarí David Turrà Alberto Ferrer Ana Conesa
|
Nucleic Acids Research
|
Widespread Inducible Transcription Downstream of Human Genes.
|
2015-07-16
|
Joan A. Steitz
|
Anna Vilborg Maria C Passarelli Therese A Yario Kazimierz T Tycowski
|
Molecular Cell
|
Expression of an estrogen-regulated variant transcript of the peroxisomal branched chain fatty acid oxidase ACOX2 in breast carcinomas
|
2015-07-17
|
Anne-Lise Børresen-Dale Surendra Kumar Vessela Kristensen Bjørn Naume
|
Sunniva Stordal Bjørklund Michael Seiler Grethe I Grenaker Alnæs Yao Ming John Kerrigan Ravi Sachidanandam Gyan Bhanot Shridar Ganesan
|
BMC Cancer
|
A nonlethal sampling method to obtain, generate and assemble whole blood transcriptomes from small, wild mammals.
|
2015-07-17
|
Emma C. Teeling Sébastien J. Puechmaille Michaël Bekaert
|
Zixia Huang Aurore Gallot Nga T Lao Nicole M Foley David Jebb
|
Molecular Ecology Resources
|
Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.
|
2015-07-17
|
Dragana Vuckovic Sally J. Dawson Giorgia Girotto Anne Viljanen Taina Rantanen Marina Ciullo Diego Vozzi Teresa Nutile Ginevra Biino Anu Loukola
|
Deborah I Scheffer Anna Morgan Mariateresa Di Stazio Maria P Concas Lisa Nolan Aileen Bahl Adrian Davis David P Corey Mario Pirastu Paolo Gasparini
|
Human Molecular Genetics
|
Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.
|
2015-07-17
|
David M. Irwin
|
Dong-Dong Wu Ling-Qun Ye Yan Li Yan-Bo Sun Yi Shao Chunyan Chen Zhu Zhu Li Zhong Lu Wang Yong E Zhang Ya-Ping Zhang
|
Journal of molecular cell biology
|
QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
|
2015-07-19
|
James C Mullikin
|
Stephen W Hartley
|
BMC Bioinformatics
|
How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets
|
2015-07-21
|
Shane G. Poplawski Lucia Peixoto Davide Risso Ted Abel
|
Mathieu E Wimmer Terence P Speed Marcelo A Wood
|
Nucleic Acids Research
|
Allelome.PRO, a pipeline to define allele-specific genomic features from high-throughput sequencing data.
|
2015-07-21
|
Tomasz Kuliński
|
Daniel Andergassen Christoph P Dotter Philipp M Guenzl Philipp C Bammer Denise P Barlow Florian M Pauler Quanah J Hudson
|
Nucleic Acids Research
|
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data.
|
2015-07-23
|
Mihaela Zavolan Andreas R Gruber Foivos Gypas Alexander Kanitz
|
Georges Martin
|
Genome Biology
|
Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment.
|
2015-07-23
|
Geoffrey J. Barton Gordon G Simpson Nicholas Schurch Christian Cole Tom Owen-Hughes Karim Gharbi Mark Blaxter
|
Marek Gierliński Pietà Schofield Alexander Sherstnev Vijender Singh Nicola Wrobel
|
Bioinformatics
|
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets.
|
2015-07-23
|
Oliver H Tam
|
Ying Jin Eric Paniagua Molly Hammell
|
Bioinformatics
|
TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer.
|
2015-07-24
|
Lingxiang Liu Jun Li Leng Han
|
Paul Roebuck Lixia Diao Yuan Yuan John N Weinstein Han Liang
|
Cancer Research
|
Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq.
|
2015-07-25
|
Per Qvist Anto P. Rajkumar Mette Nyegaard Ole Mors
|
Ross Lazarus Francesco Lescai Jia Ju Anders D Børglum Qibin Li Jane H Christensen
|
BMC Genomics
|
Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia.
|
2015-07-25
|
Alex Widmer Nicolas Blavet Niklaus Zemp Jos Käfer
|
H Blavet A Muyle R Cegan C Deschamps S Mousset S Aubourg R Bergero D Charlesworth R Hobza G A B Marais
|
BMC Genomics
|
Functional Networks of Highest-Connected Splice Isoforms: From The Chromosome 17 Human Proteome Project.
|
2015-07-28
|
Gil Omenn
|
Hong-Dong Li Rajasree Menon Brandon Govindarajoo Bharat Panwar Yang Zhang Yuanfang Guan
|
Journal of Proteome Research
|
Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription
|
2015-07-30
|
Siamon Gordon
|
Kaur Alasoo Fernando O Martinez Christine Hale Fiona Powrie Gordon Dougan Subhankar Mukhopadhyay Daniel J Gaffney
|
Scientific Reports
|
Transcriptome Dynamics of Developing Photoreceptors in Three-Dimensional Retina Cultures Recapitulates Temporal Sequence of Human Cone and Rod Differentiation Revealing Cell Surface Markers and Gene Networks
|
2015-07-31
|
Anand Swaroop Kohei Homma Jizhong Zou Matthew Brooks
|
Rossukon Kaewkhaw Koray Dogan Kaya Vijender Chaitankar Mahendra Rao
|
Stem Cells
|
DNA hypomethylation-mediated activation of Cancer/Testis Antigen 45 (CT45) genes is associated with disease progression and reduced survival in epithelial ovarian cancer.
|
2015-08-01
|
Kunle Odunsi
|
Wa Zhang Carter J Barger Petra A Link Paulette Mhawech-Fauceglia Austin Miller Stacey N Akers Adam R Karpf
|
Epigenetics
|
Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer
|
2015-08-03
|
Mathias Uhlén Linn Fagerberg William M Gallagher Karin Jirström
|
Gillian O'Hurley Christer Busch Björn M Hallström Charlotte Stadler Anna Tolf Emma Lundberg Jochen M Schwenk Anders Bjartell Fredrik Pontén
|
PLOS ONE
|
Similarities in Gene Expression Profiles during In Vitro Aging of Primary Human Embryonic Lung and Foreskin Fibroblasts.
|
2015-08-03
|
Peter Hemmerich Reinhard Guthke
|
Shiva Marthandan Steffen Priebe Mario Baumgart Marco Groth Alessandro Cellerino Stephan Diekmann
|
BioMed Research International
|
Dynamics of gene silencing during X inactivation using allele-specific RNA-seq.
|
2015-08-03
|
Tahsin Stefan Barakat Hendrik Marks Wouter de Laat Austin Smith
|
Hindrik H D Kerstens Erik Splinter René A M Dirks Guido van Mierlo Onkar Joshi Shuang-Yin Wang Tomas Babak Cornelis A Albers Tüzer Kalkan Alice Jouneau Joost Gribnau Hendrik G Stunnenberg
|
Genome Biology
|
RNA-seq reveals the critical role of OtpR in regulating Brucella melitensis metabolism and virulence under acidic stress.
|
2015-08-05
|
Yongqun He
|
Wenxiao Liu Hao Dong Jing Li Qixing Ou Yujin Lv Xiaolei Wang Zuoshuang Xiang Qingmin Wu
|
Scientific Reports
|
Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line.
|
2015-08-05
|
Carl J Schmidt
|
Liang Sun Susan J Lamont Amanda M Cooksey Fiona McCarthy Catalina O Tudor K Vijay-Shanker Rachael M DeRita Max Rothschild Chris Ashwell Michael E Persia
|
Cell Stress & Chaperones
|
RNASeq in C. elegans Following Manganese Exposure.
|
2015-08-06
|
Michael Aschner
|
Nancy L Parmalee Shahina B Maqbool Bin Ye Brent Calder Aaron B Bowman
|
Current protocols in toxicology / editorial board, Mahin D. Maines (editor-in-chief) ... [et al.]
|
Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer
|
2015-08-07
|
Majid Kazemian
|
Min Ren Jian-Xin Lin Wei Liao Rosanne Spolski Warren J Leonard
|
Molecular Systems Biology
|
An RNA-Seq-based reference transcriptome for Citrus.
|
2015-08-11
|
Terol J
|
Francisco Tadeo Daniel Ventimilla Manuel Talon
|
Plant Biotechnology Journal
|
ROTS: reproducible RNA-seq biomarker detector-prognostic markers for clear cell renal cell cancer.
|
2015-08-11
|
Laura L. Elo Panu M Jaakkola
|
Fatemeh Seyednasrollah Krista Rantanen
|
Nucleic Acids Research
|
Transcriptome profiling of larvae of the marine medaka Oryzias melastigma by Illumina RNA-seq.
|
2015-08-11
|
Jae-Seong Lee
|
Bo-Mi Kim Beom-Soon Choi Hui-Soo Kim Jae-Sung Rhee Doris W T Au Rudolf S S Wu Ik-Young Choi
|
Marine Genomics
|
Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics.
|
2015-08-12
|
Jun Fan Fawaz Ghali David A. Matthews Andrew Jones
|
Shyamasree Saha Gary Barker Kate J Heesom Conrad Bessant
|
Molecular & Cellular Proteomics
|
Host and non-host roots in rice: cellular and molecular approaches reveal differential responses to arbuscular mycorrhizal fungi.
|
2015-08-13
|
Paola Bonfante
|
Valentina Fiorilli Marta Vallino Chiara Biselli Antonella Faccio Paolo Bagnaresi
|
Frontiers in Plant Science
|
Comparative RNA-seq analysis of the Tritrichomonas foetus PIG30/1 isolate from pigs reveals close association with Tritrichomonas foetus BP-4 isolate 'bovine genotype'.
|
2015-08-14
|
Ana Conesa
|
Victoria Morin-Adeline Kai Mueller Jan Šlapeta
|
Veterinary Parasitology
|
The identification and characterization of novel transcripts from RNA-seq data.
|
2015-08-17
|
Stefanie Dimmeler Tyler Weirick Shizuka Uchida
|
Giuseppe Militello Raphael Müller David John
|
Briefings in Bioinformatics
|
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.
|
2015-08-18
|
Andrea Barta Yamile Marquez Maria Kalyna Geoffrey Michael Gadd
|
John W S Brown Craig G Simpson
|
The Plant Cell
|
The mRNA expression of soluble urokinase plasminogen activator surface receptor in human adipose tissue is positively correlated with body mass index.
|
2015-08-18
|
Kok Gan Chan
|
Hien Fuh Ng Kin Fah Chin Yun Fong Ngeow
|
Genome
|
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis.
|
2015-08-19
|
Guo-Li Ming Hongjun Song Daniel A Berg David Nauen
|
Jaehoon Shin Yunhua Zhu Joseph Y Shin Juan Song Michael A Bonaguidi Grigori Enikolopov Kimberly M Christian
|
Cell Stem Cell
|
Assembly and Analysis of Differential Transcriptome Responses of Hevea brasiliensis on Interaction with Microcyclus ulei.
|
2015-08-19
|
Ibonne Aydee García Romero Dolly Montoya Castaño Silvia Restrepo
|
Uriel Alonso Hurtado Páez Fabio Ancizar Aristizábal Gutiérrez
|
PLOS ONE
|
Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
|
2015-08-19
|
Dmitry A Ovchinnikov Deanne M. Taylor Ernst J. Wolvetang
|
Yu Hasegawa Laurence de Torrenté Jessica C Mar
|
PLOS Genetics
|
Genome-wide annotation of microRNA primary transcript structures reveals novel regulatory mechanisms
|
2015-08-19
|
Mihaela Pertea Steven Salzberg
|
Tsung-Cheng Chang Sungyul Lee Joshua T Mendell
|
Genome Research
|
Regulation of alternative splicing in Drosophila by 56 RNA binding proteins.
|
2015-08-20
|
Steven E. Brenner Brenton R. Graveley
|
Angela N Brooks Michael O Duff Gemma May Li Yang Mohan Bolisetty Jane Landolin Ken Wan Jeremy Sandler Benjamin W Booth Susan E Celniker
|
Genome Research
|
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.
|
2015-08-20
|
Tim Xiaoming Hu Ignacio del Valle Kay Elder Paul Robson
|
Paul Blakeley Norah M E Fogarty Sissy E Wamaitha Philip Snell Leila Christie Kathy K Niakan
|
Development
|
Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species.
|
2015-08-22
|
Jérôme Gouzy Pascal Gamas Corinne Da Silva
|
Susete Alves-Carvalho Grégoire Aubert Sébastien Carrère Corinne Cruaud Anne-Lise Brochot Françoise Jacquin Anthony Klein Chantal Martin Karen Boucherot Jonathan Kreplak Sandra Moreau Patrick Wincker Judith Burstin
|
The Plant Journal
|
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments
|
2015-08-24
|
Christina Kendziorski
|
Ning Leng Li-Fang Chu Chris Barry Yuan Li Jeea Choi Xiaomao Li Peng Jiang Ron M Stewart James A Thomson
|
Nature Methods
|
Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis.
|
2015-08-24
|
Po-Jung Huang Petrus Tang
|
Kuo-Yang Huang Fu-Man Ku Wei-Hung Cheng Chi-Ching Lee Lichieh Julie Chu Chih-Chieh Cheng Yi-Kai Fang Hsueh-Hsia Wu
|
Antimicrobial Agents and Chemotherapy
|
Time-Course RNA-Seq Analysis Reveals Transcriptional Changes in Rice Plants Triggered by Rice stripe virus Infection.
|
2015-08-25
|
Jin Kyo Jung
|
Won Kyong Cho Sen Lian Sang-Min Kim Bo Yoon Seo Kook-Hyung Kim
|
PLOS ONE
|
Identification of miRNAs in Bovine Endometrium through RNAseq and Prediction of Regulated Pathways.
|
2015-08-25
|
Soroush Sharbati
|
S E Palma-Vera R Einspanier
|
Reproduction in Domestic Animals
|
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.
|
2015-08-25
|
Karsten Suhre Anja M Billing Anna Halama
|
Pankaj Kumar Shahina Hayat Manish Gupta Noha A Yousri Gregory M Smith
|
BioMed Research International
|
Fast and accurate approximate inference of transcript expression from RNA-seq data.
|
2015-08-26
|
Antti Honkela
|
James Hensman Panagiotis Papastamoulis Peter Glaus Antti Honkela Magnus Rattray
|
Bioinformatics
|
Stimulation of Innate and Adaptive Immunity by Using Filamentous Bacteriophage fd Targeted to DEC-205
|
2015-08-26
|
Piergiuseppe De Berardinis
|
Luciana D'Apice Valerio Costa Rossella Sartorius Maria Trovato Marianna Aprile
|
Journal of Immunology Research
|
Altered Exosomal RNA Profiles in Bronchoalveolar Lavage from Lung Transplants with Acute Rejection
|
2015-08-26
|
Aric Gregson David Sayah
|
Aki Hoji Patil Injean Steven T Poynter Claudia Briones Vyacheslav Palchevskiy S Sam Weigt Michael Y Shino Ariss Derhovanessian Rajan Saggar David Ross Abbas Ardehali Joseph P Lynch John A Belperio
|
American Journal of Respiratory and Critical Care Medicine
|
Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy.
|
2015-08-26
|
Natalia Rodríguez-Muela Shi-Yan Ng Lee L Rubin John L. Rinn
|
Boon Seng Soh David G Hendrickson Feodor Price
|
Cell Stem Cell
|
RNAseq analysis of Aspergillus fumigatus in blood reveals a just wait and see resting stage behavior
|
2015-08-27
|
Ana Conesa Sven Krappmann Gerhard H Braus
|
Henriette Irmer Sonia Tarazona Christoph Sasse Patrick Olbermann Jürgen Loeffler
|
BMC Genomics
|
The coelomic epithelium transcriptome from a clonal sea star, Coscinasterias muricata.
|
2015-08-27
|
Josep F. Abril Pedro Martinez
|
Jonatan L Gabre Helen Nilsson Sköld Olga Ortega-Martinez
|
Marine Genomics
|
RNA-Seq analysis of urea nutrition responsive transcriptome of Oryza sativa elite indica cultivar RP Bio 226.
|
2015-08-28
|
K Ulaganathan
|
Mettu Madhavi Reddy
|
Genomics Data
|
Chromatin features, RNA polymerase II and the comparative expression of lens genes encoding crystallins, transcription factors, and autophagy mediators
|
2015-08-28
|
Deyou Zheng Ales Cvekl
|
Jian Sun Shira Rockowitz Daniel Chauss Ping Wang Marc Kantorow
|
Molecular Vision
|
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts
|
2015-09
|
Brett Trost Anthony Kusalik
|
Catherine A Moir Zoe E Gillespie Jennifer A Mitchell Christopher H Eskiw
|
Royal Society Open Science
|
Relationships within Cladobranchia (Gastropoda: Nudibranchia) based on RNA-Seq data: an initial investigation
|
2015-09
|
Jessica A Goodheart Allen Collins
|
Adam L Bazinet Michael P Cummings
|
Royal Society Open Science
|
Cullin4 Is Pro-Viral during West Nile Virus Infection of Culex Mosquitoes.
|
2015-09-01
|
Peter Walker Julio Rodriguez-Andres Jean-bernard Duchemin
|
Prasad N Paradkar Lee Trinidad
|
PLOS Pathogens
|
RNA-Seq analysis identifies key genes associated with haustorial development in the root hemiparasite Santalum album.
|
2015-09-01
|
Oliver Berkowitz James Whelan
|
Xinhua Zhang Jaime A Teixeira da Silva Muhan Zhang Guohua Ma Jun Duan
|
Frontiers in Plant Science
|
Integrated methylome and transcriptome analysis reveals novel regulatory elements in pediatric acute lymphoblastic leukemia.
|
2015-09-01
|
Kristen H Taylor Stephanie McKay
|
Md Almamun Benjamin T Levinson Annette C van Swaay Nathan T Johnson Gerald L Arthur J Wade Davis
|
Epigenetics
|
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
|
2015-09-02
|
Aviv Regev Rahul Satija Roi Avraham Alex K. Shalek
|
Nathan Haseley Douglas Brown Cristina Penaranda Humberto B Jijon John J Trombetta Ramnik J Xavier Deborah T Hung
|
Cell
|
RNAseq expression analysis of resistant and susceptible mice after influenza A virus infection identifies novel genes associated with virus replication and important for host resistance to infection
|
2015-09-02
|
Claudia Pommerenke
|
Esther Wilk Ashutosh K Pandey Sarah Rebecca Leist Bastian Hatesuer Matthias Preusse Junxi Wang Klaus Schughart
|
BMC Genomics
|
Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms.
|
2015-09-02
|
Wolfgang Sadee
|
Roshan Mascarenhas Maciej Pietrzak Ryan M Smith Amy Webb Danxin Wang Audrey C Papp Julia K Pinsonneault Michal Seweryn Grzegorz Rempala
|
PLOS ONE
|
Cell type-specific transcriptomics of hypothalamic energy-sensing neuron responses to weight-loss
|
2015-09-02
|
Scott M Sternson Henry FE Ken Sugino Tozer A Branco T
|
|
eLife
|
HiCdat: a fast and easy-to-use Hi-C data analysis tool.
|
2015-09-03
|
Ueli Grossniklaus Stefan Grob Marc W Schmid
|
|
BMC Bioinformatics
|
Benchmark analysis of algorithms for determining and quantifying full-length mRNA splice forms from RNA-seq data
|
2015-09-03
|
Katharina E. Hayer Gregory R Grant
|
Angel Pizarro Nicholas F Lahens John B Hogenesch
|
Bioinformatics
|
Errors in RNA-Seq quantification affect genes of relevance to human disease.
|
2015-09-03
|
Mick Watson
|
Christelle Robert
|
Genome Biology
|
Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer.
|
2015-09-03
|
Namshin Kim
|
Byungkuk Min Sunwha Cho Jung Sun Park Yun-Gyeong Lee Yong-Kook Kang
|
G3
|
Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline
|
2015-09-04
|
Frank Emmert-Streib
|
Yasir Rahmatallah Galina Glazko
|
Briefings in Bioinformatics
|
Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors.
|
2015-09-04
|
Jun-Jun Liu
|
Rona N Sturrock Richard A Sniezko Holly Williams Ross Benton Arezoo Zamany
|
BMC Genomics
|
Function and Regulation of Cph2 in Candida albicans.
|
2015-09-04
|
Pierre Baldi
|
Shelley Lane Pietro Di Lena Kati Tormanen Haoping Liu
|
Eukaryotic Cell
|
RNA-seq analysis of the whole transcriptome of MDA-MB-231 mammary carcinoma cells exposed to the antimetastatic drug NAMI-A.
|
2015-09-04
|
Alberto Pallavicini
|
Alberta Bergamo Marco Gerdol Marianna Lucafò Chiara Pelillo Marilena Battaglia Gianni Sava
|
Metallomics
|
Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.
|
2015-09-08
|
Michael R. Barnes
|
Zhilong Jia Xiang Zhang Naiyang Guan Xiaochen Bo Zhigang Luo
|
PLOS ONE
|
Systematic identification of factors for provirus silencing in embryonic stem cells
|
2015-09-09
|
George Q. Daley Chadi A El Farran Yinghui Li Matthew C. Lorincz
|
Bin Xia Yang Hong Chao Guo Tao Yu Hai Tong Fang Hao Fei Wang Sharon Schlesinger Yu Fen Samantha Seah Germaine Yen Lin Goh Suat Peng Neo Vinay Tergaonkar Tit-Meng Lim Lingyi Chen Jayantha Gunaratne James J Collins Stephen P Goff Hu Li Frederic A Bard Yuin-Han Loh
|
Cell
|
Molecular analyses of juvenile granulosa cell tumors bearing AKT1 mutations provide insights into tumor biology and therapeutic leads.
|
2015-09-11
|
Aurélie Auguste S Caburet Sabine Sarnacki
|
Laurianne Bessière Anne-Laure Todeschini Jaime Prat Emanuela D'angelo Pierre De La Grange Olivier Ariste Fréderic Lemoine Bérangère Legois Charles Sultan Alain Zider Louise Galmiche Nicolas Kalfa Reiner A Veitia
|
Human Molecular Genetics
|
Genome-wide RNA sequencing analysis of quorum sensing-controlled regulons in the plant-associated Burkholderia glumae PG1 strain.
|
2015-09-11
|
Andreas Knapp Rolf Daniel
|
Rong Gao Dagmar Krysciak Katrin Petersen Christian Utpatel Christel Schmeisser Sonja Voget Karl-Erich Jaeger Wolfgang R Streit
|
Applied and Environmental Microbiology
|
The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4(+) T-cells.
|
2015-09-11
|
Vanessa A Evans David Powell Sharon R. Lewin
|
Nitasha A Kumar Karey Cheong Candida da Fonseca Pereira Jenny Anderson Paul U Cameron
|
Retrovirology
|
The reverse transcription signature of N-1-methyladenosine in RNA-Seq is sequence dependent
|
2015-09-13
|
Andreas Hildebrandt Marie-Luise Winz Sunny Sharma Yuri Motorin Mark Helm
|
Ralf Hauenschild Lyudmil Tserovski Katharina Schmid Kathrin Thüring Karl-Dieter Entian Ludivine Wacheul Denis L J Lafontaine James Anderson Juan Alfonzo Andres Jäschke
|
Nucleic Acids Research
|
Ancient gene duplications have shaped developmental stage-specific expression in Pristionchus pacificus.
|
2015-09-15
|
Christian Rödelsperger P Baskaran Gabriel V. Markov
|
Christian Rödelsperger Neel Prabh Vahan Serobyan Antje Hirsekorn Christoph Dieterich
|
BMC Evolutionary Biology
|
Identification of candidate gonadal sex differentiation genes in the chicken embryo using RNA-seq
|
2015-09-16
|
Alicia Oshlack Nadia M Davidson Craig A. Smith Andrew H Sinclair
|
Katie L Ayers Luke S Lambeth
|
BMC Genomics
|
RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH
|
2015-09-16
|
Jens Nielsen Verena Siewers SungSoo Kim
|
Eugene Fletcher Amir Feizi
|
Microbial Cell Factories
|
A novel workflow correlating RNA-seq data to Phythophthora infestans resistance levels in wild Solanum species and potato clones.
|
2015-09-17
|
Estelle Proux-Wéra Erik Andreasson
|
Itziar Frades Kibrom B Abreha Åsa Lankinen Erik Alexandersson
|
Frontiers in Plant Science
|
Tools and best practices for data processing in allelic expression analysis.
|
2015-09-17
|
Tuuli Lappalainen Pejman Mohammadi
|
Stephane E Castel Ami Levy-Moonshine Eric Banks
|
Genome Biology
|
RNA-seq analyses of changes in the Anopheles gambiae transcriptome associated with resistance to pyrethroids in Kenya: identification of candidate-resistance genes and candidate-resistance SNPs.
|
2015-09-17
|
Eric Ochomo Mariangela Bonnizoni Guiyun Yan
|
William Augustine Dunn Monica Britton Yaw Afrane Guofa Zhou Joshua Hartsel Ming-Chieh Lee Jiabao Xu Andrew Githeko Joseph Fass
|
Parasites & Vectors
|
Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea
|
2015-09-17
|
Cassandra G. Extavour
|
Carrie A Whittle
|
G3
|
RNAseq Analysis Highlights Specific Transcriptome Signatures of Yeast and Mycelial Growth Phases in the Dutch Elm Disease Fungus Ophiostoma novo-ulmi.
|
2015-09-17
|
Louis Bernier
|
Martha Nigg Jérôme Laroche Christian R Landry
|
G3
|
In vivo Monitoring of Transcriptional Dynamics After Lower-Limb Muscle Injury Enables Quantitative Classification of Healing
|
2015-09-18
|
Alexander Meissner
|
Carlos A Aguilar Anna Shcherbina Darrell O Ricke Ramona Pop Christopher T Carrigan Casey A Gifford Maria L Urso Melissa A Kottke
|
Scientific Reports
|
Early transcriptional events linked to induction of diapause revealed by RNAseq in larvae of drosophilid fly, Chymomyza costata.
|
2015-09-21
|
Jan Provazník Konrad Schöttner Rodolphe Poupardin
|
Jaroslava Korbelová David Doležel Dinko Pavlinic Vladimír Beneš Vladimír Koštál
|
BMC Genomics
|
Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.
|
2015-09-21
|
Sarah Teichmann Aleksandra A Kolodziejczyk Florian Buettner
|
Jason C H Tsang Yong Yu Shannon Burke Cui Wang Liming Lu Pentao Liu
|
Genome Biology
|
Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome.
|
2015-09-22
|
Andrey Ptitsyn
|
Ramzi Temanni Christelle Bouchard Peter A V Anderson
|
PLOS ONE
|
Dynamic transcriptional symmetry-breaking in pre-implantation mammalian embryo development revealed by single-cell RNA-seq.
|
2015-09-22
|
Qi Chen
|
Junchao Shi Xin Li Xiudeng Zheng Ying Zhang Jie Qiao Fuchou Tang Yi Tao Qi Zhou Enkui Duan
|
Development
|
Transcriptome Profiling of Pediatric Core Binding Factor AML.
|
2015-09-23
|
George Komatsoulis
|
Chih-Hao Hsu Cu Nguyen Chunhua Yan Rhonda E Ries Qing-Rong Chen Ying Hu Fabiana Ostronoff Derek L Stirewalt George Komatsoulis Shawn Levy Daoud Meerzaman Soheil Meshinchi
|
PLOS ONE
|
Gene expression changes in the salivary glands of Anopheles coluzzii elicited by Plasmodium berghei infection
|
2015-09-23
|
Luis Pedro Coelho Ana Domingos Alejandro Cabezas-Cruz
|
Renato Pinheiro-Silva Lara Borges James J Valdés Virgílio do Rosário José de la Fuente
|
Parasites & Vectors
|
Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.
|
2015-09-23
|
Soraya Seedat
|
Stefanie Malan-Müller Lorren Fairbairn Willie M U Daniels Mahjoubeh Jalali Sefid Dashti Edward J Oakeley Marc Altorfer Martin Kidd Junaid Gamieldien Sîan Megan Joanna Hemmings
|
Metabolic Brain Disease
|
RNA-Seq in Mytilus galloprovincialis: comparative transcriptomics and expression profiles among different tissues.
|
2015-09-24
|
David Posada Rebeca Moreira Carlos Canchaya
|
Patricia Pereiro Antonio Figueras Beatriz Novoa
|
BMC Genomics
|
Whose Gene Is It Anyway? The Effect of Preparation Purity on Neutrophil Transcriptome Studies
|
2015-09-24
|
Helen L Wright
|
Huw B Thomas Robert J Moots Steven W Edwards
|
PLOS ONE
|
Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.).
|
2015-09-25
|
RANJEET RANJAN KUMAR Viswanathan Chinnusamy
|
Suneha Goswami Sushil K Sharma Yugal K Kala Gyanendra K Rai Dwijesh C Mishra Monendra Grover Gyanendra P Singh Himanshu Pathak Anil Rai Raj D Rai
|
OMICS: A Journal of Integrative Biology
|
Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica).
|
2015-09-29
|
Heebal Kim
|
Kelsey Caetano-Anolles Minseok Seo Sandra Rodriguez-Zas Jae-Don Oh Jae Yong Han Kichoon Lee Tae Sub Park Sangsu Shin Zhang Jiao Jiao Mrinmoy Ghosh Dong Kee Jeong Seoae Cho Ki-Duk Song Hak-Kyo Lee
|
PLOS ONE
|
De novo transcriptome profiling of highly purified human lymphocytes primary cells
|
2015-09-29
|
Sergio Abrignani Massimiliano Pagani Grazisa Rossetti Ilaria Panzeri
|
Raoul J P Bonnal Valeria Ranzani Alberto Arrigoni Serena Curti Paola Gruarin
|
Scientific Data
|
Transcriptome Characteristics and X-Chromosome Inactivation Status in Cultured Rat Pluripotent Stem Cells.
|
2015-09-29
|
Irina S. Zakharova Sergey P Medvedev Fedor Kolpakov Suren M Zakian Alexander Karaskov
|
Evgeniya A Vaskova Anastasiya E Sorokina Artem A Nemudryy Evgeniy A Elisaphenko Alexander I Shevchenko Elena A Kizilova Antonina I Zhelezova Ivan S Evshin Ruslan N Sharipov Julia M Minina Natalia S Zhdanova Igor I Khegay Gennadiy T Sukhikh Evgeniy A Pokushalov Valentin V Vlasov Ludmila N Ivanova
|
Stem Cells and Development
|
Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification.
|
2015-10-01
|
Edward R. Dougherty
|
Jason Knight Ivan Ivanov Karen Triff Robert Chapkin
|
IEEE/ACM Transactions on Computational Biology and Bioinformatics
|
Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript.
|
2015-10-01
|
Tõnu Esko Carla Giner-Delgado Marta Puig Magdalena Gayà-Vidal David Castellano
|
Lorena Pantano David Izquierdo José Ignacio Lucas-Lledó Chikashi Terao Fumihiko Matsuda Mario Cáceres
|
PLOS Genetics
|
SRSF1-Regulated Alternative Splicing in Breast Cancer
|
2015-10-01
|
Frédéric H-T Allain Adrian Robert Krainer Antoine Cléry
|
Olga Anczuków Martin Akerman Jie Wu Chen Shen Nitin H Shirole Amanda Raimer Shuying Sun Mads A Jensen Yimin Hua
|
Molecular Cell
|
Prdm12 specifies V1 interneurons through cross-repressive interactions with Dbx1 and Nkx6 genes in Xenopus.
|
2015-10-01
|
Carine Van Lint Benoît Van Driessche Julie Hanotel Ian Quigley Aurore Thelie Alessandra Pierani Michael Schubert
|
Simon Desiderio Benoit Van Driessche Anthony Rodari Mark D Borromeo Sadia Kricha François Lahaye Jenifer Croce Gustavo Cerda-Moya Jesús Ordoño Fernandez Barbara Bolle Katharine E Lewis Maike Sander Jane E Johnson Christopher R Kintner Tomas Pieler Kristine A Henningfeld Eric J Bellefroid Claude Van Campenhout
|
Development
|
Different exercise modalities have distinct effects on the integrin-linked kinase (ILK) and Ca2+ signaling pathways in the male rat bone.
|
2015-10-01
|
Dharani M Sontam Peter Tsai
|
Elwyn C Firth Mark H Vickers Justin M O'Sullivan
|
Physiological Reports
|
Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells.
|
2015-10-01
|
Aviv Regev Itay Tirosh
|
Monika S Kowalczyk Itay Tirosh Dirk Heckl Tata Nageswara Rao Atray Dixit Brian J Haas Rebekka K Schneider Amy J Wagers Benjamin L Ebert
|
Genome Research
|
Complete hematologic response of early T-cell progenitor acute lymphoblastic leukemia to the γ-secretase inhibitor BMS-906024: genetic and epigenetic findings in an outlier case.
|
2015-10-01
|
Matthew Meyerson Andrew L. Kung
|
Birgit Knoechel Ami Bhatt Li Pan Chandra S Pedamallu Eric Severson Alejandro Gutierrez David M Dorfman Frank C Kuo Michael Kluk Patrick Zweidler-McKay Stephen C Blacklow Daniel J DeAngelo Jon C Aster
|
Cold Spring Harbor molecular case studies
|
Dynamic expression of long noncoding RNAs and repeat elements in synaptic plasticity.
|
2015-10-01
|
Marcel E. Dinger
|
Jesper L V Maag Debabrata Panja Ida Sporild Sudarshan Patil Dominik C Kaczorowski Clive R Bramham Karin Wibrand
|
Frontiers in Neuroscience
|
BrowserGenome.org: web-based RNA-seq data analysis and visualization.
|
2015-10-01
|
Jonathan Schmid-Burgk Veit Hornung
|
|
Nature Methods
|
Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.
|
2015-10-01
|
Tim Xiaoming Hu
|
Paul Blakeley Norah M E Fogarty Ignacio Del Valle Sissy E Wamaitha Kay Elder Philip Snell Leila Christie Paul Robson Kathy K Niakan
|
Development
|
Functional development of the adult ovine mammary gland--insights from gene expression profiling.
|
2015-10-05
|
Amy M Paten Sam W Peterson Elizabeth J. Duncan Peter Dearden
|
Sarah J Pain Paul R Kenyon Hugh T Blair
|
BMC Genomics
|
Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.
|
2015-10-05
|
Norbert Perrimon
|
Mary-Lee Dequéant Delphine Fagegaltier Yanhui Hu Kerstin Spirohn Amanda Simcox Gregory J Hannon
|
Proceedings of the National Academy of Sciences of the United States of America
|
RNA-Seq analysis for indigo biosynthesis pathway genes in Indigofera tinctoria and Polygonum tinctorium.
|
2015-10-05
|
Sanjog T Thul
|
Bijaya K Sarangi Yoshiko Minami
|
Genomics Data
|
Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context.
|
2015-10-05
|
Spencer Diamond
|
Ryan K Shultzaberger Joseph S Boyd Ralph J Greenspan Susan S Golden
|
Annual Review of Genetics
|
Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes.
|
2015-10-05
|
Dan Nettleton
|
Andrew Lithio
|
Journal of Agricultural, Biological, and Environmental Statistics
|
Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues.
|
2015-10-05
|
Susan Fanayan Ling Yen Lee
|
Julia Fangfei Yan Hoguen Kim Seul-Ki Jeong Hyoung-Joo Lee Manveen K Sethi Ronald C Beavis Hogune Im Michael P Snyder Matan Hofree Trey Ideker Shiaw-Lin Wu Young-Ki Paik William S Hancock
|
Journal of Proteome Research
|
Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons.
|
2015-10-05
|
Samuel J Allon
|
Brian S Cole Iulia Tapescu Michael J Mallory Jinsong Qiu Robert J Lake Hua-Ying Fan Xiang-Dong Fu Kristen W Lynch
|
RNA
|
Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).
|
2015-10-06
|
Matthias Heinig
|
Sebastian Schafer Kui Miao Craig C Benson Stuart A Cook Norbert Hubner
|
Current protocols in human genetics / editorial board, Nicholas C, Dracapoli ... [et al.]
|
Transition from somatic embryo to friable embryogenic callus in cassava: dynamic changes in cellular structure, physiological status, and gene expression profiles.
|
2015-10-06
|
Peng Zhang
|
Qiuxiang Ma Wenzhi Zhou
|
Frontiers in Plant Science
|
Chromatin-Remodelling Complex NURF Is Essential for Differentiation of Adult Melanocyte Stem Cells.
|
2015-10-06
|
Dana Koludrovic Gabrielle Mengus Irwin Davidson
|
Patrick Laurette Thomas Strub Céline Keime Madeleine Le Coz Sebastien Coassolo Lionel Larue
|
PLOS Genetics
|
Model of fibrolamellar hepatocellular carcinomas reveals striking enrichment in cancer stem cells
|
2015-10-06
|
Vincenzo Cardinale Guido Carpino Domenico Alvaro
|
Tsunekazu Oikawa Eliane Wauthier Timothy A Dinh Sara R Selitsky Andrea Reyna-Neyra Ronald Levine David Klimstra Eugenio Gaudio Nancy Carrasco Praveen Sethupathy Lola M Reid
|
Nature Communications
|
Identification of functional networks associated with cell death in the retina of OXYS rats during the development of retinopathy.
|
2015-10-06
|
Oyuna S. Kozhevnikova
|
Darya V Telegina Elena E Korbolina Nikita I Ershov Nataliya G Kolosova
|
Cell Cycle
|
A Semi-parametric Bayesian Approach for Differential Expression Analysis of RNA-seq Data.
|
2015-10-07
|
Chong Wang
|
Fangfang Liu Peng Liu
|
Journal of Agricultural, Biological, and Environmental Statistics
|
RNA-Seq Analysis of Abdominal Fat in Genetically Fat and Lean Chickens Highlights a Divergence in Expression of Genes Controlling Adiposity, Hemostasis, and Lipid Metabolism
|
2015-10-07
|
Chuming Chen Larry A. Cogburn Michel J Duclos
|
Christopher W Resnyk Hongzhan Huang Cathy H Wu Jean Simon Elisabeth Le Bihan-Duval
|
PLOS ONE
|
The androgen receptor controls expression of the cancer-associated sTn antigen and cell adhesion through induction of ST6GalNAc1 in prostate cancer.
|
2015-10-07
|
Daniel Vodák David J Elliott Hing Y Leung Rolf Inge Skotheim
|
Jennifer Munkley Sebastian Oltean Brian T Wilson Karen E Livermore Yan Zhou Eleanor Star Vasileios I Floros Bjarne Johannessen Bridget Knight Paul McCullagh John McGrath Malcolm Crundwell Craig N Robson Lorna W Harries Prabhakar Rajan Ian G Mills
|
Oncotarget
|
The membrane proteome of male gametophyte in Solanum lycopersicum.
|
2015-10-08
|
Enrico Schleiff Arindam Ghatak Palak Chaturvedi Wolfram Weckwerth
|
Puneet Paul Mario Selymesi Anida Mesihovic Klaus-Dieter Scharf Stefan Simm
|
Journal of Proteomics
|
B-Cell and Monocyte Contribution to Systemic Lupus Erythematosus Identified by Cell-Type-Specific Differential Expression Analysis in RNA-Seq Data.
|
2015-10-08
|
Joel M Guthridge Judith A. James
|
Mikhail G Dozmorov Nicolas Dominguez Krista Bean Susan R Macwana Virginia Roberts Edmund Glass
|
Bioinformatics and Biology Insights
|
Profiling RNA editing in human tissues: towards the inosinome Atlas
|
2015-10-09
|
Graziano Pesole Anna Maria D'Erchia Ernesto Picardi
|
Caterina Manzari Francesca Mastropasqua Italia Aiello
|
Scientific Reports
|
Molecular genetic response to varied wavelengths of light in Xiphophorus maculatus skin
|
2015-10-09
|
Jordan Chang
|
Yuan Lu William T Boswell Mikki Boswell Kaela L Caballero Ronald B Walter
|
Comparative Biochemistry and Physiology C: Toxicology and Pharmacology
|
Novel RNA variants in colorectal cancers.
|
2015-10-12
|
Andreas M Hoff Torfinn Nome Ragnhild A. Lothe Rolf Inge Skotheim
|
Bjarne Johannessen Sharmini Alagaratnam Sen Zhao Marthe Løvf Anne C Bakken Merete Hektoen Anita Sveen
|
Oncotarget
|
A basal stem cell signature identifies aggressive prostate cancer phenotypes.
|
2015-10-12
|
Robert Baertsch
|
Bryan A Smith Artem Sokolov Vladislav Uzunangelov Yulia Newton Kiley Graim Colleen Mathis Donghui Cheng Joshua M Stuart Owen N Witte
|
Proceedings of the National Academy of Sciences of the United States of America
|
Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.
|
2015-10-12
|
David J Waxman
|
Tisha Melia Pengying Hao Feyza Yilmaz
|
Molecular and Cellular Biology
|
RNA-Seq mediated root transcriptome analysis of Chlorophytum borivilianum for identification of genes involved in saponin biosynthesis.
|
2015-10-12
|
Avneesh Kumar Jagdeep Kaur
|
Sunil Kumar Shikha Kalra Baljinder Singh Kashmir Singh
|
Functional and Integrative Genomics
|
RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library.
|
2015-10-12
|
Brian D Lehmann David C Samuels
|
Yan Guo Shilin Zhao Quanhu Sheng Mingsheng Guo Jennifer Pietenpol Yu Shyr
|
BioMed Research International
|
Assessing Transcription Regulatory Elements To Evaluate the Expression Status of Missing Protein Genes on Chromosomes 11 and 19.
|
2015-10-12
|
Zhe Ren Shaohang Xu
|
Nannan Kong Yang Zhou Yamei Deng Yang Fan Yue Zhang Liang Lin Yan Ren Quanhui Wang Jin Zi Bo Wen Siqi Liu
|
Journal of Proteome Research
|
FOXM1 cistrome predicts breast cancer metastatic outcome better than FOXM1 expression levels or tumor proliferation index.
|
2015-10-12
|
Charles J Vaske Stephen Benz
|
Christina Yau Laurence Meyer Gary Scott Brian Egan Paul Labhart Nader Pourmand Christopher C Benz
|
Breast Cancer Research and Treatment
|
Spatially distinct neutrophil responses within the inflammatory lesions of pneumonic plague
|
2015-10-13
|
Nikolas M Stasulli William E. Goldman
|
Kara R Eichelberger Paul A Price Roger D Pechous Stephanie A Montgomery Joel S Parker
|
mBio
|
Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit
|
2015-10-13
|
Waqas Ahmed Malik Dan Nettleton Hans-Peter Piepho
|
Nina Opitz Caroline Marcon Anja Paschold Andrew Lithio Ronny Brandt Frank Hochholdinger
|
Journal of Experimental Botany
|
Computational analysis of stochastic heterogeneity in PCR amplification efficiency revealed by single molecule barcoding.
|
2015-10-13
|
James M Heather Benny Chain
|
Katharine Best Theres Oakes John Shawe-Taylor
|
Scientific Reports
|
Dynamic association rules for gene expression data analysis
|
2015-10-14
|
Wen-Hsiung Li
|
Shu-Chuan Chen Tsung-Hsien Tsai Cheng-Han Chung
|
BMC Genomics
|
Insights into the role of immunosenescence during varicella zoster virus infection (shingles) in the aging cell model
|
2015-10-14
|
Mukesh Kumar
|
Ji-Ae Kim Seul-Ki Park Chan-Hee Lee Ok Sarah Shin
|
Oncotarget
|
Accelerating Discovery and Functional Analysis of Small RNAs with New Technologies.
|
2015-10-14
|
Jörg Vogel Lars Barquist
|
|
Annual Review of Genetics
|
RNA-Seq workflow: gene-level exploratory analysis and differential expression.
|
2015-10-14
|
Simon Anders Wolfgang Huber Michael I Love
|
Vladislav Kim
|
F1000Research
|
Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.
|
2015-10-16
|
Peter Redder Julien Prados
|
Vanessa Khemici Patrick Linder
|
PLOS Genetics
|
Genome-wide analysis on Chlamydomonas reinhardtii reveals the impact of hydrogen peroxide on protein stress responses and overlap with other stress transcriptomes.
|
2015-10-16
|
Sabeeha Merchant Stefan Schmollinger María Esther Pérez-Pérez Crysten E Blaby-Haas Stéphane D Lemaire
|
Ian K Blaby Sorel Fitz-Gibbon
|
The Plant Journal
|
Effect of heparin on the biological properties and molecular signature of human mesenchymal stem cells
|
2015-10-17
|
Rebekah M Samsonraj Drew M Titmarsh Emily T Camilleri
|
Ling Ling Torben Helledie Ren Jie Chua Oliver Dreesen Christian Dombrowski David A Rider Mario Galindo Ian Lee Wanjin Hong James H Hui Victor Nurcombe Andre J van Wijnen Simon M Cool
|
Gene
|
CRISPR/Cas9-mediated heterozygous knockout of the autism gene CHD8 and characterization of its transcriptional networks in neurodevelopment.
|
2015-10-19
|
Deyou Zheng
|
Ping Wang Mingyan Lin Erika Pedrosa Anastasia Hrabovsky Zheng Zhang Wenjun Guo Herbert M Lachman
|
Molecular Autism
|
Elucidating drivers of oral epithelial dysplasia formation and malignant transformation to cancer using RNAseq.
|
2015-10-19
|
Jennifer L Graham Rebecca Chalkley Alastair Droop
|
Caroline Conway Preetha Chengot Catherine Daly Lisa Ross Pamela Rabbitts Lucy F Stead
|
Oncotarget
|
Functional analysis of NtMPK2 uncovers its positive role in response to Pseudomonas syringae pv. tomato DC3000 in tobacco.
|
2015-10-19
|
Qingyou Xia
|
Xingtan Zhang Genhong Wang Junping Gao Mengyun Nie Wenshan Liu
|
Plant Molecular Biology
|
Identification of a novel fusion transcript between human relaxin-1 (RLN1) and human relaxin-2 (RLN2) in prostate cancer.
|
2015-10-20
|
Sean D McGrath Marcel E. Dinger Elizabeth D. Williams Gregor Tevz Jyotsna Batra
|
Ryan Demeter Vincent Magrini Varinder Jeet Anja Rockstroh Stephen McPherson John Lai Nenad Bartonicek Jiyuan An Melanie L Lehman Colleen C Nelson
|
Molecular and Cellular Endocrinology
|
Comparative RNA seq analysis of the New Zealand glowworm Arachnocampa luminosa reveals bioluminescence-related genes.
|
2015-10-21
|
Peter Dearden
|
Miriam L Sharpe Gregory Gimenez Kurt L Krause
|
BMC Genomics
|
Modeling of autosomal-dominant retinitis pigmentosa in Caenorhabditis elegans uncovers a nexus between global impaired functioning of certain splicing factors and cell type-specific apoptosis.
|
2015-10-21
|
Karinna Rubio-Peña Sylvain Foissac Eric Cornes J Cerón
|
Laura Fontrodona David Aristizábal-Corrales Silvia Torres Francisco J García-Rodríguez Xènia Serrat David González-Knowles Montserrat Porta-De-La-Riva
|
RNA
|
The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.
|
2015-10-21
|
Linn Fagerberg Mathias Uhlén
|
Agata Zieba Evelina Sjöstedt Matts Olovsson Björn M Hallström Linda Oskarsson Karolina Edlund Anna Tolf Fredrik Ponten
|
OMICS: A Journal of Integrative Biology
|
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
|
2015-10-22
|
Aleksandra A Kolodziejczyk John C Marioni Sarah Teichmann Jong Kyoung Kim
|
Tomislav Ilicic
|
Nature Communications
|
A Diencephalic Dopamine Source Provides Input to the Superior Colliculus, where D1 and D2 Receptors Segregate to Distinct Functional Zones.
|
2015-10-22
|
Martha Constantine-Paton Rory Kirchner Yasunobu Murata Sung-Yon Kim
|
Andrew D Bolton Andrew Young Tru Dang Yuchio Yanagawa
|
Cell Reports
|
HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse.
|
2015-10-23
|
Jeffrey R Mann David L. Adelson Lee H Wong Hamish S. Scott Moira O'bryan
|
Shu Ly Lim Zhi Peng Qu R Daniel Kortschak David M Lawrence Joel Geoghegan Anna-Lena Hempfling Martin Bergmann Christopher C Goodnow Christopher J Ormandy Duangporn Jamsai
|
PLOS Genetics
|
Menadione-Induced Oxidative Stress Re-Shapes the Oxylipin Profile of Aspergillus flavus and Its Lifestyle.
|
2015-10-23
|
Walter Sanseverino
|
Marco Zaccaria Matteo Ludovici Simona Marianna Sanzani Antonio Ippolito Riccardo Aiese Cigliano Marzia Scarpari Valeria Scala Corrado Fanelli Massimo Reverberi
|
Toxins
|
Circularization restores signal recognition particle RNA functionality in Thermoproteus
|
2015-10-24
|
L Randau
|
André Plagens Michael Daume Julia Wiegel
|
eLife
|
Mapping 3' transcript ends in the bank vole (Clethrionomys glareolus) mitochondrial genome with RNA-Seq.
|
2015-10-26
|
Petr Kotlík
|
Silvia Marková Karolína Filipi Jeremy B Searle
|
BMC Genomics
|
IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival.
|
2015-10-26
|
Phillip Dexheimer
|
Allie K Adams Lyndsey C Bolanos Rebekah A Karns Bruce J Aronow Kakajan Komurov Anil G Jegga Keith A Casper Yash J Patil Keith M Wilson Daniel T Starczynowski Susanne I Wells
|
Oncotarget
|
Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue.
|
2015-10-27
|
Hao Zhang
|
Zhixiu Wang Qinggang Li Yangzom Chamba Bo Zhang Peng Shang Changxin Wu
|
PLOS ONE
|
A Database of microRNA Expression Patterns in Xenopus laevis
|
2015-10-27
|
Sara Lopez-Gomollon Simon Moxon Tamas Dalmay
|
Ayisha Ahmed Nicole J Ward Camille Viaut Matthew L Tomlinson Ilya Patrushev Michael J Gilchrist Dario Dotlic Andrea E Münsterberg Grant N Wheeler
|
PLOS ONE
|
RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics.
|
2015-10-27
|
Bauke Ylstra Pieter Wesseling Jan Koster
|
Myron G Best Nik Sol Irsan Kooi Jihane Tannous Bart A Westerman François Rustenburg Pepijn Schellen Heleen Verschueren Edward Post Najim Ameziane Josephine Dorsman Egbert F Smit Henk M Verheul David P Noske Jaap C Reijneveld R Jonas A Nilsson Bakhos A Tannous Thomas Wurdinger
|
Cancer Cell
|
Transcriptomic Changes in Coral Holobionts Provide Insights into Physiological Challenges of Future Climate and Ocean Change.
|
2015-10-28
|
Nedeljka N. Rosic David I Kline Chon-Kit Kenneth Chan Sophie Dove David Edwards Ove Hoegh-Guldberg
|
Paulina Kaniewska Edmund Yew Siang Ling
|
PLOS ONE
|
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea
|
2015-10-28
|
Igor V Grigoriev Kazuo Ishii Yuichi Sakamoto Kerrie Barry
|
Hajime Muraguchi Kiwamu Umezawa Mai Niikura Makoto Yoshida Toshinori Kozaki Kiyota Sakai Motoyuki Shimizu Kiyoshi Nakahori Cindy Choi Chew Yee Ngan Eika Lindquist Anna Lipzen Andrew Tritt Sajeet Haridas Patricia J Pukkila
|
PLOS ONE
|
Sxl-Dependent, tra/tra2-Independent Alternative Splicing of the Drosophila melanogaster X-Linked Gene found in neurons.
|
2015-10-28
|
David Sturgill
|
Xia Sun Haiwang Yang Brian Oliver Leonard Rabinow Marie-Laure Samson
|
G3
|
Transcriptomic analysis of global changes in cytokine expression in mouse spleens following acute Toxoplasma gondii infection.
|
2015-10-28
|
Xing-Quan Zhu Si-Yang Huang Dong-Hui Zhou
|
Jun-Jun He Jun Ma Hui-Qun Song Jin-Lei Wang
|
Parasitology Research
|
A high-throughput RNA-seq approach to profile transcriptional responses
|
2015-10-29
|
Xiaoquan Wen Francesca Luca Roger Pique-Regi
|
G A Moyerbrailean G O Davis C T Harvey D Watza
|
Scientific Reports
|
RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species
|
2015-10-30
|
Wenqin Wang Joachim Messing
|
Wei Zhang Yongrui Wu Pal Maliga
|
PLOS ONE
|
ccmGDB: a database for cancer cell metabolism genes
|
2015-10-30
|
Feixiong Cheng
|
Pora Kim Junfei Zhao Zhongming Zhao
|
Nucleic Acids Research
|
The vitamin D-dependent transcriptome of human monocytes.
|
2015-10-30
|
Veijo Nurminen Antonio Neme Carsten Carlberg
|
Sabine Seuter
|
The Journal of Steroid Biochemistry and Molecular Biology
|
Activation of AhR-mediated toxicity pathway by emerging pollutants polychlorinated diphenyl sulfides.
|
2015-10-30
|
John P Giesy Pu Xia Rui Zhang Guanyong Su Zunyao Wang Xiaowei Zhang
|
Junjiang Zhang Yang Wu Jie Xia Jiamin Zhang Daniel L Villeneuve Hongxia Yu
|
Chemosphere
|
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
|
2015-10-30
|
Casey S. Greene
|
Jeffrey A Thompson Jie Tan
|
|
Cross-platform normalization of microarray and RNA-seq data for machine learning applications
|
2015-10-30
|
Casey S. Greene
|
Jeffrey A Thompson Jie Tan
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Comparative blood transcriptome analysis in idiopathic and LRRK2 G2019S-associated Parkinson's disease.
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2015-10-31
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Carlos Prieto
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Jon Infante María Sierra Pascual Sánchez-Juan Isabel González-Aramburu Coro Sánchez-Quintana José Berciano Onofre Combarros Jesús Sainz
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Neurobiology of Aging
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Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems
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2015-11
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Silvana Konermann Eugene Koonin
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Sergey Shmakov Omar O. Abudayyeh Kira S. Makarova Yuri I. Wolf Jonathan S. Gootenberg Ekaterina Semenova Leonid Minakhin Julia Joung Konstantin Severinov Feng Zhang
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Molecular Cell
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LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes.
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2015-11-01
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Mamuka Kvaratskhelia Stephen H. Hughes
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Parmit Kumar Singh Matthew R Plumb Andrea L Ferris James R Iben Xiaolin Wu Hind J Fadel Brian T Luke Caroline Esnault Eric M Poeschla Henry L Levin
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Genes & Development
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Global Analysis of mRNA, Translation, and Protein Localization: Local Translation Is a Key Regulator of Cell Protrusions.
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2015-11-01
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Faraz Khosravi Mardakheh
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Angela Paul Sandra Kümper Amine Sadok Hugh Paterson Afshan Mccarthy Yinyin Yuan Christopher J Marshall
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Developmental Cell
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SOX9 modulates the expression of key transcription factors required for heart valve development.
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2015-11-02
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Olivia Alder Pamela A. Hoodless
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Victoria C Garside Rebecca Cullum Daphne Y Lu Ryan Vander Werff Mikhail Bilenky Yongjun Zhao Steven J M Jones Marco A Marra T Michael Underhill
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Development
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Global Transcriptome Analysis of Primary Cerebrocortical Cells: Identification of Genes Regulated by Triiodothyronine in Specific Cell Types.
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2015-11-02
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Juan Bernal
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Pilar Gil-Ibañez Francisco García-García Joaquín Dopazo Beatriz Morte
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Cerebral Cortex
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Multi-Scale Molecular Deconstruction of the Serotonin Neuron System.
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2015-11-04
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Rachael Brust
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Benjamin W Okaty Morgan E Freret Benjamin D Rood Morgan L Hennessy Danielle deBairos Jun Chul Kim Melloni N Cook Susan M Dymecki
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Neuron
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The Orthology Clause in the Next Generation Sequencing Era: Novel Reference Genes Identified by RNA-seq in Humans Improve Normalization of Neonatal Equine Ovary RT-qPCR Data.
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2015-11-04
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Dragos Scarlet Reinhard Ertl Christine Aurich
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Ralf Steinborn
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PLOS ONE
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Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth.
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2015-11-05
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Bertrand Servin
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Agnes Bonnet Philippe Mulsant Beatrice Mandon-Pepin
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PLOS ONE
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Full-length single-cell RNA-seq applied to a viral human cancer: applications to HPV expression and splicing analysis in HeLa S3 cells
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2015-11-05
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Zhikun Zhao Qichao Yu Liang Wu Yong Hou Karsten Kristiansen Huanming Yang Xiuqing Zhang
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Xiaolong Zhang Ling Wang Bo Li Guibo Li Michael Dean Yanhui Wang Xinxin Lin Weijian Rao Zhanlong Mei Yang Li Runze Jiang Huan Yang Fuqiang Li Guoyun Xie Liqin Xu Kui Wu Jie Zhang Jianghao Chen Ting Wang Yingrui Li Jian Wang Xun Xu
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GigaScience
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A multi-omic analysis of human naïve CD4+ T cells.
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2015-11-06
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Danielle Thierry-Mieg Tai-Chung Huang Sneha M Pinto Jun Zhong Luigi Marchionni Jean Thierry-Mieg Min-Sik Kim
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Christopher J Mitchell Derese Getnet Srikanth S Manda Praveen Kumar Raja Sekhar Nirujogi Mio Iwasaki Patrick G Shaw Xinyan Wu Raghothama Chaerkady Arivusudar Marimuthu Babylakshmi Muthusamy Nandini A Sahasrabuddhe Rajesh Raju Caitlyn Bowman Ludmila Danilova Jevon Cutler Dhanashree S Kelkar Charles G Drake T S Keshava Prasad Peter N Murakami Alan F Scott Leming Shi Rafael Irizarry Leslie Cope Yasushi Ishihama Charles Wang Harsha Gowda Akhilesh Pandey
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BMC Systems Biology
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Proper Use of Allele-Specific Expression Improves Statistical Power for cis-eQTL Mapping with RNA-Seq Data
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2015-11-07
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Charles M. Perou
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Yi-Juan Hu Wei Sun Jung-Ying Tzeng
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Journal of the American Statistical Association
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Host Transcriptional Profiling at Early and Later Stages of the Compatible Interaction Between Phaseolus vulgaris and Meloidogyne incognita.
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2015-11-09
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Mário Massayuki Inomoto Maria Lucia Carneiro Vieira
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Luciane Santini Carla de Freitas Munhoz Mauro Ferreira Bonfim Marcelo Mendes Brandão
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Phytopathology
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RNA sequencing of Sleeping Beauty transposon-induced tumors detects transposon-RNA fusions in forward genetic cancer screens
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2015-11-09
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Jesse D Riordan Adam J. Dupuy
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Nuri A Temiz Branden S Moriarity Natalie K Wolf David A Largaespada Aaron L Sarver
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Genome Research
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Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.
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2015-11-09
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Albin Sandelin Timo Lassmann Bogumil Kaczkowski Hideya Kawaji Masayoshi Itoh Piero Carninci Yoshihide Hayashizaki Robin Andersson
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Yuji Tanaka Alistair R R Forrest FANTOM5 Consortium
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Cancer Research
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Highly proliferative primitive fetal liver hematopoietic stem cells are fueled by oxidative metabolic pathways.
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2015-11-09
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Ruben Boon Alex van Vliet Sarah-maria Fendt Nick van Gastel Catherine Verfaillie Peter Carmeliet
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Javed K Manesia Zhuofei Xu Dorien Broekaert Guy Eelen Thomas Vanwelden Steve Stegen Alberto Pascual-Montano Geert Carmeliet Satish Khurana
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Stem Cell Research
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STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA.
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2015-11-09
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Aviv Regev
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Andrew Venteicher Itay Tirosh Christine Hebert Leah Escalante Brian Nahed Daniel Cahill William Curry Robert Martuza Bradley Bernstein David Louis Mario Suva
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Neuro-Oncology
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A resource of ribosomal RNA-depleted RNA-Seq data from different normal adult and fetal human tissues.
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2015-11-10
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Nicolas Bertin
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Jocelyn Y H Choy Priscilla L S Boon Melissa J Fullwood
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Scientific Data
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An effective analytic method for detecting tissue-specific genes in RNA-seq experiments.
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2015-11-10
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Xiaohua Douglas Zhang
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Guoqing Zhao Qiao Li I-Ming Wang Xiaoqiao Liu Xiangzhong Fang
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Pharmacogenomics
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Cancer genetics: RNA-seq for blood-based pan-cancer diagnostics.
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2015-11-10
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Liesbet Lieben
|
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Nature Reviews Genetics
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REST-Governed Gene Expression Profiling in a Neuronal Cell Model Reveals Novel Direct and Indirect Processes of Repression and Up-Regulation.
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2015-11-10
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Davide Cittaro
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Jose M Garcia-Manteiga Silvia Bonfiglio Lucrezia Folladori Maria L Malosio Dejan Lazarevic Elia Stupka Jacopo Meldolesi
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Frontiers in Cellular Neuroscience
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Saccular Transcriptome Profiles of the Seasonal Breeding Plainfin Midshipman Fish (Porichthys notatus), a Teleost with Divergent Sexual Phenotypes.
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2015-11-11
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Joseph A. Sisneros
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Joshua Faber-Hammond Manoj P Samanta Elizabeth A Whitchurch Dustin Manning Allison B Coffin
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PLOS ONE
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A Comprehensive RNA Sequencing Analysis of the Adeno-Associated Virus (AAV) Type 2 Transcriptome Reveals Novel AAV Transcripts, Splice Variants, and Derived Proteins
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2015-11-11
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Andreas Gogol-Döring
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Catrin Stutika Laura Botschen Mario Mietzsch Stefan Weger Mirjam Feldkamp Wei Chen Regine Heilbronn
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Journal of Virology
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Genome-Wide Transcriptome Analysis During Anthesis Reveals New Insights into the Molecular Basis of Heat Stress Responses in Tolerant and Sensitive Rice Varieties.
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2015-11-11
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Ludovico Dreni Massimo Galbiati Lucia Colombo Martin M. Kater
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Nahuel González-Schain Lovely M F Lawas Sigrid Heuer Krishna S V Jagadish
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Plant and Cell Physiology
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RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium
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2015-11-12
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Shabarinath Srikumar Siân V Owen Carsten Kröger Karsten Hokamp
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Magali Hébrard Aoife Colgan Sathesh K Sivasankaran Andrew D S Cameron Jay C D Hinton
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PLOS Pathogens
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Molecular response of chorioretinal endothelial cells to complement injury: implications for macular degeneration.
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2015-11-13
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Luke A. Wiley Budd A. Tucker Todd E. Scheetz Robert F. Mullins Elliott H Sohn Edwin M. Stone
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Shemin Zeng S Scott Whitmore Megan J Riker
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The Journal of Pathology
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Diagnosis: RNA-seq for blood-based pan-cancer diagnostics.
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2015-11-13
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Liesbet Lieben
|
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Nature Reviews Cancer
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Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis
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2015-11-14
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Gareth D Weedall
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Helen Irving Margaret A Hughes Charles S Wondji
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BMC Genomics
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miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy
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2015-11-16
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Marc K. Halushka
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Alexander S Baras Christopher J Mitchell Jason R Myers Simone Gupta Lien-Chun Weng John M Ashton Toby C Cornish Akhilesh Pandey
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PLOS ONE
|
Tumor Repression of VCaP Xenografts by a Pyrrole-Imidazole Polyamide.
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2015-11-16
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Peter Dervan
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Amanda E Hargrove Thomas F Martinez Alissa A Hare Alexis A Kurmis John W Phillips Sudha Sud Kenneth J Pienta
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PLOS ONE
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Interaction of Arabidopsis Trihelix-Domain Transcription Factors VFP3 and VFP5 with Agrobacterium Virulence Protein VirF.
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2015-11-16
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Vitaly Citovsky
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Elena García-Cano Shimpei Magori Qi Sun Zehong Ding Sondra G Lazarowitz
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PLOS ONE
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High-throughput mRNA and miRNA profiling of epithelial-mesenchymal transition in MDCK cells
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2015-11-16
|
Mathias Müller
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Priyank Shukla Claus Vogl Barbara Wallner Doris Rigler Sabine Macho-Maschler
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BMC Genomics
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Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk
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2015-11-17
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Buket Baddal Raffaele A. Calogero
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Alessandro Muzzi Stefano Censini Giulia Torricelli Silvia Guidotti Anna R Taddei Antonello Covacci Mariagrazia Pizza Rino Rappuoli Marco Soriani Alfredo Pezzicoli
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mBio
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RNA-seq is a valuable complement of conventional diagnostic tools in newly diagnosed AML patients
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2015-11-17
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Vera Magistroni Carlo Gambacorti-Passerini
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Rocco Piazza Caterina Cecchetti Alessandra Pirola
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