Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries (Q33795797)

29 July 2017

Integration of quantitated expression estimates from polyA-selected and rRNA-depleted RNA-seq libraries (English)

1 reference

29 July 2017

0 references

1 reference

Stephen J Bush

1

0 references

David A Hume

object named as

David A Hume

4

0 references

Kim M Summers

object named as

Kim M Summers

3

0 references

author name string

Mary E B McCulloch

2

1 reference

PubMed ID

28610557

29 July 2017

Emily L Clark

5

1 reference

29 July 2017

13 June 2017

1 reference

29 July 2017

1 reference

29 July 2017

18

1 reference

29 July 2017

301

1 reference

29 July 2017

1

1 reference

https://scigraph.springernature.com/pub.10.1186/s12859-017-1714-9

29 July 2017

0 references

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4 July 2018

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Gene expression profiling of non-polyadenylated RNA-seq across species.

4 July 2018

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4 July 2018

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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

4 July 2018

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How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq

4 July 2018

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Polyribosomal RNA-Seq reveals the decreased complexity and diversity of the Arabidopsis translatome

4 July 2018

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Transcriptome meta-analysis of lung cancer reveals recurrent aberrations in NRG1 and Hippo pathway genes

4 July 2018

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Comparison of the transcriptional landscapes between human and mouse tissues

4 July 2018

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4 July 2018

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Influence of RNA extraction methods and library selection schemes on RNA-seq data

4 July 2018

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RNA-Skim: a rapid method for RNA-Seq quantification at transcript level

4 July 2018

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The sheep genome illuminates biology of the rumen and lipid metabolism

4 July 2018

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Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

4 July 2018

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A promoter-level mammalian expression atlas

4 July 2018

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An atlas of active enhancers across human cell types and tissues

4 July 2018

1 reference

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A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

4 July 2018

1 reference

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Library preparation methods for next-generation sequencing: tone down the bias

4 July 2018

1 reference

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An expression atlas of human primary cells: inference of gene function from coexpression networks

4 July 2018

1 reference

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The equine alveolar macrophage: functional and phenotypic comparisons with peritoneal macrophages

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

4 July 2018

1 reference

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4 July 2018

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Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

4 July 2018

1 reference

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CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

4 July 2018

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Differentially expressed, variant U1 snRNAs regulate gene expression in human cells

4 July 2018

1 reference

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Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

4 July 2018

1 reference

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4 July 2018

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Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages

4 July 2018

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Pig bone marrow-derived macrophages resemble human macrophages in their response to bacterial lipopolysaccharide

4 July 2018

1 reference

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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

4 July 2018

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Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

4 July 2018

1 reference

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The real cost of sequencing: higher than you think!

4 July 2018

1 reference

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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

4 July 2018

1 reference

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Ensembl BioMarts: a hub for data retrieval across taxonomic space

4 July 2018

1 reference

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RNA sequencing reveals two major classes of gene expression levels in metazoan cells

4 July 2018

1 reference

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Genomewide characterization of non-polyadenylated RNAs

4 July 2018

1 reference

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A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Tackling the widespread and critical impact of batch effects in high-throughput data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

RNA-Seq Atlas of Glycine max: a guide to the soybean transcriptome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Statistical design and analysis of RNA sequencing data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

BLAST+: architecture and applications

4 July 2018

1 reference

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Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data

4 July 2018

1 reference

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The Sequence Alignment/Map format and SAMtools

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Pre-mRNA processing reaches back to transcription and ahead to translation

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

RNA-Seq: a revolutionary tool for transcriptomics

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Mapping and quantifying mammalian transcriptomes by RNA-Seq

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

The transcriptional landscape of the yeast genome defined by RNA sequencing

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Construction, visualisation, and clustering of transcription networks from microarray expression data

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Replacement, reduction and refinement.

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

EMBOSS: the European Molecular Biology Open Software Suite

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Gene ontology: tool for the unification of biology

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Recognition of protein coding regions in DNA sequences

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Assessment of protein coding measures

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

Synthesis of histone messenger RNAs by RNA polymerase II in nuclei from S phase HeLa S3 cells

4 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development.

4 July 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-017-1714-9

An RNA-Seq based gene expression atlas of the common bean

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-017-1714-9

Systematic comparison of RNA extraction techniques from frozen and fresh lung tissues: checkpoint towards gene expression studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-017-1714-9

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-017-1714-9

Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-017-1714-9

RNA-seq: technical variability and sampling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-017-1714-9

Dominance statistics: Ordinal analyses to answer ordinal questions

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2FS12859-017-1714-9

Ribosomal RNA depletion for efficient use of RNA-seq capacity

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5470212

A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28610557

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/S12859-017-1714-9

1 reference

journals/bmcbi/BushMSHC17

29 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

29 July 2017

1 reference

PubMed ID

28610557