Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer (Q30985845)

11 August 2017

Comprehensive assembly of novel transcripts from unmapped human RNA-Seq data and their association with cancer (English)

1 reference

11 August 2017

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1 reference

1

Majid Kazemian

1 reference

11 August 2017

Min Ren

2

1 reference

11 August 2017

Jian-Xin Lin

3

1 reference

11 August 2017

Wei Liao

4

1 reference

11 August 2017

Rosanne Spolski

5

1 reference

11 August 2017

Warren J Leonard

6

1 reference

11 August 2017

7 August 2015

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Molecular Systems Biology

11 August 2017

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11 August 2017

11

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11 August 2017

8

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11 August 2017

826

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describes a project that uses

11 August 2017

MUMmer

object named as

MUMmer

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

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The landscape of long noncoding RNAs in the human transcriptome

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Comparative analysis of metazoan chromatin organization

21 June 2018

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A role of autophagy in PTP4A3-driven cancer progression.

21 June 2018

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Deletion of Ptp4a3 reduces clonogenicity and tumor-initiation ability of colitis-associated cancer cells in mice

21 June 2018

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Nucleosome positioning and histone modifications define relationships between regulatory elements and nearby gene expression in breast epithelial cells

21 June 2018

1 reference

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Pim-3 promotes human pancreatic cancer growth by regulating tumor vasculogenesis

21 June 2018

1 reference

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Comprehensive functional annotation of 77 prostate cancer risk loci

21 June 2018

1 reference

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RefSeq: an update on mammalian reference sequences

21 June 2018

1 reference

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The Cancer Genome Atlas Pan-Cancer analysis project

21 June 2018

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The Genotype-Tissue Expression (GTEx) project

21 June 2018

1 reference

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Regulation of transcription through acetylation of H3K122 on the lateral surface of the histone octamer

21 June 2018

1 reference

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

21 June 2018

1 reference

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Transcriptional amplification in tumor cells with elevated c-Myc.

21 June 2018

1 reference

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GENCODE: the reference human genome annotation for The ENCODE Project

21 June 2018

1 reference

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Epigenomic enhancer profiling defines a signature of colon cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

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

21 June 2018

1 reference

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Mapping and analysis of chromatin state dynamics in nine human cell types

21 June 2018

1 reference

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PRL‐3 phosphatase and cancer metastasis

21 June 2018

1 reference

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The European Nucleotide Archive

21 June 2018

1 reference

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Long noncoding RNAs with enhancer-like function in human cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Widespread transcription at neuronal activity-regulated enhancers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Building the sequence map of the human pan-genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

The Sequence Alignment/Map format and SAMtools

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Fast and accurate short read alignment with Burrows-Wheeler transform

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

ABySS: a parallel assembler for short read sequence data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Gene-expression signatures in breast cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Long non-coding RNAs: insights into functions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Model-based analysis of ChIP-Seq (MACS)

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

RNA maps reveal new RNA classes and a possible function for pervasive transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Patterns of somatic mutation in human cancer genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Genomic maps and comparative analysis of histone modifications in human and mouse

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Versatile and open software for comparing large genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

BLAT—The BLAST-Like Alignment Tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Gene expression profiling predicts clinical outcome of breast cancer

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

The Ensembl genome database project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Basic local alignment search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

Mapping the cancer genome. Pinpointing the genes involved in cancer will help chart a new course across the complex landscape of human malignancies.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4562499

The prognostic value of platelet endothelial cell adhesion molecule-1 in non-small-cell lung cancer patients

25 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26253570

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Stromal-epithelial metabolic coupling in gastric cancer: stromal MCT4 and mitochondrial TOMM20 as poor prognostic factors

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26253570

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.15252/MSB.156172

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

26253570

1 reference