(Q29547458)

title

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

23 April 2017

1 reference

transcript quantification

1 reference

1 reference

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21816040

8 December 2024

1

Bo Li

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21816040

8 December 2024

author name string

Colin N. Dewey

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21816040

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

8 December 2024

language of work or name

1 reference

23 April 2017

publication date

4 August 2011

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

full work available at URL

23 April 2017

https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-323

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21816040

https://europepmc.org/articles/PMC3163565

8 December 2024

file format

HyperText Markup Language

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21816040

https://europepmc.org/articles/PMC3163565?pdf=render

8 December 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A21816040

https://link.springer.com/content/pdf/10.1186/1471-2105-12-323.pdf

8 December 2024

1 reference

10.1186/1471-2105-12-323

https://api.crossref.org/works/10.1186/1471-2105-12-323

https://link.springer.com/article/10.1186/1471-2105-12-323/fulltext.html

8 December 2024

file format

HyperText Markup Language

1 reference

Crossref

DOI

10.1186/1471-2105-12-323

https://api.crossref.org/works/10.1186/1471-2105-12-323

8 December 2024

0 references

12

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

23 April 2017

page(s)

323

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

describes a project that uses

23 April 2017

DESeq2

object named as

DESeq

1 reference

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

edgeR

object named as

edgeR

1 reference

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

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

23 April 2017

1 reference

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Differential expression analysis for sequence count data

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

The UCSC Genome Browser database: update 2011

23 April 2017

1 reference

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

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Biases in Illumina transcriptome sequencing caused by random hexamer priming

23 April 2017

1 reference

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

The Sequence Alignment/Map format and SAMtools

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

TopHat: discovering splice junctions with RNA-Seq

23 April 2017

1 reference

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

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

RNA-Seq: a revolutionary tool for transcriptomics

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Alternative isoform regulation in human tissue transcriptomes

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Mapping and quantifying mammalian transcriptomes by RNA-Seq

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

The transcriptional landscape of the yeast genome defined by RNA sequencing

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

The human genome browser at UCSC

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

NCBI Reference Sequences: current status, policy and new initiatives

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Improving RNA-Seq expression estimates by correcting for fragment bias

23 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Inference of Isoforms from Short Sequence Reads

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Analysis and design of RNA sequencing experiments for identifying isoform regulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

De novo assembly and analysis of RNA-seq data.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

rQuant.web: a tool for RNA-Seq-based transcript quantitation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Modeling non-uniformity in short-read rates in RNA-Seq data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Why the need for qPCR publication guidelines?--The case for MIQE.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

RNA-Seq gene expression estimation with read mapping uncertainty

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Statistical inferences for isoform expression in RNA-Seq

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Optimal spliced alignments of short sequence reads

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Identification of novel transcripts in annotated genomes using RNA-Seq

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Accurate estimation of expression levels of homologous genes in RNA-seq experiments.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3163565

26 November 2018

Identifiers

DOI

10.1186/1471-2105-12-323

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

23 April 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1021902674

0 references

170901

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

2 references

23 April 2017

170901

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=21816040

2 references

23 April 2017