Paper · 21816040

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

Li B and 1 other. BMC Bioinformatics, 2011. Cited by 16,801 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. Papers, record 21816040. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/21816040

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title: RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.; PubMed
Journal: BMC Bioinformatics; PubMed
Year: 2011; PubMed
Publication types: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't; PubMed
PubMed: https://pubmed.ncbi.nlm.nih.gov/21816040/; PubMed
DOI: https://doi.org/10.1186/1471-2105-12-323; PubMed
PMC: https://pmc.ncbi.nlm.nih.gov/articles/PMC3163565/; PubMed
The journal: https://conductscience.org/library/journal-index/100965194; PubMed
Citations, by iCite: 16,801; iCite
Relative citation ratio, by iCite: 462; iCite
Revised in PubMed: 2024-07-29; PubMed

Authors2

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

Order	Author	Forename	Kind	ORCID iD
1	Li B	Bo
2	Dewey CN	Colin N

Source PubMed

Topics9

NLM's MeSH indexing of the paper, its major topics first.

MeSH term	Major
Gene Expression Profiling	Major topic
Sequence Analysis, RNA	Major topic
Software	Major topic
Animals
Computer Simulation
Humans
Mice
Protein Isoforms
RNA

Source PubMed

Grants2

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes it	Agency	Country	NIH project	Stated by
R01 HG005232	NHGRI NIH HHS	United States	R01HG005232	PubMed and NIH
1R01HG005232-01A1	NHGRI NIH HHS	United States	R01HG005232	PubMed and NIH

Source NIH RePORTER

Trials2

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

Trial	Title	The trial lists it as	Named in the paper's record	Source
NCT03529955	Evaluating Safety & Efficacy of Apremilast in the Treatment of Cutaneous Disease in Patients With Recalcitrant Dermatomyositis	Background		ClinicalTrials.gov
NCT03990350	Gut Microbiota Composition in Hispanic and Non-Hispanic Children.	Background		ClinicalTrials.gov

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References38

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

Order	PMID	Title	Journal	Year	In Papers	Source
1	20,935,650	De novo assembly and analysis of RNA-seq data.	Nat Methods	2010	https://conductscience.org/library/papers/20935650	PubMed
2	21,697,122	Identification of novel transcripts in annotated genomes using RNA-Seq.	Bioinformatics	2011	https://conductscience.org/library/papers/21697122	PubMed
3	18,927,115	NCBI Reference Sequences: current status, policy and new initiatives.	Nucleic Acids Res	2009	https://conductscience.org/library/papers/18927115	PubMed
4	21,169,371	Using non-uniform read distribution models to improve isoform expression inference in RNA-Seq.	Bioinformatics	2011	https://conductscience.org/library/papers/21169371	PubMed
5	21,045,057	Ensembl 2011.	Nucleic Acids Res	2011	https://conductscience.org/library/papers/21045057	PubMed
6	18,516,045	Mapping and quantifying mammalian transcriptomes by RNA-Seq.	Nat Methods	2008	https://conductscience.org/library/papers/18516045	PubMed
7	21,410,973	Improving RNA-Seq expression estimates by correcting for fragment bias.	Genome Biol	2011	https://conductscience.org/library/papers/21410973	PubMed
8	19,505,943	The Sequence Alignment/Map format and SAMtools.	Bioinformatics	2009	https://conductscience.org/library/papers/19505943	PubMed
9	21,385,036	Inference of isoforms from short sequence reads.	J Comput Biol	2011	https://conductscience.org/library/papers/21385036	PubMed
10	20,150,413	Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments.	Nucleic Acids Res	2010	https://conductscience.org/library/papers/20150413	PubMed

1 to 10 of 38

See all 38 references

Cited by12,624

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 16,801 citations.

PMID	Title	Journal	Year	In Papers	Source
42,989,093	Full-length transcriptome atlas of Panax vietnamensis var. fuscidiscus reveals novel genes and alternative splicing in tissue-specific biosynthesis of ocotillol-type saponins.	BMC Plant Biol	2026	https://conductscience.org/library/papers/42989093	PubMed
42,985,447	Integrated metabolomic, transcriptomic and computational analyses reveal geographical variation and potential anti-osteoarthritis bioactive compounds in Arenga pinnata pith.	Front Plant Sci	2026	https://conductscience.org/library/papers/42985447	PubMed
42,984,670	Integrated manufacturing platform for cortical organoids reveals early phosphatase and prefoldin dysregulation in MAPT V337M neurons.	NPJ Dement	2026	https://conductscience.org/library/papers/42984670	PubMed
42,983,839	LRRK2 G2019S variant is associated with transcriptional changes in Parkinson's disease human myeloid cells under proinflammatory environment.	J Neuroinflammation	2026	https://conductscience.org/library/papers/42983839	PubMed
42,978,809	sncRNA signatures underlying HIV-1 restriction in elite controllers.	Front Cell Infect Microbiol	2026	https://conductscience.org/library/papers/42978809	PubMed
42,977,764	GATA transcription factors coordinate developmental progression in the arabidopsis root.	Nat Commun	2026	https://conductscience.org/library/papers/42977764	PubMed
42,967,953	High-efficiency antimony biomineralization by Serratia nematodiphila: process optimization and integrated genomic-transcriptomic-proteomic analysis.	World J Microbiol Biotechnol	2026	https://conductscience.org/library/papers/42967953	PubMed
42,967,936	DCAF7 regulates hematopoietic stem cell function and differentiation through polycomb repressive complex 1 modulation.	Nat Commun	2026	https://conductscience.org/library/papers/42967936	PubMed
42,967,922	Single-cell profiling uncovers a rare mesenchymal-like urothelial state associated with sarcomatoid bladder cancer.	Cell Death Dis	2026	https://conductscience.org/library/papers/42967922	PubMed
42,966,958	Multiomics insights into quinolizidine alkaloid biosynthetic architecture in narrow-leafed lupin genotypes with contrasting alkaloid regulation.	Hortic Res	2026	https://conductscience.org/library/papers/42966958	PubMed

1 to 10 of 12,624

See all 12,624 cited by

Genes0

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

None in this release.

Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed: 2026-11-06; PubMed
iCite: 2026-11-05; iCite
PMC's ID file: 2026-11-05; PMC's ID file
NIH RePORTER's grant and paper links: 2026-11-01; NIH RePORTER's grant and paper links
Trials: 2026-11-12
Gene search: 2026-11-11
Pipelines: 2026-09-18

Sources 11

ChEMBL, through Open TargetsCC BY-SA 3.0
ClinicalTrials.govNo license stated
HGNCCC0
iCiteCC BY 4.0
NCBI GenePublic domain (US government)
NIH RePORTER's grant and paper linksPublic domain
Open TargetsCC0 1.0
PMC's ID filePublic domain (US government)
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0

Each source's terms

ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
ClinicalTrials.govnone stated
HGNCCC0: https://www.genenames.org/about/license/
iCiteCC BY 4.0
NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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