Paper · 18516045

Mapping and quantifying mammalian transcriptomes by RNA-Seq.

Mortazavi A and 4 others. Nat Methods, 2008. Cited by 10,215 papers, by iCite.

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ConductScience Library. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Papers, record 18516045. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/18516045

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Paper

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

Title: Mapping and quantifying mammalian transcriptomes by RNA-Seq.; PubMed
Journal: Nat Methods; PubMed
Year: 2008; 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/18516045/; PubMed
DOI: https://doi.org/10.1038/nmeth.1226; PubMed
PMC: https://pmc.ncbi.nlm.nih.gov/articles/PMC13303166/; PubMed
The journal: https://conductscience.org/library/journal-index/101215604; PubMed
Citations, by iCite: 10,215; iCite
Relative citation ratio, by iCite: 247; iCite
Revised in PubMed: 2026-08-13; PubMed

Authors5

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

Order	Author	Forename
1	Mortazavi A	Ali
2	Williams BA	Brian A
3	McCue K	Kenneth
4	Schaeffer L	Lorian
5	Wold B	Barbara

Source PubMed

Topics21

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

MeSH term	Major
Gene Expression Profiling	Major topic
RNA	Major topic
Sequence Analysis, RNA	Major topic
3' Untranslated Regions
Algorithms
Alternative Splicing
Animals
Brain
Chromosome Mapping
Databases, Nucleic Acid
Exons
Liver
Mice
Mice, Inbred C57BL
Muscle, Skeletal
Oligonucleotide Array Sequence Analysis
Promoter Regions, Genetic
RNA Splicing
RNA, Messenger
Sensitivity and Specificity
Software

Source PubMed

Grants1

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
U54 HG004576	NHGRI NIH HHS	United States	U54HG004576	PubMed and NIH

Source NIH RePORTER

Trials0

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

None in this release.

Comments and corrections1

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

Kind	PMID	Title	In Papers
Comment in	18,587,314	The beginning of the end for microarrays?	https://conductscience.org/library/papers/18587314

Source PubMed

References23

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	16,749,918	Hybridization interactions between probesets in short oligo microarrays lead to spurious correlations.	BMC Bioinformatics	2006	https://conductscience.org/library/papers/16749918	PubMed
2	10,835,600	Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.	Nat Biotechnol	2000	https://conductscience.org/library/papers/10835600	PubMed
3	18,039,370	In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation.	BMC Bioinformatics	2007	https://conductscience.org/library/papers/18039370	PubMed
4	17,510,325	RNA maps reveal new RNA classes and a possible function for pervasive transcription.	Science	2007	https://conductscience.org/library/papers/17510325	PubMed
5	17,486,121	Genome-wide transcription and the implications for genomic organization.	Nat Rev Genet	2007	https://conductscience.org/library/papers/17486121	PubMed
6	18,423,832	Highly integrated single-base resolution maps of the epigenome in Arabidopsis.	Cell	2008	https://conductscience.org/library/papers/18423832	PubMed
7	18,488,015	Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution.	Nature	2008	https://conductscience.org/library/papers/18488015	PubMed
8	15,239,822	Analysis of alternative splicing with microarrays: successes and challenges.	Genome Biol	2004	https://conductscience.org/library/papers/15239822	PubMed
9	15,979,196	Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping.	Trends Genet	2005	https://conductscience.org/library/papers/15979196	PubMed
10	7,570,003	Serial analysis of gene expression.	Science	1995	https://conductscience.org/library/papers/7570003	PubMed

1 to 10 of 23

See all 23 references

Cited by7,670

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 10,215 citations.

PMID	Title	Journal	Year	In Papers	Source
42,985,778	Notch/NF-κB crosstalk signaling controls SASP gene expression during brain aging.	Nucleic Acids Res	2026	https://conductscience.org/library/papers/42985778	PubMed
42,943,142	Silicon Modulates the Expression of Copper-Responsive Transporters and Non-Coding RNAs in Cucumber Subjected to Copper Stress.	Plants (Basel)	2026	https://conductscience.org/library/papers/42943142	PubMed
42,938,423	SpliceCOV: Supervised Filtering of RNA-Seq-Derived Transcript Features Improves Transcriptome Assembly.	Genes (Basel)	2026	https://conductscience.org/library/papers/42938423	PubMed
42,932,063	Low Input RNA Sequencing of Freshly Isolated Muscle Stem Cells.	Methods Mol Biol	2027	https://conductscience.org/library/papers/42932063	PubMed
42,932,006	Yap1 mediates miR-143 regulation of ovarian estrogen synthesis in Larimichthys crocea‌.	Fish Physiol Biochem	2026	https://conductscience.org/library/papers/42932006	PubMed
42,919,625	Sintilimab plus eribulin and carboplatin in patients with metastatic triple-negative breast cancer (SECURE): a phase II, multicenter trial.	J Immunother Cancer	2026	https://conductscience.org/library/papers/42919625	PubMed
42,914,125	Plastid tRNA-derived small RNAs associate with AGO1 and accumulate upon sulfur deprivation in Chlamydomonas.	Plant Physiol	2026	https://conductscience.org/library/papers/42914125	PubMed
42,911,958	Adaptive metabolic reprogramming of the brain tissue during late-stage Trypanosoma brucei infection maintains host learning and memory.	PLoS Pathog	2026	https://conductscience.org/library/papers/42911958	PubMed
42,908,748	Culture medium and plant growth regulator regimes influence the transcriptome and cannabisin accumulation in Cannabis sativa cell suspension cultures.	Front Plant Sci	2026	https://conductscience.org/library/papers/42908748	PubMed
42,897,811	Microglial Labeling in Mouse Spinal Cord Injury: A Review of Timing, Efficacy, and Specificity.	Glia	2026	https://conductscience.org/library/papers/42897811	PubMed

1 to 10 of 7,670

See all 7,670 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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