Pimentel H - Search Results

1

Differential analysis of RNA-seq incorporating quantification uncertainty.

Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Pimentel H, et al. Nat Methods. 2017 Jul;14(7):687-690. doi: 10.1038/nmeth.4324. Epub 2017 Jun 5. Nat Methods. 2017. PMID: 28581496 Free article.

2

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L. Roberts A, et al. Among authors: pimentel h. Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21. Bioinformatics. 2011. PMID: 21697122

3

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

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Trapnell C, et al. Among authors: pimentel h. Nat Protoc. 2012 Mar 1;7(3):562-78. doi: 10.1038/nprot.2012.016. Nat Protoc. 2012. PMID: 22383036 Free PMC article.

4

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG. Pimentel H, et al. Nucleic Acids Res. 2014 Apr;42(6):4031-42. doi: 10.1093/nar/gkt1388. Epub 2014 Jan 17. Nucleic Acids Res. 2014. PMID: 24442673 Free PMC article.

5

A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis.

Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. Pimentel H, et al. Nucleic Acids Res. 2016 Jan 29;44(2):838-51. doi: 10.1093/nar/gkv1168. Epub 2015 Nov 3. Nucleic Acids Res. 2016. PMID: 26531823 Free PMC article.

6

Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L. Bray NL, et al. Among authors: pimentel h. Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4. Nat Biotechnol. 2016. PMID: 27043002

7

Erratum: Near-optimal probabilistic RNA-seq quantification.

Bray NL, Pimentel H, Melsted P, Pachter L. Bray NL, et al. Among authors: pimentel h. Nat Biotechnol. 2016 Aug 9;34(8):888. doi: 10.1038/nbt0816-888d. Nat Biotechnol. 2016. PMID: 27504780 No abstract available.

8

The Lair: a resource for exploratory analysis of published RNA-Seq data.

Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L. Pimentel H, et al. BMC Bioinformatics. 2016 Dec 1;17(1):490. doi: 10.1186/s12859-016-1357-2. BMC Bioinformatics. 2016. PMID: 27905880 Free PMC article.

9

Pseudoalignment for metagenomic read assignment.

Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Schaeffer L, et al. Among authors: pimentel h. Bioinformatics. 2017 Jul 15;33(14):2082-2088. doi: 10.1093/bioinformatics/btx106. Bioinformatics. 2017. PMID: 28334086 Free PMC article.

10

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.

Yi L, Pimentel H, Pachter L. Yi L, et al. Among authors: pimentel h. PLoS One. 2017 Apr 27;12(4):e0175744. doi: 10.1371/journal.pone.0175744. eCollection 2017. PLoS One. 2017. PMID: 28448519 Free PMC article.

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