Harold Pimentel

/in /by

Publications:

Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq. Nat Protoc. 2024 Oct 10. view on PubMed

Estevam GO, Linossi EM, Rao J, Macdonald CB, Ravikumar A, Chrispens KM, Capra JA, Coyote-Maestas W, Pimentel H, Collisson EA, Jura N, Fraser JS. Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv. 2024 Jul 18. view on PubMed

Pimentel H, Freimer JW, Arce MM, Garrido CM, Marson A, Pritchard JK. A model for accurate quantification of CRISPR effects in pooled FACS screens. bioRxiv. 2024 Jun 18. view on PubMed

Rao J, Xin R, Macdonald C, Howard MK, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W, Pimentel H. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biol. 2024 05 24; 25(1):138. view on PubMed

LaPierre N, Pimentel H. Accounting for isoform expression increases power to identify genetic regulation of gene expression. PLoS Comput Biol. 2024 Feb; 20(2):e1011857. view on PubMed

Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq. bioRxiv. 2024 Jan 23. view on PubMed

Nyberg WA, Ark J, To A, Clouden S, Reeder G, Muldoon JJ, Chung JY, Xie WH, Allain V, Steinhart Z, Chang C, Talbot A, Kim S, Rosales A, Havlik LP, Pimentel H, Asokan A, Eyquem J. An evolved AAV variant enables efficient genetic engineering of murine T cells. Cell. 2023 01 19; 186(2):446-460.e19. view on PubMed

Patel RA, Musharoff SA, Spence JP, Pimentel H, Tcheandjieu C, Mostafavi H, Sinnott-Armstrong N, Clarke SL, Smith CJ, V.A. Million Veteran Program, Durda PP, Taylor KD, Tracy R, Liu Y, Johnson WC, Aguet F, Ardlie KG, Gabriel S, Smith J, Nickerson DA, Rich SS, Rotter JI, Tsao PS, Assimes TL, Pritchard JK. Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits. Am J Hum Genet. 2022 07 07; 109(7):1286-1297. view on PubMed

Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cooke S, Shea T, Gienger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell. 2020 Feb 20; 180(4):816. view on PubMed

Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell. 2020 01 23; 180(2):263-277.e20. view on PubMed

Smart AC, Margolis CA, Pimentel H, He MX, Miao D, Adeegbe D, Fugmann T, Wong KK, Van Allen EM. Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018 12; 36(11):1056-1058. view on PubMed

Yi L, Pimentel H, Bray NL, Pachter L. Gene-level differential analysis at transcript-level resolution. Genome Biol. 2018 04 12; 19(1):53. view on PubMed

Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Pseudoalignment for metagenomic read assignment. Bioinformatics. 2017 Jul 15; 33(14):2082-2088. view on PubMed

Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty. Nat Methods. 2017 Jul; 14(7):687-690. view on PubMed

Yi L, Pimentel H, Pachter L. Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLoS One. 2017; 12(4):e0175744. view on PubMed

Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L. The Lair: a resource for exploratory analysis of published RNA-Seq data. BMC Bioinformatics. 2016 Dec 01; 17(1):490. view on PubMed

Bray NL, Pimentel H, Melsted P, Pachter L. Erratum: Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016 08 09; 34(8):888. view on PubMed

Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016 05; 34(5):525-7. view on PubMed

Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 2016 Jan 29; 44(2):838-51. view on PubMed

Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG. A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 2014 Apr; 42(6):4031-42. view on PubMed

Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013 Apr 25; 14(4):R36. view on PubMed

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012 Mar 01; 7(3):562-78. view on PubMed

Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011 Sep 01; 27(17):2325-9. view on PubMed