Harold Pimentel


Harold Pimentel, Ph.D.


Office Address:
5303 Life Sciences

Affiliations

Assistant Professor, Computational Medicine
Research Interests

We aim to understand gene regulation by building broadly applicable computational tools to analyze high-throughput genomic assays. This approach works by carefully investigating the experimental design and developing data-driven models using computer science and high-dimensional statistics to advance biomedical discovery.

Publications

A selected list of publications:

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. 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. PMID: 35716666; PMCID: PMC9300878.

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell. 2020 Feb 20; 180(4):816. 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. PMID: 32084344; PMCID: PMC7201975.

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. 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. PMID: 31955845; PMCID: PMC7197499.

Intron retention is a source of neoepitopes in cancer. Nat Biotechnol. 2018 12; 36(11):1056-1058. Smart AC, Margolis CA, Pimentel H, He MX, Miao D, Adeegbe D, Fugmann T, Wong KK, Van Allen EM. PMID: 30114007; PMCID: PMC6226333.

Gene-level differential analysis at transcript-level resolution. Genome Biol. 2018 04 12; 19(1):53. Yi L, Pimentel H, Bray NL, Pachter L. PMID: 29650040; PMCID: PMC5896116.

Pseudoalignment for metagenomic read assignment. Bioinformatics. 2017 Jul 15; 33(14):2082-2088. Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. PMID: 28334086; PMCID: PMC5870846.

Differential analysis of RNA-seq incorporating quantification uncertainty. Nat Methods. 2017 Jul; 14(7):687-690. Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. PMID: 28581496.

Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways. PLoS One. 2017; 12(4):e0175744. Yi L, Pimentel H, Pachter L. PMID: 28448519; PMCID: PMC5407828.

The Lair: a resource for exploratory analysis of published RNA-Seq data. BMC Bioinformatics. 2016 Dec 01; 17(1):490. Pimentel H, Sturmfels P, Bray N, Melsted P, Pachter L. PMID: 27905880; PMCID: PMC5131447.

Erratum: Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016 08 09; 34(8):888. Bray NL, Pimentel H, Melsted P, Pachter L. PMID: 27504780.

Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016 05; 34(5):525-7. Bray NL, Pimentel H, Melsted P, Pachter L. PMID: 27043002.

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. Pimentel H, Parra M, Gee SL, Mohandas N, Pachter L, Conboy JG. PMID: 26531823; PMCID: PMC4737145.

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis. Nucleic Acids Res. 2014 Apr; 42(6):4031-42. Pimentel H, Parra M, Gee S, Ghanem D, An X, Li J, Mohandas N, Pachter L, Conboy JG. PMID: 24442673; PMCID: PMC3973340.

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013 Apr 25; 14(4):R36. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. PMID: 23618408; PMCID: PMC4053844.

Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011 Sep 01; 27(17):2325-9. Roberts A, Pimentel H, Trapnell C, Pachter L. PMID: 21697122.