Harold Joseph Pimentel

Title(s)Assistant Professor, Computational Medicine
SchoolMedicine
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. Elife. 2025 Feb 17; 13. Estevam GO, Linossi E, Rao J, Macdonald CB, Ravikumar A, Chrispens KM, Capra JA, Coyote-Maestas W, Pimentel H, Collisson EA, Jura N, Fraser JS. PMID: 39960754; PMCID: PMC11832172.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. dotears: Scalable and consistent directed acyclic graph estimation using observational and interventional data. iScience. 2025 Feb 21; 28(2):111673. Xue A, Rao J, Sankararaman S, Pimentel H. PMID: 39944273; PMCID: PMC11814701.
      View in: PubMed   Mentions:
    3. Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv. 2024 Dec 05. 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. PMID: 39071407; PMCID: PMC11275805.
      View in: PubMed   Mentions:
    4. kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq. Nat Protoc. 2025 Mar; 20(3):587-607. Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. PMID: 39390263.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    5. A model for accurate quantification of CRISPR effects in pooled FACS screens. bioRxiv. 2024 Jun 18. Pimentel H, Freimer JW, Arce MM, Garrido CM, Marson A, Pritchard JK. PMID: 38948774; PMCID: PMC11213010.
      View in: PubMed   Mentions:
    6. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biol. 2024 05 24; 25(1):138. Rao J, Xin R, Macdonald C, Howard MK, Estevam GO, Yee SW, Wang M, Fraser JS, Coyote-Maestas W, Pimentel H. PMID: 38789982; PMCID: PMC11127319.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    7. Accounting for isoform expression increases power to identify genetic regulation of gene expression. PLoS Comput Biol. 2024 Feb; 20(2):e1011857. LaPierre N, Pimentel H. PMID: 38346082; PMCID: PMC10890775.
      View in: PubMed   Mentions: 2     Fields:    
    8. kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq. bioRxiv. 2024 Jan 23. Sullivan DK, Min KHJ, Hjörleifsson KE, Luebbert L, Holley G, Moses L, Gustafsson J, Bray NL, Pimentel H, Booeshaghi AS, Melsted P, Pachter L. PMID: 38045414; PMCID: PMC10690192.
      View in: PubMed   Mentions:
    9. An evolved AAV variant enables efficient genetic engineering of murine T cells. Cell. 2023 01 19; 186(2):446-460.e19. 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. PMID: 36638795; PMCID: PMC10540678.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    10. 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.
      View in: PubMed   Mentions: 33     Fields:    
    11. 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.
      View in: PubMed   Mentions: 6     Fields:    
    12. 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.
      View in: PubMed   Mentions: 43     Fields:    
    13. 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.
      View in: PubMed   Mentions: 126     Fields:    Translation:HumansCells
    14. 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.
      View in: PubMed   Mentions: 62     Fields:    Translation:Animals
    15. 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.
      View in: PubMed   Mentions: 43     Fields:    Translation:Cells
    16. 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.
      View in: PubMed   Mentions: 705     Fields:    Translation:Cells
    17. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansCells
    18. 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.
      View in: PubMed   Mentions: 8     Fields:    Translation:Humans
    19. 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.
      View in: PubMed   Mentions: 81     Fields:    
    20. Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol. 2016 05; 34(5):525-7. Bray NL, Pimentel H, Melsted P, Pachter L. PMID: 27043002.
      View in: PubMed   Mentions: 4162     Fields:    
    21. 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.
      View in: PubMed   Mentions: 103     Fields:    Translation:HumansCells
    22. 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.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    23. 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.
      View in: PubMed   Mentions: 6653     Fields:    Translation:HumansCells
    24. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012 Mar 01; 7(3):562-78. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. PMID: 22383036; PMCID: PMC3334321.
      View in: PubMed   Mentions: 6559     Fields:    
    25. 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.
      View in: PubMed   Mentions: 544     Fields:    Translation:HumansAnimals
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