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Harold Joseph Pimentel

Title(s)Adjunct Instructor, Computational Medicine
SchoolMedicine
Address612 Charles E. Young Drive, Ea 5303
Los Angeles CA 90024
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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. 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.
      View in: PubMed   Mentions:    Fields:    
    2. 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.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    3. 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.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    4. 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.
      View in: PubMed   Mentions: 10     Fields:    Translation:Animals
    5. 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.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    6. 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: 215     Fields:    Translation:Cells
    7. 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.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    8. 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.
      View in: PubMed   Mentions: 5     Fields:    Translation:Humans
    9. 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: 24     Fields:    
    10. 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: 1021     Fields:    
    11. 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.
      View in: PubMed   Mentions: 54     Fields:    Translation:HumansCells
    12. 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.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    13. 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.
      View in: PubMed   Mentions: 4294     Fields:    Translation:HumansCells
    14. 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.
      View in: PubMed   Mentions: 4192     Fields:    
    15. 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: 424     Fields:    Translation:HumansAnimals
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