Publications

• 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.
• 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.. American journal of human genetics, 2022.
• 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.
• 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.
• 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.. Nature biotechnology, 2018.
• Yi L, Pimentel H, Bray NL, Pachter L. Gene-level differential analysis at transcript-level resolution.. Genome biology, 2018.
• Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L. Pseudoalignment for metagenomic read assignment.. Bioinformatics (Oxford, England), 2017.
• Pimentel H, Bray NL, Puente S, Melsted P, Pachter L. Differential analysis of RNA-seq incorporating quantification uncertainty.. Nature methods, 2017.
• Yi L, Pimentel H, Pachter L. Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways.. PloS one, 2017.
• 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.
• Bray NL, Pimentel H, Melsted P, Pachter L. Erratum: Near-optimal probabilistic RNA-seq quantification.. Nature biotechnology, 2016.
• Bray NL, Pimentel H, Melsted P, Pachter L. Near-optimal probabilistic RNA-seq quantification.. Nature biotechnology, 2016.
• 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 research, 2015.
• 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 research, 2014.
• 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 biology, 2013.
• 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.. Nature protocols, 2012.
• Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq.. Bioinformatics (Oxford, England), 2011.