Harold Pimentel
Harold Pimentel
Assistant Professor, UCLA
Verified email at - Homepage
Cited by
Cited by
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
D Kim, G Pertea, C Trapnell, H Pimentel, R Kelley, SL Salzberg
Genome biology 14, 1-13, 2013
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
C Trapnell, A Roberts, L Goff, G Pertea, D Kim, DR Kelley, H Pimentel, ...
Nature protocols 7 (3), 562-578, 2012
Near-optimal probabilistic RNA-seq quantification
NL Bray, H Pimentel, P Melsted, L Pachter
Nature biotechnology 34 (5), 525-527, 2016
Differential analysis of RNA-seq incorporating quantification uncertainty
H Pimentel, NL Bray, S Puente, P Melsted, L Pachter
Nature methods 14 (7), 687-690, 2017
Identification of novel transcripts in annotated genomes using RNA-Seq
A Roberts, H Pimentel, C Trapnell, L Pachter
Bioinformatics 27 (17), 2325-2329, 2011
Intron retention is a source of neoepitopes in cancer
AC Smart, CA Margolis, H Pimentel, MX He, D Miao, D Adeegbe, ...
Nature biotechnology 36 (11), 1056-1058, 2018
Erratum: Near-optimal probabilistic RNA-seq quantification
NL Bray, H Pimentel, P Melsted, L Pachter
Nature Biotechnology 34 (8), 888-888, 2016
A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis
H Pimentel, M Parra, SL Gee, N Mohandas, L Pachter, JG Conboy
Nucleic acids research 44 (2), 838-851, 2016
Gene-level differential analysis at transcript-level resolution
L Yi, H Pimentel, NL Bray, L Pachter
Genome biology 19, 1-11, 2018
Pseudoalignment for metagenomic read assignment
L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter
Bioinformatics 33 (14), 2082-2088, 2017
A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis
H Pimentel, M Parra, S Gee, D Ghanem, X An, J Li, N Mohandas, ...
Nucleic acids research 42 (6), 4031-4042, 2014
Evolutionary persistence of DNA methylation for millions of years after ancient loss of a de novo methyltransferase
S Catania, PA Dumesic, H Pimentel, A Nasif, CI Stoddard, JE Burke, ...
Cell 180 (2), 263-277. e20, 2020
Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits
RA Patel, SA Musharoff, JP Spence, H Pimentel, C Tcheandjieu, ...
The American Journal of Human Genetics 109 (7), 1286-1297, 2022
Fusion detection and quantification by pseudoalignment
P Melsted, S Hateley, IC Joseph, H Pimentel, N Bray, L Pachter
BioRxiv, 166322, 2017
An evolved AAV variant enables efficient genetic engineering of murine T cells
WA Nyberg, J Ark, A To, S Clouden, G Reeder, JJ Muldoon, JY Chung, ...
Cell 186 (2), 446-460. e19, 2023
Keep me around: intron retention detection and analysis
H Pimentel, JG Conboy, L Pachter
arXiv preprint arXiv:1510.00696, 2015
The Lair: a resource for exploratory analysis of published RNA-Seq data
H Pimentel, P Sturmfels, N Bray, P Melsted, L Pachter
BMC bioinformatics 17, 1-6, 2016
Biclustering by sparse canonical correlation analysis
H Pimentel, Z Hu, H Huang
Quantitative Biology 6 (1), 56-67, 2018
Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data
WA McGee, H Pimentel, L Pachter, JY Wu
BioRxiv, 564955, 2019
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
L Yi, H Pimentel, L Pachter
PLoS One 12 (4), e0175744, 2017
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