Harold Pimentel
Harold Pimentel
Assistant Professor, UCLA
Verified email at ucla.edu - 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 (4), 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
Identification of novel transcripts in annotated genomes using RNA-Seq
A Roberts, H Pimentel, C Trapnell, L Pachter
Bioinformatics 27 (17), 2325-2329, 2011
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
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
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
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
Gene-level differential analysis at transcript-level resolution
L Yi, H Pimentel, NL Bray, L Pachter
Genome biology 19 (1), 1-11, 2018
Near-optimal RNA-Seq quantification
N Bray, H Pimentel, P Melsted, L Pachter
arXiv preprint arXiv:1505.02710, 2015
Pseudoalignment for metagenomic read assignment
L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter
Bioinformatics 33 (14), 2082-2088, 2017
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
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), 1-6, 2016
Fusion detection and quantification by pseudoalignment
P Melsted, S Hateley, IC Joseph, H Pimentel, N Bray, L Pachter
bioRxiv, 166322, 2017
Keep me around: intron retention detection and analysis
H Pimentel, JG Conboy, L Pachter
arXiv preprint arXiv:1510.00696, 2015
Biclustering by sparse canonical correlation analysis
H Pimentel, Z Hu, H Huang
Quantitative Biology 6 (1), 56-67, 2018
Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways
L Yi, H Pimentel, L Pachter
PloS one 12 (4), e0175744, 2017
TopHat2: parallel mapping of transcriptomes to detect InDels, gene fusions, and more
DG Kim, G Pertea, C Trapnell, H Pimentel, R Kelley, SL Salzberg
Genomics & Informatics 10, 263-265, 2012
Compositional data analysis is necessary for simulating and analyzing rna-seq data
WA McGee, H Pimentel, L Pachter, JY Wu
CabFriendly: A Cloud-based Mobile Web App
A Roberts, H Pimentel, S Karayevm
Amazon’s EC2, 2011
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