| 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), R36, 2013 | 7470 | 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, 2012 | 7462 | 2012 |
| Near-optimal probabilistic RNA-seq quantification NL Bray, H Pimentel, P Melsted, L Pachter Nature biotechnology 34 (5), 525, 2016 | 1897 | 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 | 808 | 2011 |
| Differential analysis of RNA-seq incorporating quantification uncertainty H Pimentel, NL Bray, S Puente, P Melsted, L Pachter Nature methods 14 (7), 687, 2017 | 362 | 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, 2015 | 79 | 2015 |
| 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 | 69 | 2014 |
| Pseudoalignment for metagenomic read assignment L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter Bioinformatics 33 (14), 2082-2088, 2017 | 40 | 2017 |
| Intron retention is a source of neoepitopes in cancer AC Smart, CA Margolis, H Pimentel, MX He, D Miao, D Adeegbe, ... Nature biotechnology, 2018 | 33 | 2018 |
| Gene-level differential analysis at transcript-level resolution L Yi, H Pimentel, NL Bray, L Pachter Genome biology 19 (1), 53, 2018 | 20 | 2018 |
| 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), 490, 2016 | 14 | 2016 |
| Keep me around: intron retention detection and analysis H Pimentel, JG Conboy, L Pachter arXiv preprint arXiv:1510.00696, 2015 | 8 | 2015 |
| TopHat2: Parallel mapping of transcriptomes to detect InDels, gene fusions, and more DG Kim, G Pertea, C Trapnell, H Pimentel, R Kelley, SL Salzberg TopHat2, 2012 | 6 | 2012 |
| Zika infection of neural progenitor cells perturbs transcription in neurodevelopmental pathways L Yi, H Pimentel, L Pachter PloS one 12 (4), e0175744, 2017 | 5 | 2017 |
| Biclustering by sparse canonical correlation analysis H Pimentel, Z Hu, H Huang Quantitative Biology 6 (1), 56-67, 2018 | 4 | 2018 |
| Fusion detection and quantification by pseudoalignment P Melsted, S Hateley, IC Joseph, H Pimentel, NL Bray, L Pachter BioRxiv, 166322, 2017 | 2 | 2017 |
| CabFriendly: A Cloud-based Mobile Web App A Roberts, H Pimentel, S Karayevm Amazon’s EC2, 2011 | 2 | 2011 |
| Near-optimal RNA-Seq quantification N Bray, H Pimentel, P Melsted, L Pachter arXiv preprint 1505, 0 | 2 | |
| Intron retention as a novel source of cancer neoantigens A Smart | 1 | 2019 |
| 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, ... bioRxiv, 149385, 2019 | 1 | 2019 |
Lior PachterBren Professor of Computational Biology, CaltechVerified email at caltech.edu
