| 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 | 13583 | 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 | 13206 | 2012 |
| Near-optimal probabilistic RNA-seq quantification NL Bray, H Pimentel, P Melsted, L Pachter Nature biotechnology 34 (5), 525-527, 2016 | 8812 | 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 | 1509 | 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 | 1234 | 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 | 278 | 2018 |
| Erratum: Near-optimal probabilistic RNA-seq quantification NL Bray, H Pimentel, P Melsted, L Pachter Nature Biotechnology 34 (8), 888-888, 2016 | 224 | 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 | 192 | 2016 |
| Gene-level differential analysis at transcript-level resolution L Yi, H Pimentel, NL Bray, L Pachter Genome biology 19, 1-11, 2018 | 151 | 2018 |
| Pseudoalignment for metagenomic read assignment L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter Bioinformatics 33 (14), 2082-2088, 2017 | 111 | 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 | 102 | 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 | 101 | 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 | 52 | 2022 |
| 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 | 40 | 2023 |
| Fusion detection and quantification by pseudoalignment P Melsted, S Hateley, IC Joseph, H Pimentel, N Bray, L Pachter BioRxiv, 166322, 2017 | 33 | 2017 |
| Keep me around: intron retention detection and analysis H Pimentel, JG Conboy, L Pachter arXiv preprint arXiv:1510.00696, 2015 | 23 | 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 | 20 | 2016 |
| Biclustering by sparse canonical correlation analysis H Pimentel, Z Hu, H Huang Quantitative Biology 6 (1), 56-67, 2018 | 16 | 2018 |
| kallisto, bustools and kb-python for quantifying bulk, single-cell and single-nucleus RNA-seq DK Sullivan, KH Min, KE Hjörleifsson, L Luebbert, G Holley, L Moses, ... Nature Protocols, 1-21, 2024 | 14 | 2024 |
| Compositional Data Analysis is necessary for simulating and analyzing RNA-Seq data WA McGee, H Pimentel, L Pachter, JY Wu BioRxiv, 564955, 2019 | 13 | 2019 |
Lior PachterBren Professor of Computational Biology, CaltechVerified email at caltech.edu
