Ultrafast and memory-efficient alignment of short DNA sequences to the human genome B Langmead, C Trapnell, M Pop, SL Salzberg Genome biology 10, 1-10, 2009 | 23495 | 2009 |
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation C Trapnell, BA Williams, G Pertea, A Mortazavi, G Kwan, MJ Van Baren, ... Nature biotechnology 28 (5), 511-515, 2010 | 15167 | 2010 |
TopHat: discovering splice junctions with RNA-Seq C Trapnell, L Pachter, SL Salzberg Bioinformatics 25 (9), 1105-1111, 2009 | 13334 | 2009 |
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 | 13248 | 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 | 12894 | 2012 |
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells C Trapnell, D Cacchiarelli, J Grimsby, P Pokharel, S Li, M Morse, ... Nature biotechnology 32 (4), 381-386, 2014 | 5114 | 2014 |
Differential analysis of gene regulation at transcript resolution with RNA-seq C Trapnell, DG Hendrickson, M Sauvageau, L Goff, JL Rinn, L Pachter Nature biotechnology 31 (1), 46-53, 2013 | 3827 | 2013 |
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses MN Cabili, C Trapnell, L Goff, M Koziol, B Tazon-Vega, A Regev, JL Rinn Genes & development 25 (18), 1915-1927, 2011 | 3743 | 2011 |
Reversed graph embedding resolves complex single-cell trajectories X Qiu, Q Mao, Y Tang, L Wang, R Chawla, HA Pliner, C Trapnell Nature methods 14 (10), 979-982, 2017 | 3058 | 2017 |
The single-cell transcriptional landscape of mammalian organogenesis J Cao, M Spielmann, X Qiu, X Huang, DM Ibrahim, AJ Hill, F Zhang, ... Nature 566 (7745), 496-502, 2019 | 2606 | 2019 |
Improving RNA-Seq expression estimates by correcting for fragment bias A Roberts, C Trapnell, J Donaghey, JL Rinn, L Pachter Genome biology 12, 1-14, 2011 | 1520 | 2011 |
Single-cell mRNA quantification and differential analysis with Census X Qiu, A Hill, J Packer, D Lin, YA Ma, C Trapnell Nature methods 14 (3), 309-315, 2017 | 1316 | 2017 |
Computational methods for transcriptome annotation and quantification using RNA-seq M Garber, MG Grabherr, M Guttman, C Trapnell Nature methods 8 (6), 469-477, 2011 | 1297 | 2011 |
Comprehensive single-cell transcriptional profiling of a multicellular organism J Cao, JS Packer, V Ramani, DA Cusanovich, C Huynh, R Daza, X Qiu, ... Science 357 (6352), 661-667, 2017 | 1296 | 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 | 1205 | 2011 |
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing DA Cusanovich, R Daza, A Adey, HA Pliner, L Christiansen, ... Science 348 (6237), 910-914, 2015 | 1197 | 2015 |
Defining cell types and states with single-cell genomics C Trapnell Genome research 25 (10), 1491-1498, 2015 | 807 | 2015 |
Joint profiling of chromatin accessibility and gene expression in thousands of single cells J Cao, DA Cusanovich, V Ramani, D Aghamirzaie, HA Pliner, AJ Hill, ... Science 361 (6409), 1380-1385, 2018 | 762 | 2018 |
A single-cell atlas of in vivo mammalian chromatin accessibility DA Cusanovich, AJ Hill, D Aghamirzaie, RM Daza, HA Pliner, JB Berletch, ... Cell 174 (5), 1309-1324. e18, 2018 | 695 | 2018 |
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre E Hacisuleyman, LA Goff, C Trapnell, A Williams, J Henao-Mejia, L Sun, ... Nature structural & molecular biology 21 (2), 198-206, 2014 | 680 | 2014 |