Cole Trapnell
Cole Trapnell
Associate Professor, Dept. of Genome Sciences, University of Washington
Verified email at - Homepage
Cited by
Cited by
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
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
TopHat: discovering splice junctions with RNA-Seq
C Trapnell, L Pachter, SL Salzberg
Bioinformatics 25 (9), 1105-1111, 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
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
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
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
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
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
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
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
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
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
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
Identification of novel transcripts in annotated genomes using RNA-Seq
A Roberts, H Pimentel, C Trapnell, L Pachter
Bioinformatics 27 (17), 2325-2329, 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
Defining cell types and states with single-cell genomics
C Trapnell
Genome research 25 (10), 1491-1498, 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
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
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
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