Cole Trapnell
TitleCited byYear
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
B Langmead, C Trapnell, M Pop, SL Salzberg
Genome biology 10 (3), R25, 2009
154282009
TopHat: discovering splice junctions with RNA-Seq
C Trapnell, L Pachter, SL Salzberg
Bioinformatics 25 (9), 1105-1111, 2009
93822009
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
90762010
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
75302013
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
75082012
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, 2013
23802013
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
23582011
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, 2014
12262014
Computational methods for transcriptome annotation and quantification using RNA-seq
M Garber, MG Grabherr, M Guttman, C Trapnell
Nature methods 8 (6), 469, 2011
9132011
Improving RNA-Seq expression estimates by correcting for fragment bias
A Roberts, C Trapnell, J Donaghey, JL Rinn, L Pachter
Genome biology 12 (3), R22, 2011
8212011
Identification of novel transcripts in annotated genomes using RNA-Seq
A Roberts, H Pimentel, C Trapnell, L Pachter
Bioinformatics 27 (17), 2325-2329, 2011
8142011
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, 2017
4372017
High-throughput sequence alignment using Graphics Processing Units
MC Schatz, C Trapnell, AL Delcher, A Varshney
BMC bioinformatics 8 (1), 474, 2007
4022007
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, 2014
3842014
Targeted RNA sequencing reveals the deep complexity of the human transcriptome
TR Mercer, DJ Gerhardt, ME Dinger, J Crawford, C Trapnell, JA Jeddeloh, ...
Nature biotechnology 30 (1), 99, 2012
3752012
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
3742015
How to map billions of short reads onto genomes
C Trapnell, SL Salzberg
Nature biotechnology 27 (5), 455, 2009
3742009
Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
CA Gifford, MJ Ziller, H Gu, C Trapnell, J Donaghey, A Tsankov, ...
Cell 153 (5), 1149-1163, 2013
3362013
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99 A
SL Salzberg, DD Sommer, MC Schatz, AM Phillippy, PD Rabinowicz, ...
BMC genomics 9 (1), 204, 2008
3362008
Long noncoding RNAs regulate adipogenesis
L Sun, LA Goff, C Trapnell, R Alexander, KA Lo, E Hacisuleyman, ...
Proceedings of the National Academy of Sciences 110 (9), 3387-3392, 2013
3312013
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Articles 1–20