David R Kelley
David R Kelley
Calico Labs
Verified email at calicolabs.com - Homepage
TitleCited byYear
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
74622012
A whole-genome assembly of the domestic cow, Bos taurus
AV Zimin, AL Delcher, L Florea, DR Kelley, MC Schatz, D Puiu, ...
Genome biology 10 (4), R42, 2009
9542009
Quake: quality-aware detection and correction of sequencing errors
DR Kelley, MC Schatz, SL Salzberg
Genome Biology 11 (11), R116, 2010
5832010
Assemblathon 1: A competitive assessment of de novo short read assembly methods
DA Earl, K Bradnam, JS John, A Darling, D Lin, J Faas, HOK Yu, B Vince, ...
Genome Research, 2011
4962011
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
3792014
Transposable elements reveal a stem cell specific class of long noncoding RNAs
DR Kelley, JL Rinn
Genome Biology 13 (11), R107, 2012
3382012
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
3352013
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
S Salzberg, D Sommer, M Schatz, A Phillippy, P Rabinowicz, S Tsuge, ...
BMC genomics 9 (1), 204, 2008
3342008
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
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
DR Kelley, J Snoek, JL Rinn
Genome research 26 (7), 990-999, 2016
3292016
cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data
L Goff, C Trapnell, D Kelley
R package version 2 (0), 2013
1502013
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering
DR Kelley, B Liu, AL Delcher, M Pop, SL Salzberg
Nucleic Acids Research 40 (1), e9-e9, 2012
1272012
Clustering metagenomic sequences with interpolated Markov models
D Kelley, S Salzberg
BMC Bioinformatics 11 (1), 544, 2010
1042010
Widespread RNA binding by chromatin-associated proteins
D Hendrickson, DR Kelley, D Tenen, B Bernstein, JL Rinn
Genome biology 17 (1), 28, 2016
942016
Detection and correction of false segmental duplications caused by genome mis-assembly
DR Kelley, SL Salzberg
Genome Biology 11 (3), R28, 2010
652010
Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions
DR Kelley, DG Hendrickson, D Tenen, JL Rinn
Genome Biology 15 (12), 537, 2014
632014
De novo assembly of large genomes using cloud computing
MC Schatz, D Sommer, D Kelley, M Pop
Proceedings of the Cold Spring Harbor Biology of Genomes Conference, 2010
462010
Genetic determinants and epigenetic effects of pioneer-factor occupancy
J Donaghey, S Thakurela, J Charlton, JS Chen, ZD Smith, H Gu, R Pop, ...
Nature genetics 50 (2), 250, 2018
422018
Sequential regulatory activity prediction across chromosomes with convolutional neural networks
DR Kelley, YA Reshef, M Bileschi, D Belanger, CY McLean, J Snoek
Genome research 28 (5), 739-750, 2018
402018
Mis-assembled “segmental duplications” in two versions of the Bos taurus genome
AV Zimin, DR Kelley, M Roberts, G Marçais, SL Salzberg, JA Yorke
PLoS One 7 (8), e42680, 2012
292012
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