David R Kelley
David R Kelley
Calico Labs
Verified email at calicolabs.com - Homepage
Cited by
Cited by
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
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), 1-10, 2009
Quake: quality-aware detection and correction of sequencing errors
DR Kelley, MC Schatz, SL Salzberg
Genome Biology 11 (11), R116, 2010
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
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
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
Transposable elements reveal a stem cell specific class of long noncoding RNAs
DR Kelley, JL Rinn
Genome Biology 13 (11), R107, 2012
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
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
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), 1-16, 2008
cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data
L Goff, C Trapnell, D Kelley
R package version 2 (0), 2013
Widespread RNA binding by chromatin-associated proteins
DG Hendrickson, DR Kelley, D Tenen, B Bernstein, JL Rinn
Genome biology 17 (1), 1-18, 2016
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
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
Clustering metagenomic sequences with interpolated Markov models
D Kelley, S Salzberg
BMC Bioinformatics 11 (1), 544, 2010
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), 250-258, 2018
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
Detection and correction of false segmental duplications caused by genome mis-assembly
DR Kelley, SL Salzberg
Genome Biology 11 (3), R28, 2010
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
Recurrent noncoding regulatory mutations in pancreatic ductal adenocarcinoma
ME Feigin, T Garvin, P Bailey, N Waddell, DK Chang, DR Kelley, S Shuai, ...
Nature genetics 49 (6), 825-833, 2017
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