David R Kelley
David R Kelley
Calico Labs
Verified email at calicolabs.com - Homepage
Title
Cited by
Cited by
Year
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
92262012
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
11022009
Quake: quality-aware detection and correction of sequencing errors
DR Kelley, MC Schatz, SL Salzberg
Genome Biology 11 (11), R116, 2010
6292010
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
5242011
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
4832016
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
4682014
Transposable elements reveal a stem cell specific class of long noncoding RNAs
DR Kelley, JL Rinn
Genome Biology 13 (11), R107, 2012
4072012
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
3682013
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
3662013
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
3592008
cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data
L Goff, C Trapnell, D Kelley
R package version 2 (0), 2013
1802013
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
1392012
Widespread RNA binding by chromatin-associated proteins
D Hendrickson, DR Kelley, D Tenen, B Bernstein, JL Rinn
Genome biology 17 (1), 28, 2016
1312016
Clustering metagenomic sequences with interpolated Markov models
D Kelley, S Salzberg
BMC Bioinformatics 11 (1), 544, 2010
1122010
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
962018
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
762014
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
692018
Detection and correction of false segmental duplications caused by genome mis-assembly
DR Kelley, SL Salzberg
Genome Biology 11 (3), R28, 2010
682010
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
482010
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
342012
The system can't perform the operation now. Try again later.
Articles 1–20