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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
126512012
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, 1-10, 2009
13552009
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
9662016
Quake: quality-aware detection and correction of sequencing errors
DR Kelley, MC Schatz, SL Salzberg
Genome Biology 11 (11), R116, 2010
7222010
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
6742014
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
6262011
Transposable elements reveal a stem cell specific class of long noncoding RNAs
DR Kelley, JL Rinn
Genome Biology 13 (11), R107, 2012
5792012
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
4812013
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
4812013
Effective gene expression prediction from sequence by integrating long-range interactions
Ž Avsec, V Agarwal, D Visentin, JR Ledsam, A Grabska-Barwinska, ...
Nature methods 18 (10), 1196-1203, 2021
4612021
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
SL Salzberg, DD Sommer, MC Schatz, AM Phillippy, PD Rabinowicz, ...
BMC genomics 9, 1-16, 2008
4162008
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
3842018
CummeRbund: visualization and exploration of Cufflinks high-throughput sequencing data
LA Goff, C Trapnell, D Kelley
R package version 2 (0), 2012
3042012
Widespread RNA binding by chromatin-associated proteins
D G Hendrickson, DR Kelley, D Tenen, B Bernstein, JL Rinn
Genome biology 17, 1-18, 2016
2092016
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
2002012
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
1562018
Predicting 3D genome folding from DNA sequence with Akita
G Fudenberg, DR Kelley, KS Pollard
Nature Methods 17 (11), 1111-1117, 2020
1552020
Clustering metagenomic sequences with interpolated Markov models
D Kelley, S Salzberg
BMC Bioinformatics 11 (1), 544, 2010
1382010
Cross-species regulatory sequence activity prediction
DR Kelley
PLOS Computational Biology 16 (7), e1008050, 2020
1312020
Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning
NJ Bernstein, NL Fong, I Lam, MA Roy, DG Hendrickson, DR Kelley
Cell Systems 11 (1), 95-101. e5, 2020
1222020
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Articles 1–20