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David R Kelley
David R Kelley
Calico Labs
在 calicolabs.com 的电子邮件经过验证 - 首页
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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
113072012
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
12592009
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
7632016
Quake: quality-aware detection and correction of sequencing errors
DR Kelley, MC Schatz, SL Salzberg
Genome Biology 11 (11), R116, 2010
6852010
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
5922014
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
5792011
Transposable elements reveal a stem cell specific class of long noncoding RNAs
DR Kelley, JL Rinn
Genome Biology 13 (11), R107, 2012
5002012
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
4322013
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
4222013
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), 1-16, 2008
3872008
CummeRbund: visualization and exploration of Cufflinks high-throughput sequencing data
LA Goff, C Trapnell, D Kelley
R package version 2 (0), 2012
2992012
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
2282018
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
1772012
Widespread RNA binding by chromatin-associated proteins
D G Hendrickson, DR Kelley, D Tenen, B Bernstein, JL Rinn
Genome biology 17 (1), 1-18, 2016
1732016
Clustering metagenomic sequences with interpolated Markov models
D Kelley, S Salzberg
BMC Bioinformatics 11 (1), 544, 2010
1322010
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
1102018
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
1022021
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
862014
Detection and correction of false segmental duplications caused by genome mis-assembly
DR Kelley, SL Salzberg
Genome Biology 11 (3), R28, 2010
852010
Predicting 3D genome folding from DNA sequence with Akita
G Fudenberg, DR Kelley, KS Pollard
Nature Methods 17 (11), 1111-1117, 2020
662020
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