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David R. Kelley

Genome Biology, Nature Methods, Nature Protocols, Genome Research, Nature Structural &Molecular Biology, Cell, Proceedings of the National Academy of Sciences of the United States of America, BMC Genomics Show more
14
Role
Title
Level Year L/R
🐜 Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
10 auth. C. Trapnell, Adam Roberts, L. Goff, G. Pertea, Daehwan Kim, David R. Kelley, ... Harold Pimentel, S. Salzberg, J. Rinn, L. Pachter 		13 2012
13
🐜
🐜 A whole-genome assembly of the domestic cow, Bos taurus
15 auth. A. Zimin, A. Delcher, L. Florea, David R. Kelley, M. Schatz, D. Puiu, Finnian Hanrahan, G. Pertea, C. V. Van Tassell, T. Sonstegard, ... G. Marçais, Michael Roberts, P. Subramanian, J. Yorke, S. Salzberg 		10 2009
10
🐜
🦁 Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks
David R. Kelley, Jasper Snoek, J. Rinn 		9 2015
9
🦁
🐒 Effective gene expression prediction from sequence by integrating long-range interactions
10 auth. Ε½iga Avsec, Vikram Agarwal, D. Visentin, J. Ledsam, A. Grabska-Barwinska, Kyle R. Taylor, ... Yannis Assael, J. Jumper, Pushmeet Kohli, David R. Kelley 		9 2021
9
🐒
🦁 Quake: quality-aware detection and correction of sequencing errors
David R. Kelley, M. Schatz, S. Salzberg 		9 2010
9
🦁
🐜 Assemblathon 1: a competitive assessment of de novo short read assembly methods.
71 auth. Dent Earl, K. Bradnam, John A St John, A. Darling, D. Lin, Joseph N. Fass, H. O. Yu, Vince Buffalo, D. Zerbino, M. Diekhans, N. Nguyen, P. Ariyaratne, W. Sung, Z. Ning, M. Haimel, ... J. Simpson, Nuno A. Fonseca, I. Birol, T. R. Docking, Isaac Y. Ho, D. Rokhsar, R. Chikhi, D. Lavenier, Guillaume Chapuis, D. Naquin, Nicolas Maillet, M. Schatz, David R. Kelley, A. Phillippy, S. Koren, Shiaw-Pyng Yang, Wei Wu, Wen-Chi Chou, Anuj Srivastava, T. Shaw, J. Ruby, Peter Skewes-Cox, Miguel Betegon, M. Dimon, Victor V. Solovyev, I. Seledtsov, P. D. Kosarev, D. Vorobyev, R. Ramirez-Gonzalez, R. Leggett, D. MacLean, Fangfang Xia, Ruibang Luo, Zhenyu Li, Yinlong Xie, Binghang Liu, S. Gnerre, Iain MacCallum, Dariusz Przybylski, Filipe J. Ribeiro, Shuangye Yin, Ted Sharpe, Giles Hall, P. Kersey, R. Durbin, S. Jackman, Jarrod Chapman, Xiaoqiu Huang, J. Derisi, M. CΓ‘ccamo, Yingrui Li, D. Jaffe, R. Green, D. Haussler, I. Korf, B. Paten 		9 2011
9
🐜
🐜 Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
18 auth. Ezgi Hacisuleyman, L. Goff, C. Trapnell, Adam Williams, Jorge Henao-Mejia, Lei Sun, P. McClanahan, David G Hendrickson, Martin Sauvageau, David R. Kelley, ... Michael Morse, J. Engreitz, E. Lander, M. Guttman, H. Lodish, R. Flavell, A. Raj, J. Rinn 		8 2014
8
🐜
🦁 Transposable elements reveal a stem cell-specific class of long noncoding RNAs
David R. Kelley, J. Rinn 		8 2012
8
🦁
🐜 Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
24 auth. Casey A. Gifford, M. Ziller, H. Gu, C. Trapnell, Julie Donaghey, Alexander M. Tsankov, A. Shalek, David R. Kelley, Alexander A. Shishkin, Robbyn Issner, ... Xiaolan Zhang, Michael J. Coyne, Jennifer L. Fostel, Laurie Holmes, J. Meldrim, M. Guttman, C. Epstein, Hongkun Park, O. Kohlbacher, Johannes Rinn, A. Gnirke, E. Lander, B. Bernstein, A. Meissner 		8 2013
8
🐜
🦁 Sequential regulatory activity prediction across chromosomes with convolutional neural networks
David R. Kelley, Yakir A. Reshef, Maxwell L. Bileschi, David Belanger, Cory Y. McLean, Jasper Snoek 		8 2017
8
🦁
🐜 Long noncoding RNAs regulate adipogenesis
14 auth. Lei Sun, L. Goff, C. Trapnell, Ryan K. Alexander, Kinyui A. Lo, Ezgi Hacisuleyman, Martin Sauvageau, B. TazΓ³n-Vega, David R. Kelley, David G Hendrickson, ... Bingbing Yuan, Manolis Kellis, H. Lodish, J. Rinn 		8 2013
8
🐜
🐜 Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A
37 auth. S. Salzberg, Daniel D. Sommer, M. Schatz, A. Phillippy, P. Rabinowicz, S. Tsuge, Ayako Furutani, H. Ochiai, A. Delcher, David R. Kelley, R. Madupu, D. Puiu, D. Radune, Martin Shumway, C. Trapnell, ... G. Aparna, G. Jha, A. Pandey, P. Patil, H. Ishihara, D. Meyer, B. Szurek, V. Verdier, R. Koebnik, J. Dow, R. Ryan, H. Hirata, S. Tsuyumu, Sang Won Lee, Young-Su Seo, Malinee Sriariyanum, P. Ronald, R. V. Sonti, M. van Sluys, J. Leach, F. White, A. Bogdanove 		8 2008
8
🐜
🐬 Widespread RNA binding by chromatin-associated proteins
David G Hendrickson, David R. Kelley, D. Tenen, B. Bernstein, J. Rinn 		7 2016
7
🐬
🐬 Predicting 3D genome folding from DNA sequence with Akita
G. Fudenberg, David R. Kelley, K. Pollard 		7 2020
7
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