David R Kelley

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John RinnUniversity of Colorado (CU Boulder)Verified email at colorado.edu
Steven SalzbergBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at jhu.edu
Cole TrapnellAssistant Professor, University of WashingtonVerified email at uw.edu
Loyal A. GoffJohns Hopkins Institute of Genetic MedicineVerified email at jhmi.edu
David Gillis HendricksonVerified email at calicolabs.com
Geo PerteaData/Software Engineer, Lieber Institute for Brain DevelopmentVerified email at jhu.edu
Michael C. SchatzBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at cs.jhu.edu
Lior PachterBren Professor of Computational Biology, CaltechVerified email at caltech.edu
Adam RobertsGoogle BrainVerified email at google.com
Daehwan KimMichael L. Rosenberg Assistant Professor of Bioinformatics at the University of Texas SouthwesternVerified email at UTSouthwestern.edu
James YorkeDist. Univ. Research Prof of Math and Physics, Univ. of MarylandVerified email at umd.edu
Aleksey V ZiminAssociate Research Scientist, Department of Biomedical Engineering, Johns Hopkins UnviersityVerified email at jhu.edu
Martin SauvageauAssistant Professor, Montreal Clinical Research Institute - IRCMVerified email at ircm.qc.ca
Ezgi HacisuleymanPostdoctoral fellow at Rockefeller UniversityVerified email at mail.rockefeller.edu
Mihai PopProfessor of Computer Science, University of Maryland, College ParkVerified email at umd.edu
Daniel D SommerNational Biodefense Analysis and Countermeasures CenterVerified email at nbacc.dhs.gov
Carl KingsfordProfessor, Computational Biology Department, School of Computer Science, CarnegieVerified email at cs.cmu.edu
Bo LiuEngineering Manager of Data Infrastructure, Square

David R Kelley

Calico Labs

Verified email at calicolabs.com - Homepage

Computational Biology


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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	12036	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, 1-10, 2009	1304	2009
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	857	2016
Quake: quality-aware detection and correction of sequencing errors DR Kelley, MC Schatz, SL Salzberg Genome Biology 11 (11), R116, 2010	705	2010
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	647	2014
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	606	2011
Transposable elements reveal a stem cell specific class of long noncoding RNAs DR Kelley, JL Rinn Genome Biology 13 (11), R107, 2012	540	2012
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	456	2013
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	456	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, 1-16, 2008	407	2008
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	307	2018
CummeRbund: visualization and exploration of Cufflinks high-throughput sequencing data LA Goff, C Trapnell, D Kelley R package version 2 (0), 2012	295	2012
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	252	2021
Widespread RNA binding by chromatin-associated proteins D G Hendrickson, DR Kelley, D Tenen, B Bernstein, JL Rinn Genome biology 17, 1-18, 2016	191	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	188	2012
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	138	2018
Clustering metagenomic sequences with interpolated Markov models D Kelley, S Salzberg BMC Bioinformatics 11 (1), 544, 2010	138	2010
Predicting 3D genome folding from DNA sequence with Akita G Fudenberg, DR Kelley, KS Pollard Nature Methods 17 (11), 1111-1117, 2020	112	2020
Murine single-cell RNA-seq reveals cell-identity-and tissue-specific trajectories of aging JC Kimmel, L Penland, ND Rubinstein, DG Hendrickson, DR Kelley, ... Genome research 29 (12), 2088-2103, 2019	96	2019
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	94	2014

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