| 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 | 13084 | 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 | 1375 | 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 | 1054 | 2016 |
| Quake: quality-aware detection and correction of sequencing errors DR Kelley, MC Schatz, SL Salzberg Genome Biology 11 (11), R116, 2010 | 737 | 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 | 698 | 2014 |
| 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 | 666 | 2021 |
| 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 | 637 | 2011 |
| Transposable elements reveal a stem cell specific class of long noncoding RNAs DR Kelley, JL Rinn Genome Biology 13 (11), R107, 2012 | 604 | 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 | 497 | 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 | 489 | 2013 |
| 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 | 454 | 2018 |
| 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 | 432 | 2008 |
| Widespread RNA binding by chromatin-associated proteins D G Hendrickson, DR Kelley, D Tenen, B Bernstein, JL Rinn Genome biology 17, 1-18, 2016 | 232 | 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 | 216 | 2012 |
| Predicting 3D genome folding from DNA sequence with Akita G Fudenberg, DR Kelley, KS Pollard Nature Methods 17 (11), 1111-1117, 2020 | 205 | 2020 |
| 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 | 178 | 2018 |
| Cross-species regulatory sequence activity prediction DR Kelley PLOS Computational Biology 16 (7), e1008050, 2020 | 173 | 2020 |
| 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 | 157 | 2020 |
| Clustering metagenomic sequences with interpolated Markov models D Kelley, S Salzberg BMC Bioinformatics 11 (1), 544, 2010 | 143 | 2010 |
| 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 | 138 | 2019 |
Steven SalzbergBloomberg Distinguished Professor, Johns Hopkins UniversityVerified email at jhu.edu
