| An integrated encyclopedia of DNA elements in the human genome EP Consortium Nature 489 (7414), 57–74, 2012 | 11603 | 2012 |
| Integrative analysis of 111 reference human epigenomes A Kundaje, W Meuleman, J Ernst, M Bilenky, A Yen, A Heravi-Moussavi, ... Nature 518 (7539), 317-330, 2015 | 3801 | 2015 |
| ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ... Genome research 22 (9), 1813-1831, 2012 | 1562 | 2012 |
| Architecture of the human regulatory network derived from ENCODE data MB Gerstein, A Kundaje, M Hariharan, SG Landt, KK Yan, C Cheng, ... Nature 489 (7414), 91-100, 2012 | 1387 | 2012 |
| A comparative encyclopedia of DNA elements in the mouse genome F Yue, Y Cheng, A Breschi, J Vierstra, W Wu, T Ryba, R Sandstrom, Z Ma, ... Nature 515 (7527), 355-364, 2014 | 1304 | 2014 |
| A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS Biol 9 (4), e1001046, 2011 | 1216 | 2011 |
| Learning important features through propagating activation differences A Shrikumar, P Greenside, A Kundaje International Conference on Machine Learning, 3145-3153, 2017 | 1182* | 2017 |
| Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors J Wang, J Zhuang, S Iyer, XY Lin, TW Whitfield, MC Greven, BG Pierce, ... Genome research 22 (9), 1798-1812, 2012 | 856 | 2012 |
| Opportunities and obstacles for deep learning in biology and medicine T Ching, DS Himmelstein, BK Beaulieu-Jones, AA Kalinin, BT Do, ... Journal of The Royal Society Interface 15 (141), 20170387, 2018 | 760 | 2018 |
| Linking disease associations with regulatory information in the human genome MA Schaub, AP Boyle, A Kundaje, S Batzoglou, M Snyder Genome research 22 (9), 1748-1759, 2012 | 703 | 2012 |
| Defining functional DNA elements in the human genome M Kellis, B Wold, MP Snyder, BE Bernstein, A Kundaje, GK Marinov, ... Proceedings of the National Academy of Sciences 111 (17), 6131-6138, 2014 | 646 | 2014 |
| Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution MR Corces, JD Buenrostro, B Wu, PG Greenside, SM Chan, JL Koenig, ... Nature genetics 48 (10), 1193-1203, 2016 | 533 | 2016 |
| An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues MR Corces, AE Trevino, EG Hamilton, PG Greenside, ... Nature methods 14 (10), 959-962, 2017 | 493 | 2017 |
| Integrative annotation of chromatin elements from ENCODE data MM Hoffman, J Ernst, SP Wilder, A Kundaje, RS Harris, M Libbrecht, ... Nucleic acids research 41 (2), 827-841, 2013 | 485 | 2013 |
| Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers S Onengut-Gumuscu, WM Chen, O Burren, NJ Cooper, AR Quinlan, ... Nature genetics 47 (4), 381-386, 2015 | 413 | 2015 |
| Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease E Gjoneska, AR Pfenning, H Mathys, G Quon, A Kundaje, LH Tsai, ... Nature 518 (7539), 365-369, 2015 | 413 | 2015 |
| Long noncoding RNAs are rarely translated in two human cell lines B Bánfai, H Jia, J Khatun, E Wood, B Risk, WE Gundling, A Kundaje, ... Genome research 22 (9), 1646-1657, 2012 | 370 | 2012 |
| Extensive variation in chromatin states across humans M Kasowski, S Kyriazopoulou-Panagiotopoulou, F Grubert, JB Zaugg, ... Science 342 (6159), 750-752, 2013 | 338 | 2013 |
| Comparative analysis of metazoan chromatin organization JWK Ho, YL Jung, T Liu, BH Alver, S Lee, K Ikegami, KA Sohn, A Minoda, ... Nature 512 (7515), 449-452, 2014 | 306 | 2014 |
| H3K4me3 breadth is linked to cell identity and transcriptional consistency BA Benayoun, EA Pollina, D Ucar, S Mahmoudi, K Karra, ED Wong, ... Cell 158 (3), 673-688, 2014 | 300 | 2014 |
Peyton GreensideStanford UniversityVerified email at stanford.edu
