| An integrated encyclopedia of DNA elements in the human genome ENCODE Project Consortium Nature 489 (7414), 57, 2012 | 17337 | 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 | 1720 | 2012 |
| Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, ... Science 330 (6012), 1775-1787, 2010 | 1146 | 2010 |
| A user's guide to the encyclopedia of DNA elements (ENCODE) ENCODE Project Consortium PLoS biology 9 (4), e1001046, 2011 | 875 | 2011 |
| A user's guide to the encyclopedia of DNA elements (ENCODE) RM Myers, J Stamatoyannopoulos, M Snyder, I Dunham, RC Hardison, ... PLoS biology 9 (4), 2011 | 684 | 2011 |
| Comparative analysis of the transcriptome across distant species MB Gerstein, J Rozowsky, KK Yan, D Wang, C Cheng, JB Brown, ... Nature 512 (7515), 445-448, 2014 | 340 | 2014 |
| Ranking scientific publications using a model of network traffic D Walker, H Xie, KK Yan, S Maslov Journal of Statistical Mechanics: Theory and Experiment 2007 (06), P06010, 2007 | 339 | 2007 |
| Comparative analysis of regulatory information and circuits across distant species AP Boyle, CL Araya, C Brdlik, P Cayting, C Cheng, Y Cheng, K Gardner, ... Nature 512 (7515), 453-456, 2014 | 230 | 2014 |
| Understanding transcriptional regulation by integrative analysis of transcription factor binding data C Cheng, R Alexander, R Min, J Leng, KY Yip, J Rozowsky, KK Yan, ... Genome research 22 (9), 1658-1667, 2012 | 203 | 2012 |
| The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors MM Kudron, A Victorsen, L Gevirtzman, LDW Hillier, WW Fisher, ... Genetics 208 (3), 937-949, 2018 | 192 | 2018 |
| A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets C Cheng, KK Yan, KY Yip, J Rozowsky, R Alexander, C Shou, M Gerstein Genome biology 12, 1-18, 2011 | 181 | 2011 |
| Measuring the reproducibility and quality of Hi-C data GG Yardımcı, H Ozadam, MEG Sauria, O Ursu, KK Yan, T Yang, ... Genome biology 20, 1-19, 2019 | 180 | 2019 |
| Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data KY Yip, RP Alexander, KK Yan, M Gerstein PloS one 5 (1), e8121, 2010 | 147 | 2010 |
| An integrative ENCODE resource for cancer genomics J Zhang, D Lee, V Dhiman, P Jiang, J Xu, P McGillivray, H Yang, J Liu, ... Nature communications 11 (1), 3696, 2020 | 133 | 2020 |
| Measuring the evolutionary rewiring of biological networks C Shou, N Bhardwaj, HYK Lam, KK Yan, PM Kim, M Snyder, MB Gerstein PLoS computational biology 7 (1), e1001050, 2011 | 124 | 2011 |
| Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data C Cheng, KK Yan, W Hwang, J Qian, N Bhardwaj, J Rozowsky, ZJ Lu, ... PLoS computational biology 7 (11), e1002190, 2011 | 120 | 2011 |
| Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein Proceedings of National Academy of Science 107 (20), 9186, 2010 | 110 | 2010 |
| HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps MG Koon-Kiu Yan, Galip Gürkan Yardımcı, Chengfei Yan, William S. Noble Bioinformatics, 2017 | 95 | 2017 |
| Supervised enhancer prediction with epigenetic pattern recognition and targeted validation A Sethi, M Gu, E Gumusgoz, L Chan, KK Yan, J Rozowsky, I Barozzi, ... Nature methods 17 (8), 807-814, 2020 | 89 | 2020 |
| Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels N Bhardwaj, KK Yan, MB Gerstein Proceedings of the National Academy of Sciences 107 (15), 6841-6846, 2010 | 86 | 2010 |
Mark GersteinProfessor of Biomedical Informatics, Yale UniversityVerified email at yale.edu
