| Expanded encyclopaedias of DNA elements in the human and mouse genomes JE Moore, MJ Purcaro, HE Pratt, CB Epstein, N Shoresh, J Adrian, T Kawli, ... Nature 583 (7818), 699-710, 2020 | 1155 | 2020 |
| Comprehensive analysis of single cell ATAC-seq data with SnapATAC R Fang, S Preissl, Y Li, X Hou, J Lucero, X Wang, A Motamedi, AK Shiau, ... Nature communications 12 (1), 1337, 2021 | 359* | 2021 |
| Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation S Preissl, R Fang, H Huang, Y Zhao, R Raviram, DU Gorkin, Y Zhang, ... Nature neuroscience 21 (3), 432-439, 2018 | 296 | 2018 |
| An atlas of dynamic chromatin landscapes in mouse fetal development DU Gorkin*, I Barozzi*, Y Zhao*, Y Zhang*, H Huang*, AY Lee, B Li, ... Nature 583 (7818), 744-751, 2020 | 288 | 2020 |
| Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells Y Zhang*, T Li*, S Preissl*, ML Amaral, JD Grinstein, EN Farah, E Destici, ... Nature Genetics, 1-9, 2019 | 277 | 2019 |
| HPV integration in HNSCC correlates with survival outcomes, immune response signatures, and candidate drivers LA Koneva, Y Zhang, S Virani, PB Hall, JB McHugh, DB Chepeha, ... Molecular Cancer Research 16 (1), 90-102, 2018 | 182 | 2018 |
| Joint profiling of DNA methylation and chromatin architecture in single cells G Li, Y Liu, Y Zhang, N Kubo, M Yu, R Fang, M Kellis, B Ren Nature methods 16 (10), 991-993, 2019 | 177 | 2019 |
| Joint profiling of histone modifications and transcriptome in single cells from mouse brain C Zhu, Y Zhang, YE Li, J Lucero, MM Behrens, B Ren Nature Methods 18 (3), 283-292, 2021 | 174 | 2021 |
| PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data Y Zhang, YH Lin, TD Johnson, LS Rozek, MA Sartor Bioinformatics 30 (18), 2568-2575, 2014 | 134 | 2014 |
| Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number alterations, PIK3CA mutation, and pathway signatures Y Zhang, LA Koneva, S Virani, AE Arthur, A Virani, PB Hall, CD Warden, ... Clinical Cancer Research 22 (18), 4735-4745, 2016 | 132 | 2016 |
| Loss of CHD1 promotes heterogeneous mechanisms of resistance to AR-targeted therapy via chromatin dysregulation Z Zhang, C Zhou, X Li, SD Barnes, S Deng, E Hoover, CC Chen, YS Lee, ... Cancer cell 37 (4), 584-598. e11, 2020 | 107 | 2020 |
| CTCF mediates dosage-and sequence-context-dependent transcriptional insulation by forming local chromatin domains H Huang, Q Zhu, A Jussila, Y Han, B Bintu, C Kern, M Conte, Y Zhang, ... Nature Genetics 53 (7), 1064-1074, 2021 | 101 | 2021 |
| MAPS: model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments I Juric, M Yu, A Abnousi, R Raviram, R Fang, Y Zhao, Y Zhang, Y Qiu, ... PLoS computational biology 15 (4), e1006982, 2019 | 98 | 2019 |
| Perspectives on ENCODE MP Snyder, TR Gingeras, JE Moore, Z Weng, MB Gerstein, B Ren, ... Nature 583 (7818), 693-698, 2020 | 91 | 2020 |
| Cardiac cell type–specific gene regulatory programs and disease risk association JD Hocker, OB Poirion, F Zhu, J Buchanan, K Zhang, J Chiou, TM Wang, ... Science advances 7 (20), eabf1444, 2021 | 69 | 2021 |
| Genome-wide association and multi-omic analyses reveal ACTN2 as a gene linked to heart failure M Arvanitis, E Tampakakis, Y Zhang, W Wang, A Auton, D Dutta, ... Nature communications 11 (1), 1122, 2020 | 60 | 2020 |
| SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data M Yu, A Abnousi, Y Zhang, G Li, L Lee, Z Chen, R Fang, TM Lagler, ... Nature methods 18 (9), 1056-1059, 2021 | 47 | 2021 |
| Expressed HNSCC variants by HPV-status in a well-characterized Michigan cohort T Qin, Y Zhang, KR Zarins, TR Jones, S Virani, LA Peterson, JB McHugh, ... Scientific reports 8 (1), 11458, 2018 | 39 | 2018 |
| Topologically associating domain boundaries are required for normal genome function S Rajderkar, I Barozzi, Y Zhu, R Hu, Y Zhang, B Li, A Alcaina Caro, ... Communications Biology 6 (1), 435, 2023 | 24* | 2023 |
| A scalable epitope tagging approach for high throughput ChIP-Seq analysis X Xiong, Y Zhang, J Yan, S Jain, S Chee, B Ren, H Zhao ACS synthetic biology 6 (6), 1034-1042, 2017 | 21 | 2017 |
Bing Ren, Ph.D.University of California, San DiegoVerified email at ucsd.edu
