| An integrated software system for analyzing ChIP-chip and ChIP-seq data H Ji, H Jiang, W Ma, DS Johnson, RM Myers, WH Wong Nature biotechnology 26 (11), 1293-1300, 2008 | 875 | 2008 |
| TERT promotes epithelial proliferation through transcriptional control of a Myc-and Wnt-related developmental program J Choi, LK Southworth, KY Sarin, AS Venteicher, W Ma, W Chang, ... PLoS Genet 4 (1), e10, 2008 | 418 | 2008 |
| Escape from X Inactivation Varies in Mouse Tissues JB Berletch, W Ma, F Yang, J Shendure, WS Noble, CM Disteche, X Deng PLOS Genetics 11 (3), e1005079, 2015 | 346 | 2015 |
| Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks JS Park, W Ma, LL O'Brien, E Chung, JJ Guo, JG Cheng, MT Valerius, ... Developmental cell 23 (3), 637-651, 2012 | 304 | 2012 |
| The lncRNA Firre anchors the inactive X chromosome to the nucleolus by binding CTCF and maintains H3K27me3 methylation F Yang, X Deng, W Ma, JB Berletch, N Rabaia, G Wei, JM Moore, ... Genome biology 16 (1), 52, 2015 | 301 | 2015 |
| Bipartite structure of the inactive mouse X chromosome X Deng, W Ma, V Ramani, A Hill, F Yang, F Ay, JB Berletch, CA Blau, ... Genome biology 16 (1), 152, 2015 | 267 | 2015 |
| Motif-based analysis of large nucleotide data sets using MEME-ChIP W Ma, WS Noble, TL Bailey Nature protocols 9 (6), 1428-1450, 2014 | 265 | 2014 |
| Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes W Ma, F Ay, C Lee, G Gulsoy, X Deng, S Cook, J Hesson, C Cavanaugh, ... Nature methods 12 (1), 71-78, 2015 | 228 | 2015 |
| Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning KA Peterson, Y Nishi, W Ma, A Vedenko, L Shokri, X Zhang, M McFarlane, ... Genes & Development 26 (24), 2802-2816, 2012 | 200 | 2012 |
| Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis EY Lee, H Ji, Z Ouyang, B Zhou, W Ma, SA Vokes, AP McMahon, ... Proceedings of the National Academy of Sciences 107 (21), 9736-9741, 2010 | 148 | 2010 |
| Mapping 3D genome architecture through in situ DNase Hi-C V Ramani, DA Cusanovich, RJ Hause, W Ma, R Qiu, X Deng, CA Blau, ... Nature protocols 11 (11), 2104-2121, 2016 | 140 | 2016 |
| Mammalian X Upregulation Is Associated with Enhanced Transcription Initiation, RNA Half-Life, and MOF-Mediated H4K16 Acetylation X Deng, JB Berletch, W Ma, DK Nguyen, JB Hiatt, WS Noble, J Shendure, ... Developmental Cell, 2013 | 119 | 2013 |
| Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B Y Qiu, EK Pasoreck, AK Reddy, A Nagatani, W Ma, J Chory, M Chen Nature communications 8 (1), 1905, 2017 | 92 | 2017 |
| Concurrent gut transcriptome and microbiota profiling following chronic ethanol consumption in nonhuman primates T Barr, S Sureshchandra, P Ruegger, J Zhang, W Ma, J Borneman, ... Gut microbes 9 (4), 338-356, 2018 | 57 | 2018 |
| Using CisGenome to Analyze ChIP‐chip and ChIP‐seq Data H Ji, H Jiang, W Ma, WH Wong Current Protocols in Bioinformatics 2, 2, 2011 | 53 | 2011 |
| Insight into Insulin Secretion from Transcriptome and Genetic Analysis of Insulin-Producing Cells of Drosophila J Cao, J Ni, W Ma, V Shiu, LA Milla, S Park, ML Spletter, S Tang, J Zhang, ... Genetics 197 (1), 175-192, 2014 | 51 | 2014 |
| The analysis of ChIP-Seq data W Ma, WH Wong Methods in enzymology 497, 51-73, 2011 | 40 | 2011 |
| Using DNase Hi-C techniques to map global and local three-dimensional genome architecture at high resolution W Ma, F Ay, C Lee, G Gulsoy, X Deng, S Cook, J Hesson, C Cavanaugh, ... Methods 142, 59-73, 2018 | 38 | 2018 |
| Babesia duncani multi-omics identifies virulence factors and drug targets P Singh, S Lonardi, Q Liang, P Vydyam, E Khabirova, T Fang, S Gihaz, ... Nature Microbiology, 1-15, 2023 | 35 | 2023 |
| DNA sequence+ shape kernel enables alignment-free modeling of transcription factor binding W Ma, L Yang, R Rohs, WS Noble Bioinformatics 33 (19), 3003-3010, 2017 | 29 | 2017 |
