Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome

by Irene Unterman, Idit Bloch, Simona Cazacu, Gila Kazimirsky, Bruria Ben-Zeev, Benjamin P Berman, Chaya Brodie, Yuval Tabach
Published 2021-08-01

Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes

by Yueyuan Zheng, Guowei Huang, Tiago C. Silva, Qian Yang, Yan-Yi Jiang, H. Phillip Koeffler, De-Chen Lin, Benjamin P. Berman
Published 2021-06-01

A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes

by Yueyuan Zheng, Guowei Huang, Tiago C. Silva, Qian Yang, Yan-Yi Jiang, H. Phillip Koeffler, De-Chen Lin, Benjamin P. Berman
Published 2021-04-01

Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity.

by Li Jia, Benjamin P Berman, Unnati Jariwala, Xiting Yan, Jon P Cogan, Allison Walters, Ting Chen, Grant Buchanan, Baruch Frenkel, Gerhard A Coetzee
Published 2008-01-01

GENAVi: a shiny web application for gene expression normalization, analysis and visualization

by Alberto Luiz P. Reyes, Tiago C. Silva, Simon G. Coetzee, Jasmine T. Plummer, Brian D. Davis, Stephanie Chen, Dennis J. Hazelett, Kate Lawrenson, Benjamin P. Berman, Simon A. Gayther, Michelle R. Jones
Published 2019-10-01

Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation.

by Crystal N Marconett, Beiyun Zhou, Megan E Rieger, Suhaida A Selamat, Mickael Dubourd, Xiaohui Fang, Sean K Lynch, Theresa Ryan Stueve, Kimberly D Siegmund, Benjamin P Berman, Zea Borok, Ite A Laird-Offringa
Published 2013-06-01

Functional enhancers at the gene-poor 8q24 cancer-linked locus.

by Li Jia, Gilad Landan, Mark Pomerantz, Rami Jaschek, Paula Herman, David Reich, Chunli Yan, Omar Khalid, Phil Kantoff, William Oh, J Robert Manak, Benjamin P Berman, Brian E Henderson, Baruch Frenkel, Christopher A Haiman, Matthew Freedman, Amos Tanay, Gerhard A Coetzee
Published 2009-08-01

Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer

by Rosario I. Corona, Ji-Heui Seo, Xianzhi Lin, Dennis J. Hazelett, Jessica Reddy, Marcos A. S. Fonseca, Forough Abassi, Yvonne G. Lin, Paulette Y. Mhawech-Fauceglia, Sohrab P. Shah, David G. Huntsman, Alexander Gusev, Beth Y. Karlan, Benjamin P. Berman, Matthew L. Freedman, Simon A. Gayther, Kate Lawrenson
Published 2020-04-01

FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer

by Bingchen Han, Ying Qu, Yanli Jin, Yi Yu, Nan Deng, Kolja Wawrowsky, Xiao Zhang, Na Li, Shikha Bose, Qiang Wang, Sugunadevi Sakkiah, Ravinder Abrol, Tor W. Jensen, Benjamin P. Berman, Hisashi Tanaka, Jeffrey Johnson, Bowen Gao, Jijun Hao, Zhenqiu Liu, Ralph Buttyan, Partha S. Ray, Mien-Chie Hung, Armando E. Giuliano, Xiaojiang Cui
Published 2015-11-01

Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression

by Yuan Jiang, Yan-Yi Jiang, Jian-Jun Xie, Anand Mayakonda, Masaharu Hazawa, Li Chen, Jin-Fen Xiao, Chun-Quan Li, Mo-Li Huang, Ling-Wen Ding, Qiao-Yang Sun, Liang Xu, Deepika Kanojia, Maya Jeitany, Jian-Wen Deng, Lian-Di Liao, Harmik J. Soukiasian, Benjamin P. Berman, Jia-Jie Hao, Li-Yan Xu, En-Min Li, Ming-Rong Wang, Xin-Gang Bi, De-Chen Lin, H. Phillip Koeffler
Published 2018-09-01

Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway

by Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S. Damrauer, Tiago Chedraoui Silva, Christopher K. Wong, Hyo Young Choi, Ina Felau, A. Gordon Robertson, Mauro A.A. Castro, Lisui Bao, Esther Rheinbay, Eric Minwei Liu, Tuan Trieu, David Haan, Christina Yau, Toshinori Hinoue, Yuexin Liu, Ofer Shapira, Kiran Kumar, Karen L. Mungall, Hailei Zhang, Jake June-Koo Lee, Ashton Berger, Galen F. Gao, Binyamin Zhitomirsky, Wen-Wei Liang, Meng Zhou, Sitapriya Moorthi, Alice H. Berger, Eric A. Collisson, Michael C. Zody, Li Ding, Andrew D. Cherniack, Gad Getz, Olivier Elemento, Christopher C. Benz, Josh Stuart, J.C. Zenklusen, Rameen Beroukhim, Jason C. Chang, Joshua D. Campbell, D. Neil Hayes, Lixing Yang, Peter W. Laird, John N. Weinstein, David J. Kwiatkowski, Ming S. Tsao, William D. Travis, Ekta Khurana, Benjamin P. Berman, Katherine A. Hoadley, Nicolas Robine, Matthew Meyerson, Ramaswamy Govindan, Marcin Imielinski
Published 2021-02-01