Benjamin P Berman

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 25

Top Venues

Nucleic acids research

Genome biology

Proceedings of the National Academy of Sciences of the United States of America

Nature communications

Cedars-Sinai Medical Center

University of California Berkeley (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Cedars-Sinai Medical Center Oct 01 2014 - Jun 10 2020

United States

Co-director and Associate Professor :: Center for Bioinformatics and Functional Genomics

University of Southern California Sep 01 2011 - Oct 01 2014

United States

Assistant Professor :: Norris Comprehensive Cancer Center

University of Southern California Aug 01 2007 - Aug 31 2011

United States

Senior Research Associate :: Norris Comprehensive Cancer Center

Education History

University of California Berkeley Sep 01 2001 - Jul 31 2006

United States

PHD :: Molecular and Cell Biology

Publications

Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen, Efrat Katsman, Ayush Semwal, Walid Abi Habib, Lyong Heo, Peter W Laird, Benjamin P Berman, Timothy J Triche, Hui Shen
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nucleic acids research (2024)
Irene Unterman, Dana Avrahami, Efrat Katsman, Timothy J Triche, Benjamin Glaser, Benjamin P Berman
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes. Genome biology 25 (1) (2024)
Irene Unterman, Dana Avrahami, Efrat Katsman, Triche Tim, Benjamin Glaser, Benjamin P Berman
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes. Genome biology 25 (1) (2024)
Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen, Efrat Katsman, Ayush Semwal, Walid Abi Habib, Lyong Heo, Peter W Laird, Benjamin P Berman, Timothy J Triche, Hui Shen
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nucleic acids research 52 (6) (2024)
Irene Unterman, Dana Avrahami, Efrat Katsman, Triche Tim, Benjamin Glaser, Benjamin P Berman
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes. Genome biology 25 (1) (2024)
Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen, Efrat Katsman, Ayush Semwal, Walid Abi Habib, Lyong Heo, Peter W Laird, Benjamin P Berman, Timothy J Triche, Hui Shen
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nucleic acids research (2024)
Irene Unterman, Dana Avrahami, Efrat Katsman, Triche Tim, Benjamin Glaser, Benjamin P Berman
CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes. Genome biology 25 (1) (2024)
Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen, Efrat Katsman, Ayush Semwal, Walid Abi Habib, Lyong Heo, Peter W Laird, Benjamin P Berman, Timothy J Triche, Hui Shen
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nucleic acids research 52 (6) (2024)
Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen, Efrat Katsman, Ayush Semwal, Walid Abi Habib, Lyong Heo, Peter W Laird, Benjamin P Berman, Timothy J Triche, Hui Shen
BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Nucleic acids research 52 (6) (2024)
Efrat Katsman, Shari Orlanski, Filippo Martignano, Ilana Fox-Fisher, Ruth Shemer, Yuval Dor, Aviad Zick, Amir Eden, Iacopo Petrini, Silvestro Giovanni Conticello, Benjamin P Berman
Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing. Genome biology 23 (1) (2022)
Tal Falick Michaeli, Ofra Sabag, Rimma Fok, Batia Azria, Jonathan Monin, Yuval Nevo, Yuval Gielchinsky, Benjamin P Berman, Howard Cedar, Yehudit Bergman
Muscle injury causes long-term changes in stem-cell DNA methylation. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Tal Falick Michaeli, Ofra Sabag, Rimma Fok, Batia Azria, Jonathan Monin, Yuval Nevo, Yuval Gielchinsky, Benjamin P Berman, Howard Cedar, Yehudit Bergman
Muscle injury causes long-term changes in stem-cell DNA methylation. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Tal Falick Michaeli, Ofra Sabag, Rimma Fok, Batia Azria, Jonathan Monin, Yuval Nevo, Yuval Gielchinsky, Benjamin P Berman, Howard Cedar, Yehudit Bergman
Muscle injury causes long-term changes in stem-cell DNA methylation. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Tal Falick Michaeli, Ofra Sabag, Rimma Fok, Batia Azria, Jonathan Monin, Yuval Nevo, Yuval Gielchinsky, Benjamin P Berman, Howard Cedar, Yehudit Bergman
Muscle injury causes long-term changes in stem-cell DNA methylation. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Yongsheng Huang, Qian Yang, Yueyuan Zheng, Lehang Lin, Xin Xu, Xiu-E Xu, Tiago C Silva, Masaharu Hazawa, Li Peng, Haotian Cao, Yanbing Ding, Daning Lu, Benjamin P Berman, Li-Yan Xu, En-Min Li, Dong Yin
Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma. Nucleic acids research 49 (16) (2021)
Yueyuan Zheng, Guowei Huang, Tiago C Silva, Qian Yang, Yan-Yi Jiang, H Phillip Koeffler, De-Chen Lin, Benjamin P Berman
Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes. Nature communications 12 (1) (2021)
Irene Unterman, Idit Bloch, Simona Cazacu, Gila Kazimirsky, Bruria Ben-Zeev, Benjamin P Berman, Chaya Brodie, Yuval Tabach
Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome. eLife 10 (2021)
Yueyuan Zheng, Guowei Huang, Tiago C Silva, Qian Yang, Yan-Yi Jiang, H Phillip Koeffler, De-Chen Lin, Benjamin P Berman
A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes. Nature communications 12 (1) (2021)
Jian Pan, Tiago C Silva, Nicole Gull, Qian Yang, Jasmine T Plummer, Stephanie Chen, Kenji Daigo, Takao Hamakubo, Sigal Gery, Ling-Wen Ding, Yan-Yi Jiang, Shaoyan Hu, Li-Yan Xu, En-Min Li, Yanbing Ding, Samuel J Klempner, Simon A Gayther, Benjamin P Berman, H Phillip Koeffler, De-Chen Lin
Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas. Cancer research 80 (13) (2020)
M Ryan Corces, Jeffrey M Granja, Shadi Shams, Bryan H Louie, José A Seoane, Wanding Zhou, Tiago C Silva, Clarice Groeneveld, Christopher K Wong, Seung Woo Cho, Ansuman T Satpathy, Maxwell R Mumbach, Katherine A Hoadley, A Gordon Robertson, Nathan C Sheffield, Ina Felau, Mauro A A Castro, Benjamin P Berman, Louis M Staudt, Jean C Zenklusen, Peter W Laird, Christina Curtis, null null, William J Greenleaf, Howard Y Chang
The chromatin accessibility landscape of primary human cancers. Science (New York, N.Y.) 362 (6413) (2018)
Suhn Kyong Rhie, Shannon M Schreiner, Heather Witt, Chris Armoskus, Fides D Lay, Adrian Camarena, Valeria N Spitsyna, Yu Guo, Benjamin P Berman, Oleg V Evgrafov, James A Knowles, Peggy J Farnham
Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation. Science advances 4 (12) (2018)
Wanding Zhou, Huy Q Dinh, Zachary Ramjan, Daniel J Weisenberger, Charles M Nicolet, Hui Shen, Peter W Laird, Benjamin P Berman
DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nature genetics 50 (4) (2018)
Muhammad Shahid, Nicole Gull, Austin Yeon, Eunho Cho, Jooeun Bae, Hyun Seok Yoon, Sungyong You, Hana Yoon, Minjung Kim, Benjamin P Berman, Jayoung Kim
Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A. Scientific reports 8 (1) (2018)
Muhammad Shahid, Nicole Gull, Austin Yeon, Eunho Cho, Jooeun Bae, Hyun Seok Yoon, Sungyong You, Hana Yoon, Minjung Kim, Benjamin P Berman, Jayoung Kim
Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A. Scientific reports 8 (1) (2018)
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
Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression. Nature communications 9 (1) (2018)

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Publication Activity (10 Years)

Top Topics

Top Venues

Benjamin P Berman