Skip to Main Content

Author Details

Benjamin P Berman
Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem
2000
68
39
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37620896Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation.Genome Biol2023
37620896Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation.Genome Biol2023
35883104DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers.J Exp Clin Cancer Res2022
35841107Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing.Genome Biol2022
35883104DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers.J Exp Clin Cancer Res2022
35841107Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing.Genome Biol2022
34355696Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome.Elife2021
33626341Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.Cell Rep2021
33883598Mechanistic and therapeutic distinctions between cardiosphere-derived cell and mesenchymal stem cell extracellular vesicle non-coding RNA.Sci Rep2021
33931649A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.Nat Commun2021
34355696Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome.Elife2021
34183671Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.Nat Commun2021
34370013Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.Nucleic Acids Res2021
33883598Mechanistic and therapeutic distinctions between cardiosphere-derived cell and mesenchymal stem cell extracellular vesicle non-coding RNA.Sci Rep2021
33626341Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.Cell Rep2021
33931649A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.Nat Commun2021
34183671Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.Nat Commun2021
34370013Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.Nucleic Acids Res2021
31409603Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma.Gut2020
32332753Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer.Nat Commun2020
32946763Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites.Am J Hum Genet2020
31409603Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma.Gut2020
32946763Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites.Am J Hum Genet2020
32332753Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer.Nat Commun2020
30364927ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.Bioinformatics2019
31619158GENAVi: a shiny web application for gene expression normalization, analysis and visualization.BMC Genomics2019
30496486Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1.Nucleic Acids Res2019
30292564Discrimination of Pulmonary Nodule Volume Change for Low- and High-contrast Tasks in a Phantom CT Study with Low-dose Protocols.Acad Radiol2019
30364927ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles.Bioinformatics2019
30990720Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library.J Proteome Res2019
31619158GENAVi: a shiny web application for gene expression normalization, analysis and visualization.BMC Genomics2019
30990720Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library.J Proteome Res2019
30496486Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1.Nucleic Acids Res2019
30292564Discrimination of Pulmonary Nodule Volume Change for Low- and High-contrast Tasks in a Phantom CT Study with Low-dose Protocols.Acad Radiol2019
28860350Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas.Gut2018
28860350Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas.Gut2018
30361341The chromatin accessibility landscape of primary human cancers.Science2018
30555922Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.Sci Adv2018
30101756Coronary artery calcium quantification using contrast-enhanced dual-energy computed tomography scans in comparison with unenhanced single-energy scans.Phys Med Biol2018
30190462Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression.Nat Commun2018
29764999Targetable BET proteins- and E2F1-dependent transcriptional program maintains the malignancy of glioblastoma.Proc Natl Acad Sci U S A2018
29662153Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A.Sci Rep2018
29610480DNA methylation loss in late-replicating domains is linked to mitotic cell division.Nat Genet2018
29540744Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A.Sci Rep2018
30190462Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression.Nat Commun2018
30101756Coronary artery calcium quantification using contrast-enhanced dual-energy computed tomography scans in comparison with unenhanced single-energy scans.Phys Med Biol2018
30361341The chromatin accessibility landscape of primary human cancers.Science2018
30555922Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.Sci Adv2018
29610480DNA methylation loss in late-replicating domains is linked to mitotic cell division.Nat Genet2018
29662153Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A.Sci Rep2018
  • 1 - 50 of 136

Recommended Authors

Yunjiang Qiu
Ludwig Institute for Cancer Research, University of California
Career Start Year 2015
Number of shared co-authors 1
Yupeng He
Salk Institute for Biological Studies
Career Start Year 2012
Number of shared co-authors 5
Samantha Kuan
University of California San Diego
Career Start Year 2010
Number of shared co-authors 3
David U Gorkin
Center for Epigenomics, University of California San Diego
Career Start Year 2009
Number of shared co-authors 7
Chongzhi Zang
Center for Public Health Genomics, University of Virginia
Career Start Year 2008
Number of shared co-authors 5
Lukas Chavez
University of California San Diego
Career Start Year 2008
Number of shared co-authors 1
Altuna Akalin
Berlin Institute for Medical Systems Biology
Career Start Year 2006
Number of shared co-authors 1
Yue Lu
The University of Texas MD Anderson Cancer Center
Career Start Year 2006
Number of shared co-authors 0
Yassen Assenov
German Cancer Research Center (DKFZ)
Career Start Year 2006
Number of shared co-authors 2
Jun S Song
University of Illinois at Urbana-Champaign
Career Start Year 2005
Number of shared co-authors 4
Christoph Bock
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Career Start Year 2005
Number of shared co-authors 10
Yin Shen
Wenzhou Medical University
Career Start Year 2005
Number of shared co-authors 5
Duncan Sproul
Institute of Genetics and Cancer, University of Edinburgh
Career Start Year 2004
Number of shared co-authors 2
Gary C Hon
Cecil H. and Ida Green Center for Reproductive Biology Sciences
Career Start Year 2004
Number of shared co-authors 13
Lingyun Song
Center for Genomic & Computational Biology, Duke University
Career Start Year 2004
Number of shared co-authors 11
Anshul Kundaje
Stanford University.
Career Start Year 2004
Number of shared co-authors 25
Mathieu Lupien
Princess Margaret Cancer Research Centre
Career Start Year 2003
Number of shared co-authors 12
Michael J Buck
Jacobs School of Medicine and Biomedical Sciences, University at Buffalo
Career Start Year 2002
Number of shared co-authors 0
Ting Wang
Washington University School of Medicine
Career Start Year 2001
Number of shared co-authors 9
Peter J Park
Harvard Medical School
Career Start Year 2001
Number of shared co-authors 44
Stefan Bekiranov
University of Virginia
Career Start Year 2000
Number of shared co-authors 4
Terrence S Furey
University of North Carolina at Chapel Hill
Career Start Year 2000
Number of shared co-authors 41
Guo-Cheng Yuan
Dana-Farber Cancer Institute, Harvard School of Public Health
Career Start Year 2000
Number of shared co-authors 0
Kai Tan
University of Pennsylvania
Career Start Year 1999
Number of shared co-authors 3
Martin Hirst
University of British Columbia
Career Start Year 1998
Number of shared co-authors 21
Tim H-M Huang
University of Texas Health San Antonio (UTHSA)
Career Start Year 1997
Number of shared co-authors 3
Bing Ren
Center for Epigenomics, University of California San Diego
Career Start Year 1995
Number of shared co-authors 27
Peter C Scacheri
Case Western Reserve University School of Medicine
Career Start Year 1995
Number of shared co-authors 12
Bradley E Bernstein
Broad Institute of MIT and Harvard
Career Start Year 1994
Number of shared co-authors 14
Holger Heyn
Barcelona Institute of Science and Technology, Spain Universitat Pompeu Fabra
Career Start Year 1988
Number of shared co-authors 10

Collaborators

Peter W Laird
Van Andel Institute
Co-authored papers 10
Gerhard A Coetzee
Van Andel Institute
Co-authored papers 9
Tiago C Silva
University of Miami Miller School of Medicine
Co-authored papers 9
Simon G Coetzee
Co-authored papers 8
Gerald M Rubin
The University of Florida
Co-authored papers 7
Peggy J Farnham
Keck School of Medicine of USC
Co-authored papers 7
Susan E Celniker
Lawrence Berkeley National Laboratory
Co-authored papers 6
Houtan Noushmehr
Henry Ford Hospital
Co-authored papers 6
Lijing Yao
Co-authored papers 6
Simon A Gayther
Cedars-Sinai Medical Center
Co-authored papers 5
Matthew L Freedman
Dana-Farber Cancer Institute
Co-authored papers 4
Daniel J Weisenberger
Co-authored papers 4
Heather Witt
Co-authored papers 4
Nomi L Harris
Lawrence Berkely National Laboratory, Massachusetts Institute of Technology, Princeton University
Co-authored papers 3
Hui Shen
Van Andel Institute
Co-authored papers 3
Katherine A Hoadley
Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill
Co-authored papers 3
Barret D Pfeiffer
Howard Hughes Medical Institute
Co-authored papers 3
Suzanna E Lewis
Lawrence Berkeley National Laboratory
Co-authored papers 3
Jonathan L Tupy
Lawrence Berkeley National Laboratory
Co-authored papers 2
James A Knowles
Co-authored papers 2
Chris Tyler-Smith
Wellcome Sanger Institute
Co-authored papers 2
Reed A George
Howard Hughes Medical Institute
Co-authored papers 2
Leyla Bayraktaroglu
Co-authored papers 2
Michael Ashburner
University of Cambridge
Co-authored papers 2
Mauro A A Castro
Federal University of Parana
Co-authored papers 2
Michael B Eisen
Howard Hughes Medical Institute, University of California Berkeley
Co-authored papers 2
Simon Prochnik
Joint Genome Institute
Co-authored papers 2
Ina Felau
National Cancer Institute
Co-authored papers 2
Amy G Robertson
Present address: Dxige Research Inc.
Co-authored papers 2
Suhn K Rhie
Keck School of Medicine of USC
Co-authored papers 2
Release 1.2