Publications - Berman Lab Cedars-Sinai Skip to content Close Select your preferred language English عربى 简体中文 繁體中文 فارسي עִברִית 日本語 한국어 Русский Español Tagalog English English عربى 简体中文 繁體中文 فارسي עִברִית 日本語 한국어 Русский Español Tagalog Translation is unavailable for Internet Explorer Cedars-Sinai Home 1-800-CEDARS-1 1-800-CEDARS-1 Close Find a Doctor Locations Programs & Services Health Library Patient & Visitors Community My CS-Link RESEARCH clear Go Close Navigation Links Academics Faculty Development Community Engagement Calendar Research Research Areas Research Labs Departments & Institutes Find Clinical Trials Research Cores Research Administration Basic Science Research Clinical & Translational Research Center (CTRC) Technology & Innovations News & Breakthroughs Education Graduate Medical Education Continuing Medical Education Graduate School of Biomedical Sciences Professional Training Programs Medical Students Campus Life Office of the Dean Simulation Center Medical Library Program in the History of Medicine About Us All Education Programs Departments & Institutes Faculty Directory Berman Lab Back to Berman Lab Lab Members Personal Statement Publications Research Areas Publications See a complete PubMed list of publications by Benjamin Berman, PhD. Selected Key Publications Silva TC, Coetzee SG, Yao L, Hazelett DJ, Noushmehr H, Berman BP. Enhancer linking by methylation/expression relationships with the R package ELMER version 2. bioRxiv. 2017 Jun 11. https://www.biorxiv.org/content/early/2017/10/10/148726. Coetzee SG, Ramjan Z, Dinh HQ, Berman BP, Hazelett DJ. StateHub-StatePaintR: rapid and reproducible chromatin state evaluation for custom genome annotation. bioRxiv. 2017 May 23. https://www.biorxiv.org/content/early/2017/05/23/127720. Lin DC, Dinh HQ, Xie JJ, Mayakonda A, Jiang YY, Ding LW, He JZ, Xu XE, Hao JJ, Wang MR, Xu LY, Li EM, Berman BP, Koeffler HP. Identification of distinct mutational patterns and new driver genes in esophageal squamous cell carcinomas and adenocarcinomas [published online ahead of print August 31, 2017]. Gut. http://gut.bmj.com/content/early/2017/09/02/gutjnl-2017-314607. Hao JJ, Lin DC, Dinh HQ, Mayakonda A, Jiang YY, Chang C, Jiang Y, Lu CC, Shi ZZ, Xu X, Zhang Y, Cai Y, Wang JW, Zhan QM, Wei WQ, Berman BP, et al. Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma. Nat Genet. 2016 Dec;48(12):1500-1507. http://www.nature.com/ng/journal/v48/n12/full/ng.3683.html. Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, Noushmehr H, Lange CP, van Dijk CM, Tollenaar RA, et al. Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2011 Nov 27;44(1):40-46. http://www.nature.com/ng/journal/v44/n1/full/ng.969.html. Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 2015 May 21;16:105. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0668-3. Lay FD, Liu Y, Kelly TK, Witt H, Farnham PJ, Jones PA, Berman BP. The role of DNA methylation in directing the functional organization of the cancer epigenome. Genome Res. 2015;25:467-477. http://genome.cshlp.org/content/25/4/467. Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res. 2012 Dec;22(12):2497-2506. http://genome.cshlp.org/content/22/12/2497. Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012 Jul 11;13(7):R61. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-7-r61. Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29;474(7353):609-615. http://www.nature.com/nature/journal/v474/n7353/full/nature10166.html. Juve G, Deelman E, Vahi K, Mehta G, Berriman B, Berman BP, Maechling P. Scientific workflow applications on Amazon EC2. IEEE Conference on E-Science. December 9-11, 2009. http://ieeexplore.ieee.org/document/5408002/. Jia L, Berman BP, Jariwala U, Yan X, Cogan JP, Walters A, Chen T, Buchanan G, Frenkel B, Coetzee GA. Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity. PLOS One. 2008;3(11):e3645. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003645. Tomancak P, Berman BP, Beaton A, Weiszmann R, Kwan E, Hartenstein V, Celniker SE, Rubin GM. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 2007;8(7):R145. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2007-8-7-r145. Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, Eisen MB, Celniker SE. Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol. 2004;5(9):R61. https://genomebiology.biomedcentral.com/articles/10.1186/gb-2004-5-9-r61. Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci USA. 2002 Jan 22;99(2):757-762. http://www.pnas.org/content/99/2/757. Hoskins RA, Nelson CR, Berman BP, Laverty TR, George RA, Ciesiolka L, Naeemuddin M, Arenson AD, Durbin J, David RG, et al. A BAC-based physical map of the major autosomes of Drosophila melanogaster. Science. 2000 Mar 24;287(5461):2271-2274. http://science.sciencemag.org/content/287/5461/2271.long. 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