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Benjamin Berman, PhD

Associate Professor, Biomedical Sciences

Director, Center for Bioinformatics and Functional Genomics

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Benjamin Berman, PhD

Associate Professor, Biomedical Sciences

Director, Center for Bioinformatics and Functional Genomics

The research of Benjamin Berman, PhD, focuses on understanding the basic logic of non-coding regulatory sequences, and how they control the local and 3D (topological) structure of chromatin to control transcription. His past work has demonstrated that functional non-coding elements could be identified genome-wide based on sequence properties alone, and he has published the first complete DNA methylation map of a human cancer, showing that methylation alone could be used to identify non-coding regulatory elements and understand the 3D topological organization of chromosomes in clinical human tissues. He is now developing new approaches to study complex tissues at the single-cell level. These projects will allow an understanding of how individual non-coding mutations within in an individual can drive disease processes. Berman is dedicated to making these computational methods available via open standards to support adoption throughout the research community.

View NIH Biographical Sketch as a PDF

  • Undergraduate: University of California, Berkeley, 1996
  • Doctorate: University of California, Berkeley, 2006
  • Research Career Development Award, Stop Cancer!, 2013
  • Junior Faculty Institutional Research Award, American Cancer Society, 2013
  • Forbeck Scholar Award, William Guy Forbeck Research Foundation, 2010
  • National Institutes of Health T32 Cancer epidemiology Postdoctoral Fellow, 2007
  • National Institutes of Health T32 Genomics Predoctoral Trainee, University of California, Berkeley, 2002

Click here for a list of peer-reviewed publications.

  • Yao L, Shen H, Laird PW, Farnham PJ, Berman BP. Inferring regulatory element landscapes and transcription factor networks from cancer methylomes. Genome Biol. 2015;16:105.
  • Reizel Y, Spiro A, Sabag O, Skversky Y, Hecht M, Keshet I, Berman BP, Cedar H. Gender-specific postnatal demethylation and establishment of epigenetic memory. Genes Dev. 2015;29(9):923-933.
  • 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(4):467-477.
  • Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol. 2012;13(7):R61.
  • 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;22(12):2497-2506.
  • 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;44(1):40-46.

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