HPCC

Center for High-Performance Computing and Communications

Benjamin Berman

berman

Benjamin Berman is an assistant professor in the Department of Preventive Medicine at the Keck School of Medicine at USC. One of the first faculty members hired in the department’s recently formed Division of Bioinformatics, Berman’s research focuses on the computational analysis of high-throughput genetic and genomic datasets. In particular, Berman works to identify key DNA sequences that influence a normal cell’s development into a cancer cell. Identifying these sequences may lead to personalized cancer treatments in the future.

Berman also serves as an investigator and founding member of the USC Epigenome Center. Established in 2007 as the first of its kind in the nation, the center provides an interdisciplinary environment for molecular and computational scientists to work side-by-side on cutting-edge, high-throughput epigenetic and population-based research. Berman and others at the Center are at work on a five-year collaboration with Johns Hopkins University (JHU ) to gather epigenome data from each of the major types of cancer. The USC/JHU project is responsible for the epigenetic component of The Cancer Genome Atlas, a large, multi-institute effort to comprehensively map molecular changes in cancer.

DNA sequencing at the Epigenome Center can produce up to a terabyte a day of raw data; Berman and his group use HPCC resources and a parallel computational framework based on MapReduce to stitch together hundreds of billions of individual DNA sequences into a biologically meaningful genomic map of normal tissue or a single tumor. Thousands of individual compute jobs are coordinated by parallel workflow software developed by researchers at the USC Viterbi School of Engineering’s Information Sciences Institute. Berman recently led a USC Epigenome Center study that used this computational framework to analyze tumors from colorectal cancer patients. The work, published in Nature Genetics, identified novel biochemical changes occurring genome-wide in cancer cells.

Berman’s research is funded by the Kenneth T. and Eileen L. Norris Foundation and the National Institutes of Health.

ABOVE: Epigenetic map showing a small section of a colon cancer patient’s genome. A novel epigenetic signature was identified which distinguished parts of the genome that were active versus those that were inactive.