Benjamin P. Berman
University of Southern California · Software Engineering
Active 1947–2026
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About
Benjamin P. Berman is a computational imaging scientist at the MITRE Corporation. He completed his PhD at the Massachusetts Institute of Technology (MIT) between 2009 and 2015, where his dissertation focused on accelerated radial magnetic resonance imaging, exploring new applications and methods in the field. His research emphasizes advancements in computational imaging techniques, contributing to the development of innovative imaging applications and methodologies.
Research topics
- Biology
- Genetics
- Computational biology
- Evolutionary biology
- Cancer research
- Virology
- Statistics
- Mathematics
Selected publications
The repertoire of mutational signatures in human cancer
Nature · 2020 · 3673 citations
, enabled the discovery of new signatures, the separation of overlapping signatures and the decomposition of signatures into components that may represent associated-but distinct-DNA damage, repair and/or replication mechanisms. By estimating the contribution of each signature to the mutational catalogues of individual cancer genomes, we revealed associations of signatures to exogenous or endogenous exposures, as well as to defective DNA-maintenance processes. However, many signatures are of unk…
The evolutionary history of 2,658 cancers
Nature · 2020 · 1112 citations
, we reconstruct the life history and evolution of mutational processes and driver mutation sequences of 38 types of cancer. Early oncogenesis is characterized by mutations in a constrained set of driver genes, and specific copy number gains, such as trisomy 7 in glioblastoma and isochromosome 17q in medulloblastoma. The mutational spectrum changes significantly throughout tumour evolution in 40% of samples. A nearly fourfold diversification of driver genes and increased genomic instability are…
Patterns of somatic structural variation in human cancer genomes
Nature · 2020 · 976 citations
. Sixteen signatures of structural variation emerged. Deletions have a multimodal size distribution, assort unevenly across tumour types and patients, are enriched in late-replicating regions and correlate with inversions. Tandem duplications also have a multimodal size distribution, but are enriched in early-replicating regions-as are unbalanced translocations. Replication-based mechanisms of rearrangement generate varied chromosomal structures with low-level copy-number gains and frequent inve…
Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing
Nature Genetics · 2020 · 763 citations
Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies in selected cancer types have suggested that chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA), we analyze patterns of chromothrips…
Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
Nature · 2020 · 655 citations
, raise doubts about others and identify novel candidates, including point mutations in the 5' region of TP53, in the 3' untranslated regions of NFKBIZ and TOB1, focal deletions in BRD4 and rearrangements in the loci of AKR1C genes. We show that although point mutations and structural variants that drive cancer are less frequent in non-coding genes and regulatory sequences than in protein-coding genes, additional examples of these drivers will be found as more cancer genomes become available.
Recent grants
Integrative Cancer Epigenomic Data Analysis Center (ICE-DAC)
NIH · $527k · 2016–2021
Integrative Cancer Epigenomic Data Analysis Center (ICE-DAC)
NIH · $2.0M · 2016–2021
NIH · $1.1M · 2017
Frequent coauthors
- 96 shared
Rory Johnson
University Hospital of Bern
- 84 shared
Roland Eils
- 82 shared
Thomas J. Mitchell
Wellcome Sanger Institute
- 76 shared
Lars Feuerbach
German Cancer Research Center
- 73 shared
L. Sylvia
Mirai Hospital
- 72 shared
Geoff Macintyre
Spanish National Cancer Research Centre
- 70 shared
Keiran Raine
Wellcome Sanger Institute
- 70 shared
Alexander Martínez-Fundichely
Presbyterian Hospital
Education
- 2007
Postdoctoral fellowship, Norris Comprehensive Cancer Center
University of Southern California
- 2006
PhD, Molecular and Cell Biology
University of California Berkeley
- 1996
BA, Computer Science
University of California Berkeley
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