Author

B. P. Berman

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Cancer Biology· 5 Bioengineering· 1

Signature Assays, Organisms & Methods

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Organism:human· 5 Approach:statistical model· 5 Research Focus:differential expression· 4 Approach:experimental assay· 4 Assay:ChIP-seq· 3 Research Focus:chromatin & epigenetic regulation· 3 Assay:DNA methylation· 3 Research Focus:benchmarking· 2

Frequent Co-Authors

D.-C. Lin· 3 shared E.-M. Li· 2 shared H. P. Koeffler· 2 shared L.-Y. Xu· 2 shared Q. Yang· 2 shared T. C. Silva· 2 shared Y. Zheng· 2 shared A. Gusev· 1 shared

Activity by Year

2019-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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3 shared papersCancer Biology

D.-C. Lin

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Author profile →

6 papers

Recent·Most cited

Long-read sequencing identifies aberrant fragmentation patterns linked to elevated cell-free DNA levels in cancer

B. P. Berman, S. A. Erdman, C. Wheeler, J. Cayford, J.-V. Turatsinze, M. Ouzounova, M. Piecyk, M. Herzog, L. Payen-Gay, T. Walter, T. K. Kelly

The paper uses long-read sequencing to analyze cfDNA fragmentation patterns in cancer patients, identifying hypofragmentation and hyperfragmentation linked to elevated cfDNA levels.

bioRxiv · May 2, 2024Cancer Biology

Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation

Y. Zheng, B. Ziman, A. S. Ho, U. K. Sinha, L.-Y. Xu, E.-M. Li, B. P. Berman, D.-C. Lin

This study identifies cell-type- and cancer-specific epigenetic features in esophageal cancer using whole-genome bisulfite sequencing, revealing novel insights into DNA methylation dynamics.

bioRxiv · Aug 18, 2022Cancer Biology

Validation of Data Acquisition and Phase Estimation for Quantitative Susceptibility Mapping with a Rotating-Tube Phantom

K. E. Keenan, B. P. Berman, S. Carnicka, S. E. Russek, W.-T. Wang, J. A. Butman, D. L. Pham, J. Dagher

This paper evaluates MRI data acquisition and phase estimation methods for quantitative susceptibility mapping using a rotating-tube phantom, identifying reliable approaches for accurate susceptibility measurements.

bioRxiv · Jun 29, 2021Bioengineering

A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb targets

Y. Zheng, G. Huang, T. C. Silva, Q. Yang, H. P. Koeffler, B. P. Berman, D.-C. Lin

The paper analyzes CpG Island gene regulation across cancers, finding that PRC2+-CGI genes show both upregulation and hypermethylation in different cancer types, indicating regulatory plasticity.

bioRxiv · Jun 4, 2020Cancer Biology

Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

J. Pan, T. C. Silva, N. Gull, Q. Yang, J. Plummer, S. Chen, K. Daigo, T. Hamakubo, S. Gery, L.-W. Ding, Y.-Y. Jiang, S.-Y. Hu, L.-Y. Xu, E.-M. Li, Y. Ding, , D.-C. Lin

The paper identifies lineage-specific activation of HNF4A in gastrointestinal adenocarcinomas through epigenomic and genomic analysis, revealing its role in promoting cancer proliferation.

bioRxiv · Oct 21, 2019Cancer Biology

Non-coding Somatic Mutations Converge on the PAX8 Pathway in Epithelial Ovarian Cancer

R. I. Corona, J.-H. Seo, X. Lin, D. J. Hazelett, J. Reddy, F. Abassi, Y. G. Lin, P. Y. Mhawech-Fauceglia, J. Lester, S. P. Shah, D. G. Huntsman, A. Gusev, B. Y. Karlan, B. P. Berman, M. L. Freedman, , K. Lawrenson

The paper identifies histotype-specific regulatory elements in ovarian cancer by integrating chromatin landscapes and somatic mutations, highlighting the PAX8 pathway's role in tumor development.

bioRxiv · Feb 1, 2019Cancer Biology