20 core papers selected from 80 peer-reviewed Berman lab publications. A complete list of publications is available at my Google Scholar page.

Irene Unterman, Dana Avrahami, Efrat Katsman, Timothy J. Triche, Benjamin Glaser, Benjamin P. Berman "CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes". Genome Biology 25 (1) :151 2024 doi:10.1186/s13059-024-03275-x

Benjamin P. Berman, Sarah A. Erdman, Jean-Valery Turatsinze, Justin Cayford, Theresa K. Kelly "Long-read sequencing reveals aberrant fragmentation patterns and origins of circulating DNA in cancer". bioRxiv 2024 doi:10.1101/2024.05.02.592182

Yueyuan Zheng, Benjamin Ziman, Allen S Ho, Uttam K Sinha, Li-Yan Xu, En-Min Li, H Phillip Koeffler, Benjamin P Berman, De-Chen Lin "Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation". Genome Biology 24 (1) :193 2023 doi:10.1186/s13059-023-03035-3

Dror Bar, Lior Fishman, Yueyuan Zheng, Irene Unterman, Devorah Schlesinger, Amir Eden, De-Chen Lin, Benjamin P. Berman "A local sequence signature defines a subset of heterochromatin-associated CpGs with minimal loss of methylation in healthy tissues but extensive loss in cancer". bioRxiv 2022 doi:10.1101/2022.08.16.504069

Efrat Katsman, Shari Orlanski, Filippo Martignano, Ilana Fox-Fisher, Ruth Shemer, Yuval Dor, Aviad Zick, Amir Eden, Iacopo Petrini, Silvestro G. Conticello, Benjamin P. Berman "Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing". Genome Biology 23 (1) 2022 doi:10.1186/s13059-022-02710-1

Irene Unterman, Idit Bloch, Simona Cazacu, Gila Kazimirsky, Bruria Ben-Zeev, Benjamin P Berman, Chaya Brodie, Yuval Tabach "Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome". eLife 10 :e67085 2021 doi:10.7554/elife.67085

Yueyuan Zheng, Guowei Huang, Tiago C. Silva, Qian Yang, Yan-Yi Jiang, H Phillip Koeffler, De-Chen Lin, Benjamin P. Berman "A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes". Nature Communications 12 :2485 2021 doi:10.1038/s41467-021-22720-0

Jian Pan, Tiago C. Silva, Nicole Gull, Qian Yang, Jasmine T. Plummer, Stephanie Chen, Kenji Daigo, Takao Hamakubo, Sigal Gery, Ling-Wen Ding, Yan-Yi Jiang, Shaoyan Hu, Li-Yan Xu, En-Min Li, Yanbing Ding, Samuel J. Klempner, Simon A. Gayther, Benjamin P. Berman, H. Phillip Koeffler, De-Chen Lin "Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas". Cancer Research 80 (13) :2722-2736 2020 doi:10.1158/0008-5472.can-20-0390

Galen F. Gao, Joel S. Parker, Sheila M. Reynolds, Tiago C. Silva, Liang-Bo Wang, Wanding Zhou, Rehan Akbani, Matthew Bailey, Saianand Balu, Benjamin P. Berman, Denise Brooks, Hu Chen, Andrew D. Cherniack, John A. Demchok, Li Ding, Ina Felau, Sharon Gaheen, Daniela S. Gerhard, David I. Heiman, Kyle M. Hernandez, Katherine A. Hoadley, Reyka Jayasinghe, Anab Kemal, Theo A. Knijnenburg, Peter W. Laird, Michael K.A. Mensah, Andrew J. Mungall, A. Gordon Robertson, Hui Shen, Roy Tarnuzzer, Zhining Wang, Matthew Wyczalkowski, Liming Yang, Jean C. Zenklusen, Zhenyu Zhang, Han Liang, Michael S. Noble "Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data". Cell Systems 9 (1) :24-34.e10 2019 doi:10.1016/J.CELS.2019.06.006

Tiago C Silva, Simon G Coetzee, Nicole Gull, Lijing Yao, Dennis J Hazelett, Houtan Noushmehr, De-Chen Lin, Benjamin P Berman "ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles". Bioinformatics 2019 doi:10.1093/bioinformatics/bty902

Wanding Zhou, Huy Q. Dinh, Zachary Ramjan, Daniel J. Weisenberger, Charles M. Nicolet, Hui Shen, Peter W. Laird, Benjamin P. Berman "DNA methylation loss in late-replicating domains is linked to mitotic cell division". Nature Genetics 50 (4) :591-602 2018 doi:10.1038/s41588-018-0073-4

De-Chen Lin, Huy Q Dinh, Jian-Jun Xie, Anand Mayakonda, Tiago Chedraoui Silva, Yan-Yi Jiang, Ling-Wen Ding, Jian-Zhong He, Xiu-E Xu, Jia-Jie Hao, Ming-Rong Wang, Chunquan Li, Li-Yan Xu, En-Min Li, Benjamin P Berman, H Phillip Koeffler "Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas". Gut 67 (10) :1769-1779 2018 doi:10.1136/gutjnl-2017-314607

Geoffrey de Couto, Romain Gallet, Linda Cambier, Ervin Jaghatspanyan, Nupur Makkar, James Frederick Dawkins, Benjamin P. Berman, Eduardo Marbán "Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning". Circulation 136 (2) :200-214 2017 doi:10.1161/CIRCULATIONAHA.116.024590

De-Chen Lin, Anand Mayakonda, Huy Q. Dinh, Pinbo Huang, Lehang Lin, Xiaoping Liu, Ling-wen Ding, Jie Wang, Benjamin P. Berman, Er-Wei Song, Dong Yin, H. Phillip Koeffler "Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma". Cancer Research 77 (9) :2255-2265 2017 doi:10.1158/0008-5472.CAN-16-2822

Jia-Jie Hao, De-Chen Lin, Huy Q Dinh, Anand Mayakonda, Yan-Yi Jiang, Chen Chang, Ye Jiang, Chen-Chen Lu, Zhi-Zhou Shi, Xin Xu, Yu Zhang, Yan Cai, Jin-Wu Wang, Qi-Min Zhan, Wen-Qiang Wei, Benjamin P Berman, Ming-Rong Wang, H Phillip Koeffler "Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma". Nature Genetics 48 (12) :1500-1507 2016 doi:10.1038/ng.3683

Lijing Yao, Hui Shen, Peter W Laird, Peggy J Farnham, Benjamin P Berman "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes". Genome Biology 16 (1) 2015 doi:10.1186/s13059-015-0668-3

Fides D. Lay, Yaping Liu, Theresa K. Kelly, Heather Witt, Peggy J. Farnham, Peter A. Jones, Benjamin P. Berman "The role of DNA methylation in directing the functional organization of the cancer epigenome". Genome Research 25 (4) :467-477 2015 doi:10.1101/gr.183368.114

T. K. Kelly, Y. Liu, F. D. Lay, G. Liang, B. P. Berman, P. A. Jones "Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules". Genome Research 22 (12) :2497-2506 2012 doi:10.1101/gr.143008.112

Yaping Liu, Kimberly D Siegmund, Peter W Laird, Benjamin P Berman "Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data". Genome Biology 13 (7) :R61- 2012 doi:10.1186/gb-2012-13-7-r61

Benjamin P Berman, Daniel J Weisenberger, Joseph F Aman, Toshinori Hinoue, Zachary Ramjan, Yaping Liu, Houtan Noushmehr, Christopher P E Lange, Cornelis M van Dijk, Rob A E M Tollenaar, David Van Den Berg, Peter W Laird "Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains". Nature Genetics 44 (1) :40-46 2011 doi:10.1038/ng.969