Publications


17 core papers selected from 69 peer-reviewed Berman lab publications. A complete list of publications is available at my Google Scholar page or my PubMed page.


Katsman, Efrat et al. "Detecting cell-of-origin and cancer-specific features of cell-free DNA with Nanopore sequencing". bioRxiv, 2021 doi:10.1101/2021.10.18.464684

Unterman, Irene et al. "Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome". eLife, 2021 doi:10.7554/elife.67085

Zheng, Yueyuan et al. "A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes". Nature Communications, 2021 doi:10.1038/s41467-021-22720-0

Pan, Jian et al. "Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas". Cancer Research, 2020 doi:10.1158/0008-5472.can-20-0390

Gao, Galen F. et al. "Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons’ Data". Cell Systems, 2019 doi:10.1016/J.CELS.2019.06.006

Silva, Tiago C et al. "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

Zhou, Wanding et al. "DNA methylation loss in late-replicating domains is linked to mitotic cell division". Nature Genetics, 2018 doi:10.1038/s41588-018-0073-4

Lin, De-Chen et al. "Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas". Gut, 2018 doi:10.1136/gutjnl-2017-314607

de Couto, Geoffrey et al. "Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning". Circulation, 2017 doi:10.1161/CIRCULATIONAHA.116.024590

Lin, De-Chen et al. "Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma". Cancer Research, 2017 doi:10.1158/0008-5472.CAN-16-2822

Hao, Jia-Jie et al. "Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma". Nature Genetics, 2016 doi:10.1038/ng.3683

Yao, Lijing et al. "Inferring regulatory element landscapes and transcription factor networks from cancer methylomes". Genome Biology, 2015 doi:10.1186/s13059-015-0668-3

Lay, Fides D. et al. "The role of DNA methylation in directing the functional organization of the cancer epigenome". Genome Research, 2015 doi:10.1101/gr.183368.114

Kelly, T. K. et al. "Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules". Genome Research, 2012 doi:10.1101/gr.143008.112

Liu, Yaping et al. "Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data". Genome Biology, 2012 doi:10.1186/gb-2012-13-7-r61

Berman, Benjamin P et al. "Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains". Nature Genetics, 2011 doi:10.1038/ng.969

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The Methyl Grammar lab at Hebrew University