Publications by authors named "Benjamin P Berman"

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Chromatin changes associated with neutrophil extracellular trap formation in whole blood reflect complex immune signaling.
Justin Cayford, Brandi Atteberry, Akanksha Singh-Taylor, Andrew Retter, Benjamin P Berman

Front Immunol· May 2025

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Understanding the complex chromatin dynamics in primary human neutrophils during PMA-induced NET formation.
Brandi Atteberry, Benjamin P Berman, Theresa K Kelly, Justin Cayford

Front Immunol· November 2024

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Author Correction: CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes.
Irene Unterman, Dana Avrahami, Efrat Katsman, Timothy J Triche, Benjamin Glaser, Benjamin P Berman

Genome Biol· July 2024

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CelFiE-ISH: a probabilistic model for multi-cell type deconvolution from single-molecule DNA methylation haplotypes.
Irene Unterman, Dana Avrahami, Efrat Katsman, Timothy J Triche, Benjamin Glaser, Benjamin P Berman

Genome Biol· June 2024

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BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies.
Wanding Zhou, Benjamin K Johnson, Jacob Morrison, Ian Beddows, James Eapen, Benjamin P Berman

Nucleic Acids Res· April 2024

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Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation.
Yueyuan Zheng, Benjamin Ziman, Allen S Ho, Uttam K Sinha, Li-Yan Xu, Benjamin P Berman

Genome Biol· August 2023

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Muscle injury causes long-term changes in stem-cell DNA methylation.
Tal Falick Michaeli, Ofra Sabag, Rimma Fok, Batia Azria, Jonathan Monin, Benjamin P Berman

Proc Natl Acad Sci U S A· December 2022

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Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing.
Efrat Katsman, Shari Orlanski, Filippo Martignano, Ilana Fox-Fisher, Ruth Shemer, Benjamin P Berman

Genome Biol· July 2022

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DNA methylation and transcriptomic features are preserved throughout disease recurrence and chemoresistance in high grade serous ovarian cancers.
Nicole Gull, Michelle R Jones, Pei-Chen Peng, Simon G Coetzee, Tiago C Silva, Benjamin P Berman

J Exp Clin Cancer Res· July 2022

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Activation of bivalent factor DLX5 cooperates with master regulator TP63 to promote squamous cell carcinoma.
Yongsheng Huang, Qian Yang, Yueyuan Zheng, Lehang Lin, Xin Xu, Benjamin P Berman

Nucleic Acids Res· September 2021

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Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome.
Irene Unterman, Idit Bloch, Simona Cazacu, Gila Kazimirsky, Bruria Ben-Zeev, Benjamin P Berman

Elife· August 2021

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Publisher Correction: A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.
Yueyuan Zheng, Guowei Huang, Tiago C Silva, Qian Yang, Yan-Yi Jiang, Benjamin P Berman

Nat Commun· June 2021

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A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.
Yueyuan Zheng, Guowei Huang, Tiago C Silva, Qian Yang, Yan-Yi Jiang, Benjamin P Berman

Nat Commun· April 2021

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Whole-genome characterization of lung adenocarcinomas lacking the RTK/RAS/RAF pathway.
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S Damrauer, Benjamin P Berman

Cell Rep· February 2021

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Whole-genome characterization of lung adenocarcinomas lacking alterations in the RTK/RAS/RAF pathway.
Jian Carrot-Zhang, Xiaotong Yao, Siddhartha Devarakonda, Aditya Deshpande, Jeffrey S Damrauer, Benjamin P Berman

Cell Rep· February 2021

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Ovarian Cancer Risk Variants Are Enriched in Histotype-Specific Enhancers and Disrupt Transcription Factor Binding Sites.
Michelle R Jones, Pei-Chen Peng, Simon G Coetzee, Jonathan Tyrer, Alberto Luiz P Reyes, Benjamin P Berman

Am J Hum Genet· October 2020

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Lineage-Specific Epigenomic and Genomic Activation of Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas.
Jian Pan, Tiago C Silva, Nicole Gull, Qian Yang, Jasmine T Plummer, Benjamin P Berman

Cancer Res· July 2020

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Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma.
Li Chen, Moli Huang, Jasmine Plummer, Jian Pan, Yan Yi Jiang, Benjamin P Berman

Gut· April 2020

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Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer.
Rosario I Corona, Ji-Heui Seo, Xianzhi Lin, Dennis J Hazelett, Jessica Reddy, Benjamin P Berman

Nat Commun· April 2020

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RNA-Binding Protein Suppresses Hypoxia and Cell-Cycle Signaling.
Xin-Yi Loh, Qiao-Yang Sun, Ling-Wen Ding, Anand Mayakonda, Nachiyappan Venkatachalam, Benjamin P Berman

Cancer Res· January 2020

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GENAVi: a shiny web application for gene expression normalization, analysis and visualization.
Alberto Luiz P Reyes, Tiago C Silva, Simon G Coetzee, Jasmine T Plummer, Brian D Davis, Benjamin P Berman

BMC Genomics· October 2019

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Before and After: Comparison of Legacy and Harmonized TCGA Genomic Data Commons' Data.
Galen F Gao, Joel S Parker, Sheila M Reynolds, Tiago C Silva, Liang-Bo Wang, Benjamin P Berman

Cell Syst· July 2019

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Mapping Citrullinated Sites in Multiple Organs of Mice Using Hypercitrullinated Library.
Justyna Fert-Bober, Vidya Venkatraman, Christie L Hunter, Ruining Liu, Erin L Crowgey, Benjamin P Berman

J Proteome Res· May 2019

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Super-enhancer-associated MEIS1 promotes transcriptional dysregulation in Ewing sarcoma in co-operation with EWS-FLI1.
Lehang Lin, Moli Huang, Xianping Shi, Anand Mayakonda, Kaishun Hu, Benjamin P Berman

Nucleic Acids Res· February 2019

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Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation.
Suhn K Rhie, Shannon Schreiner, Heather Witt, Chris Armoskus, Fides D Lay, Benjamin P Berman

Sci Adv· December 2018

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