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List of works by Benjamin P Berman

A BAC-based physical map of the major autosomes of Drosophila melanogaster.

scientific article

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

scientific article published on 30 April 2021

Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A.

scientific article

An Evaluation of the Cost and Performance of Scientific Workflows on Amazon EC2

An integrated computational pipeline and database to support whole-genome sequence annotation

scientific article

Androgen receptor responsive enhancers are flanked by consistently-positioned H3-acetylated nucleosomes.

scientific article

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

scientific article

Author Correction: Alpha-oxoglutarate inhibits the proliferation of immortalized normal bladder epithelial cells via an epigenetic switch involving ARID1A.

scientific article published on 16 April 2018

Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data

scientific article

Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue

scientific article published on 27 February 2014

Co-activation of super-enhancer-driven CCAT1 by TP63 and SOX2 promotes squamous cancer progression

scientific article published in Nature Communications

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

scientific article

DNA methylation loss in late-replicating domains is linked to mitotic cell division.

scientific article published on 2 April 2018

Data Sharing Options for Scientific Workflows on Amazon EC2

Demystifying the secret mission of enhancers: linking distal regulatory elements to target genes

scientific article published on 08 October 2015

Dynamic nucleosome-depleted regions at androgen receptor enhancers in the absence of ligand in prostate cancer cells

scientific article published on 3 October 2011

Exosomal MicroRNA Transfer Into Macrophages Mediates Cellular Postconditioning.

scientific article published on 14 April 2017

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome

scientific article

FOXC1 Activates Smoothened-Independent Hedgehog Signaling in Basal-like Breast Cancer

scientific article

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs

scientific article

Functional annotation of colon cancer risk SNPs

scientific article

Functional enhancers at the gene-poor 8q24 cancer-linked locus.

scientific article published on 14 August 2009

Gender-specific postnatal demethylation and establishment of epigenetic memory

scientific article published on May 2015

Genome-wide Mapping of Nucleosome Positioning and DNA Methylation Within Individual DNA Molecules

Genome-wide Runx2 occupancy in prostate cancer cells suggests a role in regulating secretion

scientific article published on 19 December 2011

Genomic and Epigenomic Heterogeneity of Hepatocellular Carcinoma.

scientific article

Genomic androgen receptor-occupied regions with different functions, defined by histone acetylation, coregulators and transcriptional capacity

scientific article

Global analysis of patterns of gene expression during Drosophila embryogenesis

scientific article published on January 2007

Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes

scientific article

H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes ⬇️

scientific article published on September 24, 2010

Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1.

scientific article

Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas.

scientific article published on 31 August 2017

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

scientific article published on 21 May 2015

Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation.

scientific article

Lineage-specific epigenomic and genomic activation of oncogene HNF4A promotes gastrointestinal adenocarcinomas

scientific article published on 24 April 2020

Locking in on the human methylome.

scientific article published in April 2009

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains

scientific article

Scientific workflow applications on Amazon EC2

Spatial intratumoral heterogeneity and temporal clonal evolution in esophageal squamous cell carcinoma

scientific article published on 17 October 2016

The PsychENCODE project

scientific article

The chromatin accessibility landscape of primary human cancers

scientific article

The genome sequence of Drosophila melanogaster

scientific article

The role of DNA methylation in directing the functional organization of the cancer epigenome

scientific article

Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

article

Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells

scientific article published on October 2010

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