Epigenetic and transcriptional profiling of triple negative breast cancer

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq

(2017) Joseph G. Azofeifa et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Paused RNA polymerase II inhibits new transcriptional initiation

(2017) Wanqing Shao et al.   NATURE GENETICS

Identification of active miRNA promoters from nuclear run-on RNA sequencing

(2017) Qi Liu et al.   NUCLEIC ACIDS RESEARCH

RTFBSDB: an integrated framework for transcription factor binding site analysis

(2016) Zhong Wang et al.   BIOINFORMATICS

High-throughput «Omics» technologies: New tools for the study of triple-negative breast cancer

(2016) Gaëlle Judes et al.   CANCER LETTERS

Monoubiquitination of Histone H2B Blocks Eviction of Histone Variant H2A.Z from Inducible Enhancers

(2016) Gregory Segala et al.   MOLECULAR CELL

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

(2016) Yun Chen et al.   NATURE GENETICS

Genomic Organization of Human Transcription Initiation Complexes

(2016) B. Franklin Pugh et al.   PLoS One

High-Resolution Mapping of RNA Polymerases Identifies Mechanisms of Sensitivity and Resistance to BET Inhibitors in t(8;21) AML

(2016) Yue Zhao et al.   Cell Reports

groHMM: a computational tool for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

(2015) Minho Chae et al.   BMC BIOINFORMATICS

Clinical implications of molecular heterogeneity in triple negative breast cancer

(2015) Brian D. Lehmann et al.   BREAST

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells

(2015) Miao Sun et al.   MOLECULAR CELL

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

Histone exchange, chromatin structure and the regulation of transcription

(2015) Swaminathan Venkatesh et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Subnucleosomal Structures and Nucleosome Asymmetry across a Genome

(2014) Ho Sung Rhee et al.   CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Dynamics of histone variant H3.3 and its coregulation with H2A.Z at enhancers and promoters

(2014) Ping Chen et al.   Nucleus

An Interactive Analysis and Exploration Tool for Epigenomic Data

(2013) H. Younesy et al.   COMPUTER GRAPHICS FORUM

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription

(2012) D. B. Beck et al.   GENES & DEVELOPMENT

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE