Prediction of histone post-translational modification patterns based on nascent transcription data

Anomalous collapses of Nares Strait ice arches leads to enhanced export of Arctic sea ice

(2021) G. W. K. Moore et al.   Nature Communications

The Dryas iulia Genome Supports Multiple Gains of a W Chromosome from a B Chromosome in Butterflies

(2021) James J Lewis et al.   Genome Biology and Evolution

Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size

(2021) Francesco Cicconardi et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA is essential for PRC2 chromatin occupancy and function in human pluripotent stem cells

(2020) Yicheng Long et al.   NATURE GENETICS

Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation

(2020) Marc A. J. Morgan et al.   NATURE GENETICS

Efficient chromatin accessibility mapping in situ by nucleosome-tethered tagmentation

(2020) Steven Henikoff et al.   eLife

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts

(2019) Surag Nair et al.   BIOINFORMATICS

WashU Epigenome Browser update 2019

(2019) Daofeng Li et al.   NUCLEIC ACIDS RESEARCH

Functionally Annotating Regulatory Elements in the Equine Genome Using Histone Mark ChIP-Seq

(2019) N. B. Kingsley et al.   Genes

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition

(2018) Timothy J. Durham et al.   Nature Communications

Dynamic evolution of regulatory element ensembles in primate CD4+ T cells

(2018) Charles G. Danko et al.   Nature Ecology & Evolution

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies

(2018) Rohan N. Shah et al.   MOLECULAR CELL

Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project

(2018) E. N. Burns et al.   ANIMAL GENETICS

Identification of regulatory elements from nascent transcription using dREG

(2018) Zhong Wang et al.   GENOME RESEARCH

Single-molecule nascent RNA sequencing identifies regulatory domain architecture at promoters and enhancers

(2018) Jacob M. Tome et al.   NATURE GENETICS

Chromatin run-on and sequencing maps the transcriptional regulatory landscape of glioblastoma multiforme

(2018) Tinyi Chu et al.   NATURE GENETICS

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

(2018) Elisabetta Giuffra et al.   Annual Review of Animal Biosciences

Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes

(2017) Justin S. Becker et al.   MOLECULAR CELL

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity

(2016) Arnau Sebé-Pedrós et al.   CELL

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

(2016) Yun Chen et al.   NATURE GENETICS

Histone H3 globular domain acetylation identifies a new class of enhancers

(2016) Madapura M Pradeepa et al.   NATURE GENETICS

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

High-Resolution Chromatin Dynamics during a Yeast Stress Response

(2015) Assaf Weiner et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Identification of active transcriptional regulatory elements from GRO-seq data

(2015) Charles G Danko et al.   NATURE METHODS

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

(2015) Melina Claussnitzer et al.   NEW ENGLAND JOURNAL OF MEDICINE

Joint Analysis of Functional Genomic Data and Genome-wide Association Studies of 18 Human Traits

(2014) Joseph K. Pickrell   AMERICAN JOURNAL OF HUMAN GENETICS

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

(2014) N. Bonhoure et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Site-specific human histone H3 methylation stability: fast K4me3 turnover

(2014) Yupeng Zheng et al.   PROTEOMICS

A Brief History of Epigenetics

(2014) G. Felsenfeld   Cold Spring Harbor Perspectives in Biology

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

(2014) Mary Ann Allen et al.   eLife

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

EZH2 Is Required for Germinal Center Formation and Somatic EZH2 Mutations Promote Lymphoid Transformation

(2013) Wendy Béguelin et al.   CANCER CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

(2013) H. Kwak et al.   SCIENCE

Balancing of Histone H3K4 Methylation States by the Kdm5c/SMCX Histone Demethylase Modulates Promoter and Enhancer Function

(2013) Nikolay S. Outchkourov et al.   Cell Reports

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma

(2012) Jeremy Schwartzentruber et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Exploring Massive, Genome Scale Datasets with the GenometriCorr Package

(2012) Alexander Favorov et al.   PLoS Computational Biology

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

(2011) Jason Ernst et al.   NATURE

XPB, a subunit of TFIIH, is a target of the natural product triptolide

(2011) Denis V Titov et al.   Nature Chemical Biology

The Human Epigenome Browser at Washington University

(2011) Xin Zhou et al.   NATURE METHODS

Histone modification: cause or cog?

(2011) Steven Henikoff et al.   TRENDS IN GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Triptolide is an inhibitor of RNA polymerase I and II-dependent transcription leading predominantly to down-regulation of short-lived mRNA

(2009) S. Vispe et al.   MOLECULAR CANCER THERAPEUTICS

Mapping accessible chromatin regions using Sono-Seq

(2009) R. K. Auerbach et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

DOT1L/KMT4 Recruitment and H3K79 Methylation Are Ubiquitously Coupled with Gene Transcription in Mammalian Cells

(2008) D. J. Steger et al.   MOLECULAR AND CELLULAR BIOLOGY

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics