High-resolution mapping of transcription factor binding sites on native chromatin

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins

(2013) L. Teytelman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring Chromatin Interaction Dynamics on the Second Time Scale at Single-Copy Genes

(2013) K. Poorey et al.   SCIENCE

ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies

(2013) Gabriel E. Zentner et al.   PLoS Genetics

Limitations and possibilities of low cell number ChIP-seq

(2012) Gregor D Gilfillan et al.   BMC GENOMICS

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

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

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

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Surveying the epigenomic landscape, one base at a time

(2012) Gabriel E Zentner et al.   GENOME BIOLOGY

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

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

(2011) Ho Sung Rhee et al.   CELL

Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide

(2011) S. S. Teves et al.   GENES & DEVELOPMENT

ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species

(2011) Aaron T. Spivak et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

H2A.Z nucleosomes enriched over active genes are homotypic

(2010) Christopher M Weber et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast

(2010) Mythily Ganapathi et al.   NUCLEIC ACIDS RESEARCH

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Mechanisms that Specify Promoter Nucleosome Location and Identity

(2009) Paul D. Hartley et al.   CELL

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Where Does Mediator Bind In Vivo?

(2009) Xiaochun Fan et al.   PLoS One

Impact of Chromatin Structures on DNA Processing for Genomic Analyses

(2009) Leonid Teytelman et al.   PLoS One

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

Genome-wide profiling of salt fractions maps physical properties of chromatin

(2008) S. Henikoff et al.   GENOME RESEARCH

Analysis of transcription factor interactions in osteoblasts using competitive chromatin immunoprecipitation

(2008) H. Roca et al.   NUCLEIC ACIDS RESEARCH