Optimization of transcription factor binding map accuracy utilizing knockout-mouse models

MKL1/2 and ELK4 co-regulate distinct serum response factor (SRF) transcription programs in macrophages

(2014) Lan Xie   BMC GENOMICS

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

(2014) Richard I Sherwood et al.   NATURE BIOTECHNOLOGY

Efficient genome engineering by targeted homologous recombination in mouse embryos using transcription activator-like effector nucleases

(2014) Daniel Sommer et al.   Nature Communications

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

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

(2013) Sivakanthan Kasinathan et al.   NATURE METHODS

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

Large-Scale Quality Analysis of Published ChIP-seq Data

(2013) Georgi K. Marinov et al.   G3-Genes Genomes Genetics

Computational Identification of Diverse Mechanisms Underlying Transcription Factor-DNA Occupancy

(2013) Qiong Cheng et al.   PLoS Genetics

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Rev-erb  and Rev-erb  coordinately protect the circadian clock and normal metabolic function

(2012) A. Bugge et al.   GENES & DEVELOPMENT

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

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

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

Systematic evaluation of factors influencing ChIP-seq fidelity

(2012) Yiwen Chen et al.   NATURE METHODS

A travel guide to Cytoscape plugins

(2012) Rintaro Saito et al.   NATURE METHODS

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types

(2011) Gang Wei et al.   IMMUNITY

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

Discovering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data

(2011) Dongjun Chung et al.   PLoS Computational Biology

The Essential Function for Serum Response Factor in T-Cell Development Reflects Its Specific Coupling to Extracellular Signal-Regulated Kinase Signaling

(2010) A. Mylona et al.   MOLECULAR AND CELLULAR BIOLOGY

Serum Response Factor Utilizes Distinct Promoter- and Enhancer-Based Mechanisms To Regulate Cytoskeletal Gene Expression in Macrophages

(2010) A. L. Sullivan et al.   MOLECULAR AND CELLULAR BIOLOGY

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY