Non-canonical protein-DNA interactions identified by ChIP are not artifacts

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

FRUIT, a Scar-Free System for Targeted Chromosomal Mutagenesis, Epitope Tagging, and Promoter Replacement in Escherichia coli and Salmonella enterica

(2012) Anne M. Stringer et al.   PLoS One

cis-Antisense RNA, Another Level of Gene Regulation in Bacteria

(2011) J. Georg et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

ChIP on Chip: surprising results are often artifacts

(2010) Torsten Waldminghaus et al.   BMC GENOMICS

Identification of the Regulatory Logic Controlling Salmonella Pathoadaptation by the SsrA-SsrB Two-Component System

(2010) Ana M. Tomljenovic-Berube et al.   PLoS Genetics

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing

(2009) Philippe Lefrançois et al.   BMC GENOMICS

NsrR targets in theEscherichia coligenome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility

(2009) Jonathan D. Partridge et al.   MOLECULAR MICROBIOLOGY

Inherent Signals in Sequencing-Based Chromatin-ImmunoPrecipitation Control Libraries

(2009) Vinsensius B. Vega 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

The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

(2008) Tomohiro Shimada et al.   NUCLEIC ACIDS RESEARCH

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY