High-Resolution Mapping of In vivo Genomic Transcription Factor Binding Sites Using In situ DNase I Footprinting and ChIP-seq

The lac Repressor Displays Facilitated Diffusion in Living Cells

(2012) P. Hammar et al.   SCIENCE

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

(2011) Ho Sung Rhee et al.   CELL

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Genome-wide binding profiles of the Bacillus subtilis transition state regulator AbrB and its homolog Abh reveals their interactive role in transcriptional regulation

(2010) Onuma Chumsakul et al.   NUCLEIC ACIDS RESEARCH

 X Is Involved in Controlling Bacillus subtilis Biofilm Architecture through the AbrB Homologue Abh

(2009) E. J. Murray et al.   JOURNAL OF BACTERIOLOGY

Protein Occupancy Landscape of a Bacterial Genome

(2009) Tiffany Vora et al.   MOLECULAR CELL

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

Insights into the Nature of DNA Binding of AbrB-like Transcription Factors

(2008) Daniel M. Sullivan et al.   STRUCTURE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY