Inferring transcription factor complexes from ChIP-seq data

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

(2010) Luca Giorgetti et al.   MOLECULAR CELL

Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

(2009) Ming Yu et al.   MOLECULAR CELL

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors

(2009) Michael F Berger et al.   Nature Protocols

Measuring spatial preferences at fine-scale resolution identifies known and novel cis-regulatory element candidates and functional motif-pair relationships

(2009) Ken Daigoro Yokoyama et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

Discovering Sequence Motifs with Arbitrary Insertions and Deletions

(2008) Martin C. Frith et al.   PLoS Computational Biology

Krüppel-like transcription factors: A functional family

(2007) Richard Pearson et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY