GREAT improves functional interpretation of cis-regulatory regions

Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements

(2009) Leila Taher et al.   BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

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

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Extracting transcription factor targets from ChIP-Seq data

(2009) Geetu Tuteja et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets

(2008) C. Linhart et al.   GENOME RESEARCH

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

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

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Fine mapping of regulatory loci for mammalian gene expression using radiation hybrids

(2008) Christopher C Park et al.   NATURE GENETICS

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

(2008) Anton Valouev et al.   NATURE METHODS

The Mouse Genome Database genotypes::phenotypes

(2008) J. A. Blake et al.   NUCLEIC ACIDS RESEARCH