Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

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

(2009) Philippe Lefrançois et al.   BMC GENOMICS

Dynamic and complex transcription factor binding during an inducible response in yeast

(2009) L. Ni et al.   GENES & DEVELOPMENT

Distinguishing direct versus indirect transcription factor-DNA interactions

(2009) R. Gordan et al.   GENOME RESEARCH

Systematic identification of yeast cell cycle transcription factors using multiple data sources

(2008) Wei-Sheng Wu et al.   BMC BIOINFORMATICS

Cross-species de novo identification of cis-regulatory modules with GibbsModule: Application to gene regulation in embryonic stem cells

(2008) D. Xie et al.   GENOME RESEARCH

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

(2008) Peter Van Loo et al.   GENOME BIOLOGY