CENTDIST: discovery of co-associated factors by motif distribution

Genomic Analyses of Hormone Signaling and Gene Regulation

(2010) Edwin Cheung et al.   Annual Review of Physiology

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

Close association of RNA polymerase II and many transcription factors with Pol III genes

(2010) Debasish Raha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

(2008) Matthew S Hestand et al.   BMC BIOINFORMATICS

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

(2008) Xi Chen et al.   CELL

Upregulation of Activator Protein-4 in Human Colorectal Cancer With Metastasis

(2008) Jie Cao et al.   INTERNATIONAL JOURNAL OF SURGICAL PATHOLOGY

ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species

(2008) Bart Hooghe et al.   NUCLEIC ACIDS RESEARCH

Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing

(2008) Elizabeth D. Wederell et al.   NUCLEIC ACIDS RESEARCH

Stat3 and c-Myc Genome-Wide Promoter Occupancy in Embryonic Stem Cells

(2008) Benjamin L. Kidder et al.   PLoS One

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY