Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Crystal Structure of Mouse Elf3 C-terminal DNA-binding Domain in Complex with Type II TGF-β Receptor Promoter DNA

(2010) Vinod B. Agarkar et al.   JOURNAL OF MOLECULAR BIOLOGY

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

Finding distal regulatory elements in the human genome

(2009) Nathaniel D Heintzman et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery

(2009) J. Boros et al.   GENOME RESEARCH

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

EMAGE mouse embryo spatial gene expression database: 2010 update

(2009) Lorna Richardson et al.   NUCLEIC ACIDS RESEARCH

DNA Specificity Determinants Associate with Distinct Transcription Factor Functions

(2009) Peter C. Hollenhorst et al.   PLoS Genetics

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

(2008) David A Nix et al.   BMC BIOINFORMATICS

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

(2008) Michael F. Berger et al.   CELL

Analysis of Homeodomain Specificities Allows the Family-wide Prediction of Preferred Recognition Sites

(2008) Marcus B. Noyes et al.   CELL

Regulation of the transcription factor Ets-1 by DNA-mediated homo-dimerization

(2008) Ekaterina P Lamber et al.   EMBO JOURNAL

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

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

(2008) Anton Valouev et al.   NATURE METHODS

Microsatellites as EWS/FLI response elements in Ewing's sarcoma

(2008) K. Gangwal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE