Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes

(2010) Manonmani Arunachalam et al.   BIOINFORMATICS

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

Genome-wide identification of cis-regulatory motifs and modules underlying gene coregulation using statistics and phylogeny

(2010) H. Rouault et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Leila Taher et al.   BIOINFORMATICS

Motif-Blind, Genome-Wide Discovery of cis-Regulatory Modules in Drosophila and Mouse

(2009) Miriam R. Kantorovitz et al.   DEVELOPMENTAL CELL

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Identifying Cis-Regulatory Sequences by Word Profile Similarity

(2009) Garmay Leung et al.   PLoS One

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs

(2008) Andra Ivan et al.   GENOME BIOLOGY