Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

(2008) Lucas D. Ward et al.   BIOINFORMATICS

PASTAA: identifying transcription factors associated with sets of co-regulated genes

(2008) Helge G. Roider et al.   BIOINFORMATICS

Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast

(2008) Uri Keich et al.   BMC BIOINFORMATICS

Transcriptional co-expression and co-regulation of genes coding for components of the oxidative phosphorylation system

(2008) Corina van Waveren et al.   BMC GENOMICS

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

(2008) Marcus B. Noyes et al.   CELL

Antagonistic roles for Ultrabithorax and Antennapedia in regulating segment-specific apoptosis of differentiated motoneurons in the Drosophila embryonic central nervous system

(2008) A. Rogulja-Ortmann et al.   DEVELOPMENT

Systematic functional characterization of cis-regulatory motifs in human core promoters

(2008) S. Sinha et al.   GENOME RESEARCH

Associating transcription factor-binding site motifs with target GO terms and target genes

(2008) Mikael Bodén et al.   NUCLEIC ACIDS RESEARCH

A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system

(2008) Marcus B. Noyes et al.   NUCLEIC ACIDS RESEARCH

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger 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

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

(2008) Stephen A. Ramsey et al.   PLoS Computational Biology

Stability and Dynamics of Polycomb Target Sites in Drosophila Development

(2008) Camilla Kwong et al.   PLoS Genetics