SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions.

MapGL: inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony.

Predicting the effects of SNPs on transcription factor binding affinity.

CGIMP: Real-time exploration and covariate projection for self-organizing map datasets.

A proximity-based graph clustering method for the identification and application of transcription factor clusters.

Mango: a bias-correcting ChIA-PET analysis pipeline.

Comparative analysis of regulatory information and circuits across distant species Open.

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.

F-Seq: a feature density estimator for high-throughput sequence tags.