An algorithm for inferring gene regulatory networks from a set of microarray experiments.

A network of protein-protein, protein-DNA, and modulatory interactions in human B cells.

An efficient and accurate method for determining a drug's mechanism of action, including both direct drug targets and other gene products involved in implementing its effect or modulating its activity.

A Bioconductor package for identifying genetic variants that lie upstream of master regulators and drive cellular phenotypes.

Software for inferring feature-based protein-DNA interaction models from protein binding microarray (PBM) data; used in Cis-BP database.

A motif discovery and characterization program based on mutual information.

A motif discovery and characterization program for proteins based on mutual information.

Predicts competing endogenous RNA (ceRNA) interactions from expression profiles of candidate RNAs and their common miRNA regulators using conditional mutual information.

A functional and categorical enrichment program based on mutual information.

Generates “energy logos” representing the DNA binding specificity of transcription factors in a biophysically interpretable manner (letter height equals ddG/RT).

Network analysis framework that identifies adverse event (AE) neighborhoods within the human interactome (protein-protein interaction network).

The Master Regulator Inference Algorithm identifies transcription factors (TFs) that control the transition between the two phenotypes, A and B, and the maintenance of the latter phenotype.

Arguably the first “deep learning” model for fitting position-specific affinity matrix (PSAM) models to (continuously distributed) functional genomics data.

An algorithm for the genome-wide discovery of modulators of transcriptional interactions.

A set of software tools for modeling the regulation of gene expression by transcription factors (TF); includes MatrixREDUCE, LogoGenerator, and Transfactivity.

A web-based tool that uses the t-test to interpret genome-wide mRNA expression changes at the level of Gene Ontology categories or ChIP-based regulons.

A de-novo motif discovery tool for finding informative structural elements in RNA.

A tool for finding probes that measures significantly expressed loci in a genomic array experiment.

R-system package including the Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER) and the MAster Regulator INference Analysis (MARINA) algorithms.