ARACNE
Lead Investigator(s) Andrea Califano
An algorithm for inferring gene regulatory networks from a set of microarray experiments.
Software Page
B Cell Interactome
Lead Investigator(s) Andrea Califano
A network of protein-protein, protein-DNA, and modulatory interactions in human B cells.
Software Page
DeMAND
Lead Investigator(s) Andrea Califano
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.
Software Page
DIGGIT
Lead Investigator(s) Andrea Califano
A Bioconductor package for identifying genetic variants that lie upstream of master regulators and drive cellular phenotypes.
Software Page
FIRE
Lead Investigator(s) Saeed Tavazoie
A motif discovery and characterization program based on mutual information.
Software Page
FIRE-pro
Lead Investigator(s) Saeed Tavazoie
A motif discovery and characterization program for proteins based on mutual information.
Software Page
HERMES
Lead Investigator(s) Andrea Califano
Predicts competing endogenous RNA (ceRNA) interactions from expression profiles of candidate RNAs and their common miRNA regulators using conditional mutual information.
Software Page
iPAGE
Lead Investigator(s) Saeed Tavazoie
A functional and categorical enrichment program based on mutual information.
Software Page
MADSS
Lead Investigator(s) Nicholas Tatonetti
Network analysis framework that identifies adverse event (AE) neighborhoods within the human interactome (protein-protein interaction network).
Software Page
MARINa
Lead Investigator(s) Andrea Califano
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.
Software Page
MatrixREDUCE
Lead Investigator(s) Harmen Bussemaker
Uses genome-wide occupancy data for a transcription factor and associated nucleotide sequences to discover the sequence-specific binding affinity of the transcription factor.
Software Page
MINDy2/CINDY
Lead Investigator(s) Andrea Califano
An algorithm for the genome-wide discovery of modulators of transcriptional interactions.
Software Page
REDUCE Suite
Lead Investigator(s) Harmen Bussemaker
A set of software tools for modeling the regulation of gene expression by transcription factors (TF).
Software Page
TEISER
Lead Investigator(s) Saeed Tavazoie
A de-novo motif discovery tool for finding informative structural elements in RNA.
Software Page
VIPER
Lead Investigator(s) Andrea Califano
R-system package including the Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER) and the MAster Regulator INference Analysis (MARINA) algorithms.
Software Page