ARACNE
Lead Investigator(s) Andrea Califano
An algorithm for inferring gene regulatory networks from a set of microarray experiments.
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B Cell Interactome
Lead Investigator(s) Andrea Califano
A network of protein-protein, protein-DNA, and modulatory interactions in human B cells.
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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.
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DIGGIT
Lead Investigator(s) Andrea Califano
A Bioconductor package for identifying genetic variants that lie upstream of master regulators and drive cellular phenotypes.
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FeatureREDUCE
Lead Investigator(s) Harmen Bussemaker
Software for inferring feature-based protein-DNA interaction models from protein binding microarray (PBM) data; used in Cis-BP database.
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FIRE
Lead Investigator(s) Saeed Tavazoie
A motif discovery and characterization program based on mutual information.
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FIRE-pro
Lead Investigator(s) Saeed Tavazoie
A motif discovery and characterization program for proteins based on mutual information.
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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.
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iPAGE
Lead Investigator(s) Saeed Tavazoie
A functional and categorical enrichment program based on mutual information.
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LogoGenerator
Lead Investigator(s) Harmen Bussemaker
Generates “energy logos” representing the DNA binding specificity of transcription factors in a biophysically interpretable manner (letter height equals ddG/RT).
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MADSS
Lead Investigator(s) Nicholas Tatonetti
Network analysis framework that identifies adverse event (AE) neighborhoods within the human interactome (protein-protein interaction network).
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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.
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MatrixREDUCE
Lead Investigator(s) Harmen Bussemaker
Arguably the first “deep learning” model for fitting position-specific affinity matrix (PSAM) models to (continuously distributed) functional genomics data.
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MINDy2/CINDY
Lead Investigator(s) Andrea Califano
An algorithm for the genome-wide discovery of modulators of transcriptional interactions.
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REDUCE Suite
Lead Investigator(s) Harmen Bussemaker
A set of software tools for modeling the regulation of gene expression by transcription factors (TF); includes MatrixREDUCE, LogoGenerator, and Transfactivity.
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T-profiler
Lead Investigator(s) Harmen Bussemaker
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.
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TEISER
Lead Investigator(s) Saeed Tavazoie
A de-novo motif discovery tool for finding informative structural elements in RNA.
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TranscriptionDetector
Lead Investigator(s) Harmen Bussemaker
A tool for finding probes that measures significantly expressed loci in a genomic array experiment.
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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.
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