JACKAL
Lead Investigator(s)Barry Honig
A collection of programs for the modeling and analysis of protein structures.
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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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mCarts
Lead Investigator(s)Chaolin Zhang

A hidden Markov model (HMM)-based method for predicting clusters of RNA motif sites.

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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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MODEST
Lead Investigator(s)Harris Wang

Developed with Morten Sommer, MODEST allows the rapid and effective design of optimal oligos for achieving specific mutations using the MAGE genome engineering platform.

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mRIN
Lead Investigator(s)Chaolin Zhang

A method for assessing a quantitative measure of mRNA integrity directly from RNA-seq data.

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MutaGeneSys
Lead Investigator(s)Itsik Pe'er

Uses genome-wide genotype data to estimate individual disease susceptibility.

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MVP
Lead Investigator(s)Yufeng Shen

Method to predict deleterious genetic effect of missense variants.

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Nest
Lead Investigator(s)Barry Honig
An algorithm for modeling protein structure based on a sequence-template alignment.
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NORI
Lead Investigator(s)Raul Rabadan

NORI (Non-coding RNA Identification) is a computational tool that identifies lncRNAs using next generation sequencing.

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OLego
Lead Investigator(s)Chaolin Zhang

A program for mapping RNA-seq reads, including de novo identification of exon junctions.

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OPERA
Lead Investigator(s)Itsik Pe'er

A tool for power estimation and design of whole-genome resequencing projects aimed at rare variant associations.

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P-HIPSTer
Lead Investigator(s)Barry Honig, Sagi Shapira
P-HIPSTer (Pathogen-Host Interactome Prediction using STructurE similaRity) is an algorithm that exploits both sequence- and structure-based information to infer interactions between pathogen and human proteins.
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Pandora
Lead Investigator(s)Raul Rabadan

A multi-step pipeline for finding pathogen sequences in RNA-seq data.

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Pegasus
Lead Investigator(s)Raul Rabadan

Enables annotation and prediction of oncogenic gene fusions using RNA-seq data.

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PoolDesign
Lead Investigator(s)Itsik Pe'er

A tool for designing overlapping pools for variant-carrier identification.

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PredUs
Lead Investigator(s)Barry Honig
A tool for the prediction of protein-protein interfaces based on interface conservation among structurally similar protein neighbors.
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PrePPI
Lead Investigator(s)Barry Honig
A database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
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