JACKAL
Lead Investigator(s) Zhexin Xiang, 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) Zhexin Xiang, 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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OnTheFly
Lead Investigator(s) Barry Honig, Richard Mann
A database of Drosophila melanogaster transcription factors and their binding sites.
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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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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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PrISM
Lead Investigator(s) Barry Honig
An integrated computational system where computational tools are implemented for protein sequence and structure analysis and modeling.
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Protein-DNA Interface Alignment Software
Lead Investigator(s) Barry Honig
Aligns the interfacial amino acids from two protein-DNA complexes based on the geometric relationship of each amino acid to its local DNA.
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