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- Reverse Engineering and Analysis of Regulatory Networks
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- Integration of Genomics Data
- Immuno-Genomics Data Analysis
- Protein Interaction Prediction
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JACKAL
Lead Investigator(s) Barry Honig
A collection of programs for the modeling and analysis of protein structures.
▶ Software Page 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).
▶ 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
Arguably the first “deep learning” model for fitting position-specific affinity matrix (PSAM) models to (continuously distributed) functional genomics data.
▶ Software Page mCarts
Lead Investigator(s) Chaolin Zhang
A hidden Markov model (HMM)-based method for predicting clusters of RNA motif sites.
▶ Software Page MINDy2/CINDY
Lead Investigator(s) Andrea Califano
An algorithm for the genome-wide discovery of modulators of transcriptional interactions.
▶ Software Page 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.
▶ Software Page mRIN
Lead Investigator(s) Chaolin Zhang
A method for assessing a quantitative measure of mRNA integrity directly from RNA-seq data.
▶ Software Page MutaGeneSys
Lead Investigator(s) Itsik Pe'er
Uses genome-wide genotype data to estimate individual disease susceptibility.
▶ Software Page MVP
Lead Investigator(s) Yufeng Shen
Method to predict deleterious genetic effect of missense variants.
▶ Software Page Nest
Lead Investigator(s) Barry Honig
An algorithm for modeling protein structure based on a sequence-template alignment.
▶ Software Page NORI
Lead Investigator(s) Raul Rabadan
NORI (Non-coding RNA Identification) is a computational tool that identifies lncRNAs using next generation sequencing.
▶ Software Page OLego
Lead Investigator(s) Chaolin Zhang
A program for mapping RNA-seq reads, including de novo identification of exon junctions.
▶ Software Page OPERA
Lead Investigator(s) Itsik Pe'er
A tool for power estimation and design of whole-genome resequencing projects aimed at rare variant associations.
▶ Software Page 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.
▶ Software Page Pandora
Lead Investigator(s) Raul Rabadan
A multi-step pipeline for finding pathogen sequences in RNA-seq data.
▶ Software Page Pegasus
Lead Investigator(s) Raul Rabadan
Enables annotation and prediction of oncogenic gene fusions using RNA-seq data.
▶ Software Page PoolDesign
Lead Investigator(s) Itsik Pe'er
A tool for designing overlapping pools for variant-carrier identification.
▶ Software Page PredUs
Lead Investigator(s) Barry Honig
A tool for the prediction of protein-protein interfaces based on interface conservation among structurally similar protein neighbors.
▶ Software Page PrePPI
Lead Investigator(s) Barry Honig
A database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.
▶ Software Page