JACKAL
Lead Investigator(s) Zhexin Xiang, Barry Honig
A collection of programs for the modeling and analysis of protein structures.
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JISTIC
Lead Investigator(s) Dana Pe'er
A tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. It is an improvement over the widely used GISTIC algorithm.
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LitVAn
Lead Investigator(s) Dana Pe'er
An algorithm that searches for over-represented terms in papers associated with genes in a gene set.
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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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MarkUs
Lead Investigator(s) Barry Honig
A web server that can assist in the assessment of the biochemical function for a given protein structure.
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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.
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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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Model Quality Assessment: Global and Local Quality Assessment of Protein Models
Lead Investigator(s) Barry Honig
Three protocols for model quality assessment (MQA), including direct assessment of local qualities using statistical potentials and two machine learning-based protocols.
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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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Nest
Lead Investigator(s) Zhexin Xiang, Barry Honig
An algorithm for modeling protein structure based on a sequence-template alignment.
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OLego
Lead Investigator(s) Chaolin Zhang
A program for de novo spliced mapping of mRNA-seq reads.
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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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PhenoGraph
Lead Investigator(s) Dana Pe'er
A computationally efficient graph-based method for identifying subpopulations in high-dimensional single-cell 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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Protein-DNA Modeling Interface Software
Lead Investigator(s) Barry Honig
This program can be used predict the conformation of the sidechains within a protein-DNA binding interface.
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PUDGE
Lead Investigator(s) Barry Honig
An algorithm for the computational prediction of protein structure using sequence homology.
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