ADOMETA
Lead Investigator(s) Dennis Vitkup
A bioinformatics resource designed to predict genes for orphan metabolic activities — known biochemical activities not currently assigned to genes in some or all organisms.
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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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Bias Removal
Lead Investigator(s) Andrea Califano
Two R scripts for removing location biases from a multiwell dataset.
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Biolearn 1.0
Lead Investigator(s) Dana Pe'er
A package for applying probabilistic graphical models to biological applications.
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Camelot
Lead Investigator(s) Dana Pe'er
CAusal Modeling with Expression Linkage for cOmplex Traits (Camelot) provides a framework to both model complex traits and identify the potential underlying causal factors.
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CANOES
Lead Investigator(s) Yufeng Shen
A method for calling copy number variants from exome sequencing data with an arbitrary number of reference samples.
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CIMS
Lead Investigator(s) Chaolin Zhang
A computational method for HITS-CLIP data analysis to determine the exact protein-RNA crosslink sites and thereby map protein-RNA interactions at single-nucleotide resolution.
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CLEANER
Lead Investigator(s) Mariano Alvarez
An R-system software package for the assembly of informative, transcript-specific probe-clusters for Affymetrix expression microarrays.
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CONDEX (condr)
Lead Investigator(s) Itsik Pe'er
A hidden Markov model for detecting copy number variants in exome sequence data.
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CONEXIC
Lead Investigator(s) Dana Pe'er
COpy Number and EXpression In Cancer (CONEXIC) is an algorithm that integrates matched copy number (amplifications and deletions) and gene expression data from tumor samples to identify driving mutations and the processes they influence.
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cryoEM Refinement Tools
Lead Investigator(s) Barry Honig
Programs and protocols for refining atomic structures — either experimentally determined or computationally constructed — within cryo-electron microscopy (cryoEM) density maps of macromolecular complexes.
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DASH
Lead Investigator(s) Itsik Pe'er
DASH (DASH Associates Shared Haplotypes) is a tool for detecting association to clusters of identity by descent (IBD) segments detected by the Germline software tool.
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DelPhi
Lead Investigator(s) Barry Honig
Provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.
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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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DREVI and DREMI
Lead Investigator(s) Dana Pe'er
Algorithms for visualizing and scoring the strengths of pairwise interactions in single-cell data.
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EDGI
Lead Investigator(s) Barry Honig
EDGI (Enhancer Detection using only Genomic Information) identifies large regulatory elements that consist of evolutionarily conserved, order-independent clusters of short conserved motifs.
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Energy Functions
Lead Investigator(s) Barry Honig
Programs for evaluating or comparing protein structure predictions.
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EVE
Lead Investigator(s) Saeed Tavazoie
A simulation framework for microbial populations in complex dynamic environments.
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FASD
Lead Investigator(s) Raul Rabadan
Frequency Analysis of Sequence Data (FASD)
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FeatureREDUCE
Lead Investigator(s) Harmen Bussemaker
Quantifies relative protein-NA binding affinities using sequence and structural features.
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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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GAMToC
Lead Investigator(s) Raul Rabadan
Uses copy number and mutation data from a cohort of patients, for example from TCGA, to find modules of genes with a related mutation pattern.
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Genatomy
Lead Investigator(s) Dana Pe'er
A visualization tool for biological data related to gene expression, genotypes, growth curves, and copy number variation.
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Germline
Lead Investigator(s) Itsik Pe'er
An algorithm for discovering long shared segments of identity by descent (IBD) between pairs of (unrelated) individuals in a large population.
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geWorkbench
Lead Investigator(s) Aris Floratos
Provides an integrated suite of genomics tools.
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GRASP
Lead Investigator(s) Anthony Nicholls, Barry Honig
A molecular visualization and analysis program useful for displaying and manipulating the surfaces of molecules and their electrostatic properties.
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GRASP2
Lead Investigator(s) Donald Petrey, Barry Honig
An updated version of the GRASP program used for macromolecular structure and surface visualization.
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GRASS
Lead Investigator(s) Barry Honig
A web-based server that exploits many of the features of the GRASP program, providing interactive molecular graphics and quantitative analysis tools with a simple web-based interface.
HADiT
Lead Investigator(s) Itsik Pe'er
HADiT (Haplotype Amplification Distortion in Tumors) is a tool for computing and visualizing allelic distortion in tumor SNP data.
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HATS
Lead Investigator(s) Itsik Pe'er
A tool for calling amplified alleles and constructing the amplified haplotype within called tumor amplicons.
HELIOS
Lead Investigator(s) Dana Pe'er
Integrates genomic data from primary tumors with data from functional RNAi screens to pinpoint driver genes within large recurrently amplified regions of DNA.
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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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HLA-IBD
Lead Investigator(s) Itsik Pe'er
A method for inferring per-locus human leukocyte antigen types using shared segments that are identical by descent (IBD), inferred from genotype data.
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HMAP
Lead Investigator(s) Barry Honig
A method for hybrid multidimensional alignment of profiles that combines sequence, secondary, and tertiary information in protein structures into profiles to facilitate the detection of remote homologs and perform sequence-to-sequence alignments.
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Inference of Modules Associated with eQTL's
Lead Investigator(s) Itsik Pe'er
A tool for constructing modules regulated by eQTLs using gene expression and SNP variation data across multiple individuals.
INFOSTIP
Lead Investigator(s) Itsik Pe'er
A tool for selecting individual for sequencing by total information potential, based on GERMLINE output.
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iPAGE
Lead Investigator(s) Saeed Tavazoie
A functional and categorical enrichment program based on mutual information.
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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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Quantas
Lead Investigator(s) Chaolin Zhang
A pipeline for analysing alternative splicing using RNA-seq.
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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).
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Repertoire
Lead Investigator(s) Yufeng Shen
Scripts for analyzing T cell receptor repertoire sequencing data.
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SAVI
Lead Investigator(s) Raul Rabadan
A program for calling variants in high-throughput sequencing data, particularly paired tumor-normal samples.
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SCREEN
Lead Investigator(s) Barry Honig
A tool for identifying protein cavities and computing cavity attributes that can be applied for classification and analysis.
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ShareViz
Lead Investigator(s) Itsik Pe'er
A tool for graphical visualization of hidden relatedness based on GERMLINE output.
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SIXPAC
Lead Investigator(s) Itsik Pe'er
An efficient, scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets.
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SkyBase
Lead Investigator(s) Barry Honig
A database that stores homology models built by SkyLine analysis.
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SkyLine
Lead Investigator(s)
A high-throughput pipeline for homology modeling of protein structures.
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SPIN-PP
Lead Investigator(s) Barry Honig
A database of all protein-protein interfaces present in the Protein Data Bank.
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SPLASH
Lead Investigator(s) Andrea Califano
A deterministic pattern discovery algorithm that can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences.
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STING Millennium
Lead Investigator(s) Barry Honig
A web-based suite of programs for the comprehensive and simultaneous analysis of structure and sequence.
SURFace
Lead Investigator(s) Barry Honig
Programs that calculate solvent accessible surface area and curvature-corrected solvent accessible surface area.
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T-profiler
Lead Investigator(s) Harmen Bussemaker
A web-based tool that uses the t-test to score changes in the average activity of pre-defined groups of genes.
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TARGet
Lead Investigator(s) Raul Rabadan
A light-weight application for reconstructing non-vertical evolutionary histories from sampled genetic sequences using persistent homology, a tool from topological data analysis.
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Target Explorer
Lead Investigator(s) Barry Honig, Richard Mann
Automates the process of predicting the complex regulatory elements for a specified set of transcription factors in the Drosophila melanogaster genome.
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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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ViSNE
Lead Investigator(s) Dana Pe'er
Maps high-dimensional mass cytometry data onto two dimensions while conserving the high-dimensional structure of the data.
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VISTAL
Lead Investigator(s) Barry Honig
A two-dimensional visualization tool for structural alignments.
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Wanderlust
Lead Investigator(s) Dana Pe'er
A graph-based trajectory detection algorithm that receives multiparameter single-cell events as input and maps them onto a one-dimensional developmental trajectory.
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Wishbone
Lead Investigator(s) Dana Pe'er
An algorithm to align single cells from differentiation systems with bifurcating branches.
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Xplorigin
Lead Investigator(s) Itsik Pe'er
A tool for parsing population ancestry of admixed individuals.
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Zinfandel
Lead Investigator(s) Itsik Pe'er, Yufeng Shen
A tool for detecting CNVs from low-pass whole genome sequencing data.
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