3DNA
Lead Investigator(s) Xiang-Jun Lu, Harmen Bussemaker
3DNA is a versatile, integrated software system for the analysis, rebuilding, and visualization of 3D nucleic-acid-containing structures. The 3DNA suite contains DSSR, an integrated software tool for dissecting the spatial structure of RNA, and SNAP for analyzing structures of nucleic acid-protein complexes.
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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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Atlas-SNP
Lead Investigator(s) Yufeng Shen
Bioinformatics analysis of next-generation sequencing.
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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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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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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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CTK
Lead Investigator(s) Chaolin Zhang
A software package for comprehensive and streamlined analysis of CLIP data, including peak calling and identification of precise protein-RNA crosslink sites.
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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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Episcore
Lead Investigator(s) Yufeng Shen
A method to predict gene haploinsufficiency based on human epigenomic profiles under normal conditions.
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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
Software for inferring feature-based protein-DNA interaction models from protein binding microarray (PBM) data; used in Cis-BP database.
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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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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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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.
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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HotSpots
Lead Investigator(s) Yufeng Shen
A method to infer cancer somatic mutation hotspots.
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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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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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Quantas
Lead Investigator(s) Chaolin Zhang
A pipeline for analyzing alternative splicing using RNA-seq data.
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Randomly
Lead Investigator(s) Raul Rabadan
Randomly is a python package for denoising single-cell data using Random Matrix Theory.
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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); includes MatrixREDUCE, LogoGenerator, and Transfactivity.
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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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scTDA
Lead Investigator(s) Raul Rabadan
An object-oriented python library for topological data analysis of high-throughput single-cell RNA-seq data.
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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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Ska
Lead Investigator(s) Barry Honig
A program to compare and align protein structures.
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SkyLine
Lead Investigator(s)
A high-throughput pipeline for homology modeling of protein structures.
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Splicescope
Lead Investigator(s) Chaolin Zhang
A method to evaluate neuronal maturation based on alternative splicing profiles.
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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 interpret genome-wide mRNA expression changes at the level of Gene Ontology categories or ChIP-based regulons.
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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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TOBI
Lead Investigator(s) Raul Rabadan
TOBI predicts somatic variants from .vcf or .bam input.
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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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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 copy number variants (CNVs) whole genome data based on both depth of coverage and mate pair information.
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