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.

A bioinformatics resource designed to predict genes for orphan metabolic activities — known biochemical activities not currently assigned to genes in some or all organisms.

An algorithm for inferring gene regulatory networks from a set of microarray experiments.

Bioinformatics analysis of next-generation sequencing.

A network of protein-protein, protein-DNA, and modulatory interactions in human B cells.

Two R scripts for removing location biases from a multiwell dataset.

A method for calling copy number variants from exome sequencing data with an arbitrary number of reference samples.

A hidden Markov model for detecting copy number variants in exome sequence data.

A software package for comprehensive and streamlined analysis of CLIP data, including peak calling and identification of precise protein-RNA crosslink sites.

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.

Provides numerical solutions to the Poisson-Boltzmann equation (both linear and nonlinear form) for molecules of arbitrary shape and charge distribution.

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.

A Bioconductor package for identifying genetic variants that lie upstream of master regulators and drive cellular phenotypes.

A method to predict gene haploinsufficiency based on human epigenomic profiles under normal conditions.

A simulation framework for microbial populations in complex dynamic environments.

Frequency Analysis of Sequence Data (FASD)

Software for inferring feature-based protein-DNA interaction models from protein binding microarray (PBM) data; used in Cis-BP database.

A motif discovery and characterization program based on mutual information.

A motif discovery and characterization program for proteins based on mutual information.

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.

An algorithm for discovering long shared segments of identity by descent (IBD) between pairs of (unrelated) individuals in a large population.

Provides an integrated suite of genomics tools.

HADiT (Haplotype Amplification Distortion in Tumors) is a tool for computing and visualizing allelic distortion in tumor SNP data.

A tool for calling amplified alleles and constructing the amplified haplotype within called tumor amplicons.

Predicts competing endogenous RNA (ceRNA) interactions from expression profiles of candidate RNAs and their common miRNA regulators using conditional mutual information.

A method for inferring per-locus human leukocyte antigen types using shared segments that are identical by descent (IBD), inferred from genotype data.

A method to infer cancer somatic mutation hotspots.

A tool for constructing modules regulated by eQTLs using gene expression and SNP variation data across multiple individuals.

A tool for selecting individual for sequencing by total information potential, based on GERMLINE output.

A functional and categorical enrichment program based on mutual information.

Generates “energy logos” representing the DNA binding specificity of transcription factors in a biophysically interpretable manner (letter height equals ddG/RT).

Network analysis framework that identifies adverse event (AE) neighborhoods within the human interactome (protein-protein interaction network).

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.

Arguably the first “deep learning” model for fitting position-specific affinity matrix (PSAM) models to (continuously distributed) functional genomics data.

A hidden Markov model (HMM)-based method for predicting clusters of RNA motif sites.

An algorithm for the genome-wide discovery of modulators of transcriptional interactions.

Developed with Morten Sommer, MODEST allows the rapid and effective design of optimal oligos for achieving specific mutations using the MAGE genome engineering platform.

A method for assessing a quantitative measure of mRNA integrity directly from RNA-seq data.

Uses genome-wide genotype data to estimate individual disease susceptibility.

Method to predict deleterious genetic effect of missense variants.

NORI (Non-coding RNA Identification) is a computational tool that identifies lncRNAs using next generation sequencing.

A program for mapping RNA-seq reads, including de novo identification of exon junctions.

A tool for power estimation and design of whole-genome resequencing projects aimed at rare variant associations.

A multi-step pipeline for finding pathogen sequences in RNA-seq data.

Enables annotation and prediction of oncogenic gene fusions using RNA-seq data.

A tool for designing overlapping pools for variant-carrier identification.

A pipeline for analyzing alternative splicing using RNA-seq data.

Randomly is a python package for denoising single-cell data using Random Matrix Theory.

A set of software tools for modeling the regulation of gene expression by transcription factors (TF); includes MatrixREDUCE, LogoGenerator, and Transfactivity.

Scripts for analyzing T cell receptor repertoire sequencing data.

A program for calling variants in high-throughput sequencing data, particularly paired tumor-normal samples.

An object-oriented python library for topological data analysis of high-throughput single-cell RNA-seq data.

A tool for graphical visualization of hidden relatedness based on GERMLINE output.

An efficient, scalable search algorithm that finds synergy between pairs of physically unlinked SNPs (genome-wide) in large case-control datasets.

A program to compare and align protein structures.

A high-throughput pipeline for homology modeling of protein structures.

A method to evaluate neuronal maturation based on alternative splicing profiles.

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.

A light-weight application for reconstructing non-vertical evolutionary histories from sampled genetic sequences using persistent homology, a tool from topological data analysis.

A de-novo motif discovery tool for finding informative structural elements in RNA.

TOBI predicts somatic variants from .vcf or .bam input.

A tool for finding probes that measures significantly expressed loci in a genomic array experiment.

R-system package including the Virtual Inference of Protein-activity by Enriched Regulon analysis (VIPER) and the MAster Regulator INference Analysis (MARINA) algorithms.

A tool for parsing population ancestry of admixed individuals.

A tool for detecting copy number variants (CNVs) whole genome data based on both depth of coverage and mate pair information.