A collection of programs for the modeling and analysis of protein structures.

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.

An algorithm for modeling protein structure based on a sequence-template alignment.

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.

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.

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 tool for the prediction of protein-protein interfaces based on interface conservation among structurally similar protein neighbors.

A database of predicted and experimentally determined protein-protein interactions (PPIs) for yeast and human.