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

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.

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

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

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

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

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.

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

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

An integrated computational system where computational tools are implemented for protein sequence and structure analysis and modeling.