Here are some software packages developed by my group.

Genomics (RNAseq, search, etc.)

Salmon – fast, accurate isoform abundance estimation from RNA-seq data (spiritualy Sailfish 2.0).

Sailfish – ultrafast isoform abundance estimation from RNA-seq reads.

JELLYFISH – count k-mers in large sequence databases very fast.

Sequence Bloom Trees – search for large raw read collections.

Ribomap – mapping for riboseq reads.

MINCE – reference-free compression of short-read sequencing data.

PathEnc – reference-based compression of short read data sets.

GiRaF – find reassortments in collections of influenza genome sequences.

TransTermHP – find rho-independent transcription terminators in bacterial genomes.

Hi-C & Genome Structure

Armatus – multi-scale topological domain detection from Hi-C data.

STARFISH – Identify rigid components with the pebble game and a body-bar-and-hinge reduction

Biological Networks

PARANA 2 – parsimonious estimates of ancestral networks.

CORAL – system for interactive visualizations of differences between clusterings.

PARANA – parsimonious reconstruction of ancestral interaction networks.

GHOST – Global alignment between two graphs.

Network Archaeology – infer evolutionary history of a network.

VI-Cut – find a clustering that best matches imperfectly-known cluster hints.


Map of Jazz Musicians – web application to explore recorded collaborations between jazz musicians.