HAPCOMPASS: A fast algorithm for accurate haplotype assembly

• Given a set of aligned sequence reads in a SAM file and a set of variant calls in VCF format, HAPCOMPASS will assemble reads into haplotypes

Tractatus: an exact and subquadratic algorithm for inferring identity-by-descent multi-shared haplotype tracts

• Given a set of haplotypes or genotypes, Tractatus will compute a set of identical-by-descent multi-shared haplotypes or runs of homozygosity

DELISHUS: An algorithm for detecting deletions in shared haplotypes using SNPs

• An algorithmic framework for finding inherited and de novo deletions in a GWAS SNP dataset consisting of trios or pairs

Long-range Trio-Phaser

• A long-range haplotype phasing tool developed for GWAS SNP datasets consisting of trios

Imperfect Ancestral Recombination Graph (iARG)

• A collection of tools to reconstruct evolutionary histories which include recombination and back/recurrent mutation events

Smapper: Solexa Read Mapper

Cyrene - cis-Lexicon and cis-Browser

• A database and genome browser for cis-regulatory information
• sea urchin developmental gene regulatory networks
• building a high-resolution transcriptome map of the embryo
• inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation

Virtual Sea Urchin

• 4D Map of the purple sea urchin developmental process

Ariadne

• A browser for processing population genomics workflows

Cancer Diagnosis

• An automated algorithm to determine the level of malignancy of images of tumor biopsies

Viral Immunology and Comparative Immunopeptidomics of Humans and their Pathogens

Rabbit genome project (Genetic determinants of sudden cardiac death)

ProFOLDING

• Discrete models and algorithms for protein folding
• Graph Theory of Self avoiding Walks
• Contact Maps and Protein Structure
• Energy Function Inference
• PDB Structure Alignment
• Lattice Protein Folding Algorithms with mathematically guaranteed Error Bound

The Rise and Fall of the Search for the Three-Dimensional Exactly Solvable Statistical Mechanics Models

Von Neumann Research Program in Biological Complex Systems

John von Neumann Page

Ising Page

Assembly Simulator

• A genome assembly simulator written in Mathematica

Genomathica

• A library of Mathematica tools and software for bioinformatics education and simulation.
• Genomathica is currently under construction in preparation for its first release.