GINOM is a statistical framework for assessing interval overlap of multiple genomic features [manuscript in revision].

3DC-Browser is a visualization and annotation tool for 3D structures of chromosomes [manuscript in preparation].

FISH-MDS Multidimensional scaling (MDS) for chromosome structure inference from chromosome conformation capture (3C) techniques, with constraints from Fluorescence In Situ Hybridization (FISH) [manuscript in preparation].

RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data. [manuscript]

CORaL is a software application for comparing expression profiles across experiments by using the rank of genes in the different datasets. [manuscript]