Structural and Functional Genomics Laboratory

Highly experimental playground version of 3D-GNOME derived from original paper and source code

The Biobank Of Our Own - scripts that recreate access patterns of UK Biobank using data from 1000 Genomes and Simons Genome Diversity Project

Updated version of the stochastic loop extrusion model: LoopSage with capability to run incredibly fast, parallelized across CPU cores. This package is even more user-friendly and it can be installed via PyPI.

Model for simultaneous 3D chromatin modeling from scHi-C maps

dcHiChIP is Nextflow pipeline for analysis of HiChIP data. It supports loop detection, peak calling, TADs, compartments, stripes, motif analysis, and 3D chromatin modeling.

A genomewide multiscale energy minimization model.

A software that simulates the dynamics of DNA replication by following a sofisticated Hamiltonian Monte Carlo approach.

A database of 3D chromatin model ensembles and enhancer-promoter distance profiles for archaic (Neanderthal, Denisovan) and modern human genomes (GM12878, H1-ESC, HFFc6)

Pipeline for processing HiChIP data.

The web pages of the Structural and Functional Genomics Laboratory