Software

We actively develop computational tools with the Open Chromosome Collective (Open2C).

Open2C repositories under active development include:

• polychrom-hoomd: GPU-accelerated polymer simulations for biophysical models of chromosome folding.

Published Open2C repositories include:

• bioframe: flexible workflows with genomic interval dataframes.
• cooltools: analysis of chromosome conformation data stored in the cooler format.
• pairtools: extraction and processing of chromosome contact pairs from sequencing data.

For neural network models of genome folding see:

• akita: for predicting mammalian interphase genome folding from DNA sequence
• akita-pytorch: PyTorch implementation of Akita models for genome folding

Talks and Slides

• Predicting 3D genome folding from DNA sequence (poster & talk, zenodo link)

• Akita tutorial

• Loop extrusion, genome organization, and evidence for the roles of CTCF & cohesin (figshare link)

Movies

• “Letting go of chromosome 3” (orange thread on white paper)