loop-extrusion

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Chromosome polymer simulations and in silico capture experiments

polymer simulation hi-c chromatin chromosomes loop-extrusion

High-performance stochastic modeling of DNA loop extrusion interactions

bioinformatics cpp tad biology high-performance dna cpp17 hic loop-extrusion stochastic-model topologically-associated-domains

StripePy recognizes architectural stripes in 3C and Hi-C contact maps using geometric reasoning

Loop extrusion module with LAMMPS

Code to model active loop extrusion on chromatin using hybrid MD-MC.

LAMMPS code to simulate loop extrusion of DNA by SMC complexes

Scripts for running OpenMM polychrom-based coarse-grained polymer simulations of chromatin

Analysis scripts and other code written during my time at Penn.

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