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This project holds the source code for my MPP coursework

Statistical Experimental Design for Traveltime Tomography Problems

MD simulations in LAMMPS based on AFM data

This Snakemake pipeline implements the GATK best-practices workflow

Genome-wide association analysis of COVID-19 patients vs. controls.

This is a repo for codes to simulate trans-grabbing loop extrusion factors (developed by Andrea Bonato)

Codes to simulate condensins and loop extruders that can grab polymer segments in 3D. Developed by Andrea Bonato

Codes to run "superstructure" a modified version of DBSCAN. See https://rupress.org/jcb/article/220/5/e202010003/211893/Parameter-free-molecular-super-structures

NUMT removal and variant caller benchmarking for low mtDNA heteroplasmies.

The code repo for the Changing of the Guards empirical framework for investigating Tor path selection.

Comparison of PCAWG "TNT" deletion rates vs housekeeping gene expression.