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MathOnco

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Location 🇺🇸 United States
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valis

Virtual Alignment of pathoLogy Image Series

NeoPredPipe

Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

HAL

HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs

Mistic

Multiplexed image tSNE visualizer

EvoFreq

Evolutionary frequency visualization tool of temporal data

Curvogram

Method for plotting histograms on a curve using a West Transform

Jupyter Notebook

IsoMaTrix

A framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations (MATLAB, Java)

Lenia-in-HAL

Repository for Lenia framework, implemented in Hybrid Automata Library (HAL)

scRNAseqITH

Single-cell RNA sequencing pipeline for quantifying intratumor heterogeneity

strobl2021_space_modulates_competition_AT

This repository contains the code and data for our publication Strobl et al (2022). Spatial structure impacts adaptive therapy by shaping intra-tumoral competition. Commun Med 2, 46, available at: https://rdcu.be/cL5bi.

Jupyter Notebook

flipflopblood

Whole Blood Simulations of Hematopoietic Stem Cells

nonlinearPGG

This repository contains the data and code for the paper "Neighborhood size-effects shape growing population dynamics in evolutionary public goods games"

AT_costOfResistance_LVModel

This repository contains the code to generate the figures in our research paper: Strobl et al (2020), Turnover modulates the need for a cost of resistance in adaptive therapy published in Cancer Research.

Jupyter Notebook

CARTecology

Gattaca

Base pair resolution mutation tracking for somatic evolution studies using agent based simulations

immune-checkpoint-kickstart

The code (MATLAB) for the paper "The Immune Checkpoint Kick Start: Optimization of Neoadjuvant Combination Therapy Using Game Theory" published in JCO Clinical Cancer Informatics.

Newsletter-Bibliography

LaTeX bibliography of the "This week in Math Onco" newsletter (https://mathematical-oncology.org/newsletter)

ploidyEvolution

A general N-compartment model of ploidy states is developed and analyzed.

DRL_Personalized_AT

Learning to Adapt - Deep Reinforcement Learning in Treatment-Resistant Prostate Cancer (https://doi.org/10.1101/2023.04.28.538766)

Jupyter Notebook

tissue-structure-modulates-evolution

Code repository associated with the paper "Tissue structure modulates evolution: premalignant sweeps precede neutral expansion"

multiscaleGBM

PARPi_Model

Jupyter Notebook

MIEmodel

Simplified version of a deterministic framework for modeling whole chromosome missegregations. This model is more amendable to theoretical analysis to investigate conditions for missegregation-induced extinction (MIE).