R. O. Schenck

Molecular phenotyping of colorectal neoplasia shows dynamic and adaptive cancer stem cell population admixture

The paper examines stem cell population dynamics in colorectal tumors, showing that CBC-RSC admixture correlates with mutations and microenvironmental changes, and is linked to chemoresistance.

Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models

Gattaca generates base-pair resolution artificial genomes to track somatic mutations in agent-based models, enabling in-silico studies comparable to human somatic evolution.

Evolutionary dynamics of neoantigens in growing tumours

This study develops a mathematical model of neoantigen evolution in tumors and validates it with colorectal cancer data, showing how negative selection shapes tumor immunogenotype and clonality.

EvoFreq: Visualization of the Evolutionary Frequencies of Sequence and Model Data

EvoFreq is a tool for visualizing evolutionary frequencies of sequence and model data across time, offering flexible methods for analyzing clonal dynamics.

How Homeostasis Limits Keratinocyte Evolution

This study presents a mechanistic epidermal model showing homeostasis leads to log-linear subclone size distributions in skin cells, with larger subclones being older due to persistence of driver mutations.

Niche engineering drives early passage through an immune bottleneck in progression to colorectal cancer

The paper models tumor-immune dynamics in colorectal cancer progression, showing immune evasion enables transition from immune-hot adenomas to immune-cold carcinomas.

Hybrid Automata Library: A modular platform for efficient hybrid modeling with real-time visualization

The paper introduces the Hybrid Automata Library (HAL), a Java platform for building hybrid models in mathematical oncology, with real-time visualization and modular components.