This week in MathOnco 202

Optimizing adaptive therapy, perturbation, analysis, evolution of resistance, intermittent therapy, and more.

“This week in Mathematical Oncology” — Mar. 24, 2022

> mathematical-oncology.org

From the editor:

Lots of interesting publications from the field this week: optimizing adaptive therapy, perturbation, analysis, evolution of resistance, intermittent therapy, and more.

Jeffrey West
jeffrey.west@moffitt.org

1. Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models
   Ryan O Schenck, Gabriel Brosula, Jeffrey West, Simon Leedham, Darryl Shibata, Alexander RA Anderson

2. Identifying Optimal Adaptive Therapeutic Schedules for Prostate Cancer through Combining Mathematical Modeling and Dynamic Optimization
   Ruiyang Liu, Shun Wang, Xuewen Tan, Xiufen Zou

3. Intermittent treatment of BRAFV600E melanoma cells delays resistance by adaptive resensitization to drug rechallenge
   Andrew J. Kavran, Scott A. Stuart, Kristyn R. Hayashi, Joel M. Basken, Barbara J. Brandhuber, Natalie G. Ahn

4. Anti-cancer treatment schedule optimization based on tumor dynamics modelling incorporating evolving resistance
   Anyue Yin, Johan G. C. van Hasselt, Henk-Jan Guchelaar, Lena E. Friberg, Dirk Jan A. R. Moes

5. Adaptive Evolution: How Bacteria and Cancer Cells Survive Stressful Conditions and Drug Treatment
   Mariangela Russo, Alberto Sogari, Alberto Bardelli

6. Weak Selection and the Separation of Eco-evo Time Scales using Perturbation Analysis
   Philip Gerlee

1. Acid-Base Homeostasis and Implications to the Phenotypic Behaviors of Cancer
   Yi Zhou, Wennan Chang, Xiaoyu Lu, Jin Wang, Chi Zhang, Ying Xu

2. Does deterministic coexistence theory matter in a finite world?
   Sebastian J. Schreiber, Jonathan M. Levine, Oscar Godoy, Nathan J.B. Kraft, Simon P. Hart

3. On optimal temozolomide scheduling for slowly growing gliomas
   Berta Segura-Collar, Juan Jiménez-Sánchez, Ricardo Gargini, Miodrag Dragoj, Juan M. Sepúlveda, Milica Pešić, Pilar Sánchez-Gómez, Víctor M. Pérez-García

4. Invasiveness of Cancer Populations in a Two-dimensional Percolation cluster: a Stochastic Mathematical Approach
   Renlong Yang, Yuanzhi Shao, Chongming Jiang

The newsletter now has a dedicated homepage where we post the cover artwork for each issue. We encourage submissions that coincide with the release of a recent paper from your group.

Caption: This artwork is a representation of our recent manuscript published in Molecular Biology and Evolution illustrating our new base pair resolution in silico genome tool for agent-based modeling, Gattaca. Gattaca is named after the four bases, Adenine, Cytosine, Guanine, and Thymine. The artwork represents this by depicting a Clustal multiple sequence alignment of sequences generated from randomly sampling nucleotides from the tumor suppressor gene, TP53. This gene will almost always be used as a gene of interest in the set of genes that Gattaca would use during simulations. We insert the bases GATTACA at a random site within these generated sequences to ensure sequence identity for this motif prior to alignment. The colors pay homage to sequence alignment visualizers that always use a specific color pattern when visualizing sequence data in a GUI. Although fun to visualize, Gattaca serves as a novel and powerful tool that provides us with the ability to directly compare mechanistic agent-based model genomes with patient sequence data.

Created by: Ryan Schenck & Sandy Anderson

Visit the mathematical oncology page to view jobs, meetings, and special issues. We will post new additions here, but the full list can found at mathematical-oncology.org.

1. Jobs

• PhD position: Mechanistic modeling of circulating DNA combined to machine learning for prediction of response and survival following immunotherapy (Benzekry Sebastien) - Deadline: April 29, 2022

• Sr. Research Investigator, Hematologic Malignancy Quantitative Systems Pharmacology (Bristol Myers Squibb) - Open until filled.

• Postdoctoral position in evolutionary modeling of Tasmanian devil facial tumor disease (Andrew Storfer, Washington State University) - Due: 15th Apr 2022

2. Conferences / Meetings

3. Special issues

Current subscriber count: >1.1k