This week in MathOnco 199

Ecological theory, personalization, Genie genetic drift, predictive uncertainty, and more..

“This week in Mathematical Oncology” — Mar. 3, 2022

> mathematical-oncology.org

From the editor:

Today’s issue represents advances in topics such as ecological theory, personalization, genetic drift, predictive uncertainty, and more..

Jeffrey West
jeffrey.west@moffitt.org

1. Biallelic mutations in cancer genomes reveal local mutational determinants
   Jonas Demeulemeester, Stefan C. Dentro, Moritz Gerstung, Peter Van Loo

2. Mathematical model of hormone sensitive prostate cancer treatment using leuprolide: A small step towards personalization
   Urszula Foryś, Alon Nahshony, Moran Elishmereni

3. Genie: an interactive real-time simulation for teaching genetic drift
   Andreina I. Castillo, Ben H. Roos, Michael S. Rosenberg, Reed A. Cartwright, Melissa A. Wilson

4. Effective drug combinations in breast, colon and pancreatic cancer cells
   Patricia Jaaks, Elizabeth A. Coker, Daniel J. Vis, Olivia Edwards, …, Andrea Bertotti, Livio Trusolino, Lodewyk Wessels & Mathew J. Garnett

1. Data-driven simulation of Fisher-Kolmogorov tumor growth models using Dynamic Mode Decomposition
   Alex Viguerie, Malú Grave, Gabriel F. Barros, Guillermo Lorenzo, Alessandro Reali, Alvaro L.G.A. Coutinho

2. Predictive uncertainty in mechanistic models of cellular processes calibrated to experimental data
   Michael Irvin, Arvind Ramanathan, Carlos F Lopez

3. Transmissible Cancer Evolution: The Under-Estimated Role of Environmental Factors in the “Perfect Storm” Theory
   Sophie Tissot, Anne-Lise Gérard, Justine Boutry, Antoine M. Dujon, …, Rodrigo Hamede, Benjamin Roche, Beata Ujvari, Frédéric Thomas

4. Mathematical model of a cytokine storm
   Irina Kareva, Faina Berezovskaya, Georgy Karev

5. Individual-based and continuum models of phenotypically heterogeneous growing cell populations
   Fiona R Macfarlane, Xinran Ruan, Tommaso Lorenzi

6. Borrowing ecological theory to infer interactions between sensitive and resistant breast cancer cell populations
   Zachary Susswein, Surojeet Sengupta, Robert Clarke, Shweta Bansal

1. How to use transcriptomic data for game-theoretic modeling of treatment-induced resistance in cancer cells?

   The Mathematical Oncology Blog — The “Behind the Paper” series
   Rachel Cavill, Kateřina Staňková: “We decided we would like to understand how to get beyond models of cancer and its treatment that are fitted with volumetric information only, to be able to predict the effect of anti-cancer treatments and improve therapy through game-theoretic modeling.”

2. Evolutionary therapy
   Wikipedia
   Evolutionary therapy has its own Wikipedia page now, thanks to Luka Opasic and Jake Scott. Check it out!

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: Do tumor cells sometimes make the same mistake twice? In our Nature Genetics paper, we identify biallelic mutations, where the same base is mutated independently on both parental alleles, across 2,658 cancer genomes and highlight the processes behind them. These mutations violate the infinite sites model of molecular evolution, a cornerstone of tumor phylogenetic analysis which is also often implied when calling, phasing and interpreting variants or studying the mutational landscape as a whole. The cover shows copy number estimates for chromosomes and mutations across part of a melanoma whole genome. Biallelic parallel mutations (blue circles) can be identified when their copy number is equal to the total copy number (red bars) in heterozygous regions of the tumor genome.

Created by: Jonas Demeulemeester (@zeunas & @VanLooLab)

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

• Graduate Summer Intern in Machine Learning, Pfizer Oncology La Jolla (or remote), CA (Blerta Shtylla, Email: Blerta.Shtylla@pfizer.com or Kamrine Poels Email: Kamrine.Poels@pfizer.com ), please contract directly if interested.

• Postdoctoral Fellow in Quantitative Systems Pharmacology, Pfizer Oncology La Jolla, CA (Blerta Shtylla, Email: Blerta.Shtylla@pfizer.com)

2. Conferences / Meetings

• The many faces of cancer evolution - 20-22 May 2022

3. Special issues

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