This week in MathOnco 247

Evolutionary models, quantitative systems pharmacology, first passage time analysis

“This week in Mathematical Oncology” — Mar. 23, 2023

> mathematical-oncology.org

From the editor:

Today we feature articles on evolutionary models, quantitative systems pharmacology, first passage time analysis, and more.

Enjoy,

Jeffrey West
jeffrey.west@moffitt.org

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“I not only use all the brains that I have, but all I can borrow."
- W. Wilson

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1. State-dependent evolutionary models reveal modes of solid tumour growth
   Maya A. Lewinsohn, Trevor Bedford, Nicola F. Müller, Alison F. Feder

2. An oncospace for human cancers
   Guim Aguadé-Gorgorió, José Costa, Ricard Solé

3. Fascination with Fluctuation: Luria and Delbrück’s Legacy
   Raina S. Robeva, John R. Jungck

4. Quantitative systems pharmacology model of GITR-mediated T cell dynamics in tumor microenvironment
   Yan Ji, Kumpal Madrasi, Deborah A. Knee, Lore Gruenbaum, Joshua F. Apgar, John M. Burke, Bruce Gomes

5. Development of a coupled modeling for tumor growth, angiogenesis, oxygen delivery, and phenotypic heterogeneity
   Mahmood Borzouei, Mohammad Mardaani, Modjtaba Emadi-Baygi & Hassan Rabani

6. First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer
   Magnus J. Haughey, Aleix Bassolas, Sandro Sousa, Ann-Marie Baker, Trevor A. Graham, Vincenzo Nicosia, Weini Huang

1. Clonal phylogenies inferred from bulk, single cell, and spatial transcriptomic analysis of cancer
   Andrew Erickson, Sandy Figiel, Timothy Rajakumar, Srinivasa Rao, …, Freddie C Hamdy, Dan Woodcock, Ian G Mills, Alastair D Lamb

2. Nasopharyngeal Carcinoma Ecology Theory: Cancer as Multidimensional Spatiotemporal “Unity of Ecology and Evolution” Pathological Ecosystem
   Weiren Luo

3. Exploring the onset and progression of prostate cancer through a multicellular agent-based model
   Margot Passier, Maisa van Genderen, Anniek Zaalberg, Jeroen Kneppers, Elise Bekers, Andries M Bergman, Wilbert Zwart, Federica Eduati

4. Molecular cartography uncovers evolutionary and microenvironmental dynamics in sporadic colorectal tumors
   Cody N. Heiser, Alan J. Simmons, Frank Revetta, Eliot T. McKinley, …, Qi Liu, Martha J. Shrubsole, Robert J. Coffey, Ken S. Lau

5. A phenotype-structured model for the tumour-immune response
   Zineb Kaid, Jean Clairambault, Camille Pouchol

6. Rigorous results of limiting behaviors of total tumor size under cyclic intermittent therapy for the system of reversible phenotype-switchable tumor cells
   Jaewook Joo

1. New feature: List of datasets for MathOnco research
   The Mathematical Oncology Blog
   Guillermo Lorenzo, David Hormuth: “As MathOnco researchers, we often find ourselves in need of specific data to test a new idea, calibrate our models, or validate our patient-specific predictions and novel cancer mechanisms. In order to facilitate the search for data to bring forth our models and as well as to foster the development of new ideas and collaborations, we are glad to introduce a new feature of the MathOnco website: the MathOnco Datasets.“

2. Modelling evolution at the boundaries of solid tumours
   Nature Ecology & Evolution: News & Views
   Subhayan Chattopadhyay & David Gisselsson: “A mathematical model of eco-evolutionary dynamics estimates different birth rates of cells at the periphery of a tumour versus its centre, giving insight into locally stable evolutionary mechanisms that arise as a result of boundary-driven growth.”

3. Insilico UK
   Evidence and Impact: “What is the UK and international evidence and impact behind in-silico technologies based? By 2025 at least £2.6 billion worth of Pharma and Med Devices underpinned by in-silico methods will be made in the UK, even at our current share of the global manufacturing. In-silico technologies will be critical to the future of the 111,200 directly employed in 2010 UK manufacturing sites in the Pharmaceutical and Med-Tech sectors.”

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. This week’s artwork:

Based on the paper: “State-dependent evolutionary models reveal modes of solid tumour growth” in Nature Ecology & Evolution

Artist: Maya A. Lewinsohn (@MayaLewinsohn)

Caption: "Computational biology is accomplished through trial and error. Mistakes can bring frustration, but also unexpected insights. This artwork is inspired by plotting blunders that resulted in “accidental art” — plots that were fairly useless at communicating data, but that were surprisingly aesthetic."

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

2. Conferences / Meetings

3. Special issues

• NPJ Systems Biology and Applications: Systems Immunology
  (Editors: Mohit Kumar Jolly, Jishnu Das; Deadline: 30 September 2023)

• Translational Oncology: Non-genetic heterogeneity and adaptive mechanisms in cancer evolution and drug resistance (Editors: Mohit Kumar Jolly, Subhajyoti De; Deadline: 30 June 2023)

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