test_issue_353.html

<h6>
 <code>
  “This week in Mathematical Oncology” — Dec 4, 2025
 </code>
</h6>
<h5>
 <code>
  &gt; mathematical-oncology.org
 </code>
</h5>
<h5>
 <code>
  From the editor:
 </code>
</h5>
<p>
 This is the last issue of the Math Oncology newsletter for 2025. As such, I’d like to take the opportunity to personally say thank you to our volunteers who help run this newsletter and the
 <a href="https://mathematical-oncology.org/">
  mathematical-oncology.org
 </a>
 website:
</p>
<ul>
 <li>
  <p>
   Sandy Anderson
  </p>
 </li>
 <li>
  <p>
   David Basanta
  </p>
 </li>
 <li>
  <p>
   Maximilian Strobl
  </p>
 </li>
 <li>
  <p>
   Alexander Zeilmann
  </p>
 </li>
 <li>
  <p>
   David A. Hormuth
  </p>
 </li>
 <li>
  <p>
   Guillermo Lorenzo
  </p>
 </li>
 <li>
  <p>
   Dhananjay Bhaskar
  </p>
 </li>
 <li>
  <p>
   Franco Pradelli
  </p>
 </li>
 <li>
  <p>
   Sara Hamis
  </p>
 </li>
 <li>
  <p>
   François de Kermenguy
  </p>
 </li>
 <li>
  <p>
   Veronika Hofmann
  </p>
 </li>
</ul>
<p>
 See you next year,
</p>
<p>
 Jeffrey West
 <br/>
 jeffrey.west@moffitt.org
</p>
<p>
 PS. If you’re interested, the special issue in MBS on “
 <a href="https://www.sciencedirect.com/special-issue/321305/in-memory-of-siv-sivaloganathan-perspectives-on-mathematical-oncology">
  In memory of Siv Sivaloganathan: Perspectives on Mathematical Oncology
 </a>
 ” has been extended to June 30, 2026. Take a look!
</p>
<div class="captioned-image-container">
 <figure>
  <a class="image-link image2" href="https://substackcdn.com/image/fetch/$s_!2LbH!,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2Ffabab95d-eefe-45a0-b47e-77fc63cde5de_1024x250.png" target="_blank">
   <div class="image2-inset">
    <source type="image/webp"/>
    <img alt="" class="sizing-normal" height="250" src="https://substackcdn.com/image/fetch/$s_!2LbH!,w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2Ffabab95d-eefe-45a0-b47e-77fc63cde5de_1024x250.png" title="" width="1024"/>
    <div>
    </div>
   </div>
  </a>
 </figure>
</div>
<ol>
 <li>
  <p>
   <a href="https://aacrjournals.org/cancerrescommun/article/doi/10.1158/2767-9764.CRC-25-0277/769935/Cell-state-transitions-drive-the-evolution-of">
    Cell state transitions drive the evolution of disease progression in B-lymphoblastic leukemia
   </a>
   <br/>
   <em>
    Curtis Gravenmier, Sadegh Marzban, Yi-Han Tang, Nancy Gillis, Bijal D. Shah, Lynn C. Moscinski, Ling Zhang, Jeffrey West
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://doi.org/10.1186/s43556-025-00340-0">
    Multi-omics strategies for biomarker discovery and application in personalized oncology
   </a>
   <br/>
   <em>
    Ziming Jiang, Haoxuan Zhang, Yibo Gao, Yingli Sun
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://www.cell.com/biophysj/fulltext/S0006-3495(25)00772-6">
    A multilevel formalism to model the hybrid E/M phenotypes in Epithelial-Mesenchymal Plasticity
   </a>
   <br/>
   <em>
    Kishore Hari, Shubham Tripathi, Vaibhav Anand, Mohit Kumar Jolly, Herbert Levine
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://rdcu.be/eSWvR">
    Advances in surrogate modeling for biological agent-basedsimulations: trends, challenges, and future prospects
   </a>
   <br/>
   <em>
    Kerri-Ann Norton, Daniel Bergman, Harsh Vardhan Jain, Trachette Jackson
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://www.sciencedirect.com/science/article/pii/S030438352500446X?via%3Dihub">
    Energetics of whole genome doubling and genomic instability
   </a>
   <br/>
   <em>
    Richard J. Beck, Vural Tagal, Samirkumar Amin, Samuel F. Bakhoum, Carlo C. Maley, Roel G.W. Verhaak, Ana P. Gomes, Noemi Andor
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://www.sciencedirect.com/science/article/pii/S2666166725005696?via%3Dihub">
    Protocol to model tumor hypoxia in vitro using real-time phosphorescence-based sensing of O2 gradients generated by metastatic cancer cells
   </a>
   <br/>
   <em>
    Noreen Hosny, Kimberly Shen, Yihua Zhao, Junle Qu, …, Trung V. Phan, Stephano Boyer-Paulet, Shengkai Li, Robert H. Austin
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://academic.oup.com/genetics/advance-article/doi/10.1093/genetics/iyaf255/8343559">
    Preventing evolutionary rescue in cancer using two-strike therapy
   </a>
  </p>
  <p>
   <em>
    Srishti Patil, Armaan Ahmed, Yannick Viossat, Robert Noble
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://www.sciencedirect.com/science/article/pii/S0025556425002093?dgcid=coauthor">
    Integrating machine learning into the in silico clinical trial pipeline
   </a>
   <br/>
   <em>
    Rebecca A. Bekker, Renee Brady-Nicholls, Lisette de Pillis, Jana L. Gevertz, Harsh Vardhan Jain
   </em>
  </p>
 </li>
</ol>
<div class="captioned-image-container">
 <figure>
  <a class="image-link image2" href="https://substackcdn.com/image/fetch/$s_!UZho!,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F58c80455-f0b6-43db-830a-0f73b96ead1e_1024x250.png" target="_blank">
   <div class="image2-inset">
    <source type="image/webp"/>
    <img alt="" class="sizing-normal" height="250" src="https://substackcdn.com/image/fetch/$s_!UZho!,w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F58c80455-f0b6-43db-830a-0f73b96ead1e_1024x250.png" title="" width="1024"/>
    <div>
    </div>
   </div>
  </a>
 </figure>
</div>
<ol>
 <li>
  <p>
   <a href="https://arxiv.org/abs/2511.15932">
    How Mathematical Forms of Chemotherapy and Radiotherapy Bias Model-Optimized Predictions: Implications for Model Selection
   </a>
   <br/>
   <em>
    Changin Oh, Kathleen P. Wilkie
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://arxiv.org/abs/2510.13431v1">
    Modeling Adoptive Cell Therapy in Bladder Cancer from Sparse Biological Data using PINNs
   </a>
   <br/>
   <em>
    Kayode Olumoyin, Katarzyna Rejniak
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://doi.org/10.1101/2025.11.16.688737">
    Multi-scale Network Topology Analysis Reveals Metabolic Reprogramming and Therapeutic Vulnerabilities in the Tumor Microenvironment
   </a>
   <br/>
   <em>
    Handan Cetin, Paul Bogdan, Shannon M Mumenthaler, Stacey D Finley
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://doi.org/10.1101/2025.11.17.688873">
    Rethinking the seven-day treatment-free interval in T-cell engager therapy using agent-based modeling
   </a>
   <br/>
   <em>
    Nina Obertopp, Matthew Froid, Shari Pilon-Thomas, David Basanta
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://doi.org/10.1101/2025.10.10.681641">
    Probability Distribution for Rare Neutral Mutations in Cancers and Application to Dynamic Precision Medicine of Cancer
   </a>
  </p>
  <p>
   <em>
    Wei He, Matthew D. McCoy, Chen-Hsiang Yeang, Rebecca B. Riggins, Robert A. Beckman
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://doi.org/10.1101/2025.01.31.636013">
    Population structure reverses selection of variants with proportionally scaled birth and death rates
   </a>
  </p>
  <p>
   <em>
    Natalia L. Komarova, Dominik Wodarz
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://doi.org/10.1101/2025.02.19.639193">
    Intracellular competition shapes plasmid population dynamics
   </a>
  </p>
  <p>
   <em>
    Fernando Rossine, Carlos Sanchez, Daniel Eaton, Johan Paulsson, Michael Baym
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://arxiv.org/html/2510.21325">
    Cell Competition Driven by Secreted Ligands: Modeling Liver Metastasis of Colorectal Cancer
   </a>
   <br/>
   <em>
    Hossein Nemati, Saskia Jacoba Elisabeth Suijkerbuijk, Joost de Graaf
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://doi.org/10.1101/2025.11.17.688895">
    Cellular turnover can increase or decrease the mutant burden in expanding cell population
   </a>
  </p>
  <p>
   <em>
    Samrat S. Mondal, Natalia L. Komarova, Dominik Wodarz
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://www.biorxiv.org/content/10.1101/2025.11.21.689767v1">
    Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations
   </a>
   <br/>
   <em>
    Josiah Kratz, Zihang Wen, Shiladitya Banerjee, Oana Carja
   </em>
  </p>
 </li>
</ol>
<div class="captioned-image-container">
 <figure>
  <a class="image-link image2" href="https://substackcdn.com/image/fetch/$s_!PCmY!,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F104440ac-3cbf-4dd2-bf8b-a4f8b11035f5_1024x250.png" target="_blank">
   <div class="image2-inset">
    <source type="image/webp"/>
    <img alt="" class="sizing-normal" height="250" src="https://substackcdn.com/image/fetch/$s_!PCmY!,w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F104440ac-3cbf-4dd2-bf8b-a4f8b11035f5_1024x250.png" title="" width="1024"/>
    <div>
    </div>
   </div>
  </a>
 </figure>
</div>
<ol>
 <li>
  <p>
   <a href="https://www.asimov.press/p/read-biology">
    Read Something Wonderful (about Biology)
   </a>
  </p>
  <p>
   <em>
    A curated list of 100+ essays about biology and science
   </em>
  </p>
 </li>
 <li>
  <p>
   <a href="https://jkms.org/DOIx.php?id=10.3346/jkms.2025.40.e300">
    Fifty Years of Retracted Medical Publications From 1975 to 2024: A Comprehensive Analysis of Trends, Reasons, and Countries Using the Retraction Watch Database
   </a>
  </p>
 </li>
</ol>
<div class="captioned-image-container">
 <figure>
  <a class="image-link image2" href="https://substackcdn.com/image/fetch/$s_!4buk!,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F0feba771-e36d-4595-9841-f9ee8872be92_1024x250.jpeg" target="_blank">
   <div class="image2-inset">
    <source type="image/webp"/>
    <img alt="" class="sizing-normal" height="250" src="https://substackcdn.com/image/fetch/$s_!4buk!,w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F0feba771-e36d-4595-9841-f9ee8872be92_1024x250.jpeg" title="" width="1024"/>
    <div>
    </div>
   </div>
  </a>
 </figure>
</div>
<p>
 The newsletter now has a dedicated homepage where we post the cover
 <a href="https://mathematical-oncology.org/art">
  artwork
 </a>
 for each issue, curated by Maximilian Strobl, Sarah Groves, and Veronika Hofmann. We encourage submissions that coincide with the release of a recent paper from your group. This week’s artwork:
</p>
<div class="captioned-image-container">
 <figure>
  <a class="image-link image2 is-viewable-img" href="https://substackcdn.com/image/fetch/$s_!qqqw!,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F704acad6-a7ad-4022-80db-ac2e1613e35f_843x563.png" target="_blank">
   <div class="image2-inset">
    <source type="image/webp"/>
    <img alt="" class="sizing-normal" height="563" src="https://substackcdn.com/image/fetch/$s_!qqqw!,w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fsubstack-post-media.s3.amazonaws.com%2Fpublic%2Fimages%2F704acad6-a7ad-4022-80db-ac2e1613e35f_843x563.png" width="843"/>
    <div class="image-link-expand">
     <div class="pencraft pc-display-flex pc-gap-8 pc-reset">
      <button class="pencraft pc-reset pencraft icon-container restack-image" tabindex="0" type="button">
       <svg fill="none" height="20" stroke="var(--color-fg-primary)" stroke-linecap="round" stroke-linejoin="round" stroke-width="1.5" viewbox="0 0 20 20" width="20" xmlns="http://www.w3.org/2000/svg">
        <g>
         <title>
         </title>
         <path d="M2.53001 7.81595C3.49179 4.73911 6.43281 2.5 9.91173 2.5C13.1684 2.5 15.9537 4.46214 17.0852 7.23684L17.6179 8.67647M17.6179 8.67647L18.5002 4.26471M17.6179 8.67647L13.6473 6.91176M17.4995 12.1841C16.5378 15.2609 13.5967 17.5 10.1178 17.5C6.86118 17.5 4.07589 15.5379 2.94432 12.7632L2.41165 11.3235M2.41165 11.3235L1.5293 15.7353M2.41165 11.3235L6.38224 13.0882">
         </path>
        </g>
       </svg>
      </button>
      <button class="pencraft pc-reset pencraft icon-container view-image" tabindex="0" type="button">
       <svg class="lucide lucide-maximize2 lucide-maximize-2" fill="none" height="20" stroke="currentColor" stroke-linecap="round" stroke-linejoin="round" stroke-width="2" viewbox="0 0 24 24" width="20" xmlns="http://www.w3.org/2000/svg">
        <polyline points="15 3 21 3 21 9">
        </polyline>
        <polyline points="9 21 3 21 3 15">
        </polyline>
        <line x1="21" x2="14" y1="3" y2="10">
        </line>
        <line x1="3" x2="10" y1="21" y2="14">
        </line>
       </svg>
      </button>
     </div>
    </div>
   </div>
  </a>
 </figure>
</div>
<p>
 <strong>
  Based on the paper
 </strong>
 :
 <a href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.70121">
  Ecological graph theory: Simulating competition and coexistence on graphs
 </a>
 published in
 <strong>
  Methods in Ecology and Evolution
 </strong>
</p>
<p>
 <strong>
  Artist
 </strong>
 : Ata Kalirad (
 <a href="https://x.com/ata_kalirad">
  @ata_kalirad
 </a>
 )
</p>
<p>
 <strong>
  Caption
 </strong>
 : Competition in ecosystems involves interactions of individuals in space. Incorporating the crucial spatial scale in modelling ecological competition is necessary to understand how ecological communities assemble in nature. Inspired by evolutionary graph theory (EGT), we proposed ecological graph theory (EcoGT), which translates the classic Lotka–Volterra model into a graph-based framework. We explored how spatial structure - represented by a dodecahedron, a king’s graph, or random graph - could influence the possibility of coexistence. Additionally, EcoGT can simulate competition between individuals on graphs that themselves change during simulation, a reflection of movement of the organism in the community. This method can be used to explore both the importance of space and trait variation, to understand how organisms (exemplified by nematodes in this cover) can coexist in the wild.
</p>
<div class="captioned-image-container">
 <figure>
  <a class="image-link image2" href="https://substackcdn.com/image/fetch/$s_!2Z9Y!,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F1717140c-562f-4f59-8459-4c2c1a1caa48_1024x250.png" target="_blank">
   <div class="image2-inset">
    <source type="image/webp"/>
    <img alt="" class="sizing-normal" height="250" src="https://substackcdn.com/image/fetch/$s_!2Z9Y!,w_1456,c_limit,f_auto,q_auto:good,fl_progressive:steep/https%3A%2F%2Fbucketeer-e05bbc84-baa3-437e-9518-adb32be77984.s3.amazonaws.com%2Fpublic%2Fimages%2F1717140c-562f-4f59-8459-4c2c1a1caa48_1024x250.png" title="" width="1024"/>
    <div>
    </div>
   </div>
  </a>
 </figure>
</div>
<p>
 Visit the mathematical oncology
 <a href="http://mathematical-oncology.org/">
  page
 </a>
 to view jobs, meetings, and special issues. We will post new additions here, but the full list can found at
 <a href="http://mathematical-oncology.org/">
  mathematical-oncology.org
 </a>
 .
</p>
<p>
 <em>
  1.
  <a href="http://mathematical-oncology.org/jobs.html">
   Jobs
  </a>
 </em>
</p>
<ul>
 <li>
  <p>
   <a href="https://www.cam.ac.uk/jobs/kidani-professorship-of-integrated-cancer-medicine-rd47951">
    Kidani Professorship of Integrated Cancer Medicine (Univ Cambridge)
   </a>
  </p>
 </li>
 <li>
  <p>
   <a href="https://pfizer.wd1.myworkdayjobs.com/PfizerCareers/job/United-States---California---La-Jolla/Quantitative-Systems-Pharmacologist_4946377-1">
    Quantitative Systems Pharmacologist (entry level), Pfizer, La Jolla CA (Blerta Shtylla, Email: Blerta.Shtylla@pfizer.com).
   </a>
  </p>
 </li>
 <li>
  <p>
   <a href="https://www.mathjobs.org/jobs/list/27080">
    Postdoc Position – Stochastics/Biophysics/ML – University of Utah
   </a>
  </p>
 </li>
</ul>
<p>
 <em>
  2.
  <a href="http://mathematical-oncology.org/conferences.html">
   Conferences / Meetings
  </a>
 </em>
</p>
<p>
 <em>
  3.
  <a href="http://mathematical-oncology.org/special-issues.html">
   Special issues
  </a>
 </em>
</p>
<div>
 <hr/>
</div>
<p>
 <code>
  Approximate current subscriber count, N:
  <br/>
  N(t) = 0.808t+80 (where t = days since Dec. 1st, 2017)
 </code>
</p>