This week in MathOnco 230

Cell-cell competition and communication, identifiability analysis, dose response/exposure, and more

“This week in Mathematical Oncology” — Oct. 13, 2022

> mathematical-oncology.org

From the editor:

Today we feature articles on … cell-cell competition and communication, identifiability analysis, dose response/exposure, and more.

Enjoy,

Jeffrey West
jeffrey.west@moffitt.org

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“There is no grantsmanship that will turn a bad idea into a good one, but there are many ways to disguise a good one.”
— William Raub, former deputy director NIH

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1. Cell competition in development, homeostasis and cancer
   Sanne M. van Neerven, Louis Vermeulen

2. A data assimilation framework to predict the response of glioma cells to radiation
   Junyan Liu, David A. Hormuth II, Jianchen Yang, Thomas E. Yankeelov

3. Practical identifiability analysis of a mechanistic model for the time to distant metastatic relapse and its application to renal cell carcinoma
   Arturo Álvarez-Arenas, Wilfried Souleyreau, Andrea Emanuelli, Lindsay S. Cooley, Jean-Christophe Bernhard, Andreas Bikfalvi, Sebastien Benzekry

4. Automated clinical decision support system with deep learning dose prediction and NTCP models to evaluate treatment complications in patients with esophageal cancer
   Camille Draguet, Ana M. Barragán-Montero, Macarena Chocan Vera, Melissa Thomas, …, Gilles Defraene, Karin Haustermans, John A. Lee, Edmond Sterpin

5. CYTOCON: The manually curated database of human in vivo cell and molecule concentrations
   Vladislav Leonov,Ekaterina Mogilevskaya,Elita Gerasimuk,Nail Gizzatkulov,Oleg Demin

6. Dose/exposure–response modeling in dose titration trials: Overcoming the titration paradox
   Niels Rode Kristensen, Henrik Agersø

7. Cross-Stream Interactions: Segmentation of Lung Adenocarcinoma Growth Patterns
   Xiaoxi Pan, Hanyun Zhang, Anca-Ioana Grapa, Khalid AbdulJabbar, Shan E Ahmed Raza, Ho Kwan Alvin Cheung, Takahiro Karasaki, John Le Quesne, David A. Moore, Charles Swanton & Yinyin Yuan

8. Quantitative Spatial Profiling of TILs as the Next Step beyond PD-L1 Testing for Immune Checkpoint Blockade
   Valsamo Anagnostou; Jason J. Luke

1. A lineage tree-based hidden Markov model to quantify cellular heterogeneity and plasticity
   Farnaz Mohammadi, Shakthi Visagan, Sean M. Gross, Luka Karginov, JC Lagarde, Laura M. Heiser, Aaron S. Meyer

2. Statistical inference of the rates of cell proliferation and phenotypic switching in cancer
   Einar Bjarki Gunnarsson, Jasmine Foo, Kevin Leder

3. ARCliDS: A Clinical Decision Support System for AI-assisted Decision-Making in Response-Adaptive Radiotherapy
   Dipesh Niraula, Wenbo Sun, Jionghua Jin, Ivo Dinov, …, Theodore S Lawrence, Shruti Jolly, Randall K Ten Haken, Issam El Naqa

4. Development of multi-agent-simulation models for intercellular communication via cytokines and extracellular matrices
   Ken-ichi Inoue, Satoko Kishimoto, Tomoki Mogami, Shigeru Toyoda, Masanori Hariyama

5. The Effect of Bottleneck Size on Evolution in Nested Darwinian Populations
   Matthew C. Nitschke, Andrew J. Black, Pierrick Bourrat, Paul B. Rainey

6. Phylogenetic inference from single-cell RNA-seq data
   Xuan Liu, Jason I Griffiths, Isaac Bishara, Jiayi Liu, Andrea H Bild, Jeffrey T Chang

7. Traditional phylogenetic models are insensitive to variations in the effective population size
   Rui Borges, Ioanna Kotari, Juraj Bergman, Madeline Chase, Carina Farah Mugal, Carolin Kosiol

8. Tumoroscope: a probabilistic model for mapping cancer clones in tumor tissues
   Shadi Darvish Shafighi, Agnieszka Geras, Barbara Jurzysta, Alireza Sahaf Naeini, …, Dominika Nowis, Alessandra Carbone, Jens Lagergren, Ewa Szczurek

9. Dynamic fibronectin assembly and remodeling by leader neural crest cells prevents jamming in collective cell migration
   W. Duncan Martinson, Rebecca McLennan, Jessica M. Teddy, Mary C. McKinney, Lance A. Davidson, Ruth E. Baker, Helen M. Byrne, Paul M. Kulesa, Philip K. Maini

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: “Self-assembly of tessellated tissue sheets by expansion and collision” in Nature Communications

Artist: Matthew Heinrich, Avi Wolf

Caption: Tissue tessellation inspired by the artwork "Dice lattice" of the Dutch artist M.C. Escher. This and other tessellations were assembled by letting cell monolayers expand and collide into the desired pattern. A new design tool called "TissEllate" enables the assembly of complex tessellations from initial arrays of tissues with controlled sizes, shapes, positions, and orientations.

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