This week in MathOnco 192
Spatial evolution, clonal co-occurrence, Bayesian calibration, autocrine signaling, population genetics, and much more
“This week in Mathematical Oncology” — Jan. 13, 2022
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mathematical-oncology.org
From the editor:
This week’s edition includes topics spatial evolution, clonal co-occurrence, Bayesian calibration, autocrine signaling, population genetics, and much more.
As mentioned last week, please fill out the survey below. Thank you!
Jeffrey West
jeffrey.west@moffitt.org
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Spatial structure governs the mode of tumour evolution
Robert Noble, Dominik Burri, Cécile Le Sueur, Jeanne Lemant, Yannick Viossat, Jakob Nikolas Kather, Niko BeerenwinkelSpatial patterns of tumour growth impact clonal diversification in a computational model and the TRACERx Renal study
Xiao Fu, Yue Zhao, Jose I. Lopez, Andrew Rowan, …, Charles Swanton, Erik Sahai, Kevin Litchfield, Samra Turajlic, TRACERx Renal Consortium, Paul A. BatesLACE: Inference of cancer evolution models from longitudinal single-cell sequencing data
Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani, Isabella Castiglioni, Rocco Piazza, Marco Antoniotti, Alex GraudenziStatistical tests for intra-tumour clonal co-occurrence and exclusivity
Jack Kuipers, Ariane L. Moore, Katharina Jahn, Peter Schraml, Feng Wang, Kiyomi Morita, P. Andrew Futreal, Koichi Takahashi, Christian Beisel, Holger Moch, Niko BeerenwinkelBayesian calibration of a stochastic, multiscale agent-based model for predicting in vitro tumor growth
Ernesto A. B. F. Lima, Danial Faghihi, Russell Philley, Jianchen Yang, John Virostko, Caleb M. Phillips, Thomas E. YankeelovTransition Therapy: Tackling the Ecology of Tumor Phenotypic Plasticity
Guim Aguadé-Gorgorió, Stuart Kauffman & Ricard SoléEvolution under Spatially Heterogeneous Selection in Solid Tumors
Guanghao Li, Zuyu Yang, Dafei Wu, Sixue Liu, Xuening Li, Tao Li, Yawei Li, Liji Liang, Weilong Zou, Chung-I Wu, Hurng-Yi Wang, Xuemei LuCombination treatment optimization using a pan-cancer pathway model
Robin Schmucker, Gabriele Farina, James Faeder, Fabian Fröhlich, Ali Sinan Saglam, Tuomas SandholmCancer cell heterogeneity and plasticity: A paradigm shift in glioblastoma
Yahaya A Yabo, Simone P Niclou, Anna GolebiewskaA Fractional Modeling of Tumor–Immune System Interaction Related to Lung Cancer with Real Data
Fatma Özköse, Seçil Yılmaz, Mehmet Yavuz, İlhan Öztürk, M. Tamer Şenel, Burcu Şen Bağcı, Medine Doğan, Ömer Önal
Autocrine signaling explains the emergence of Allee effects in cancer cell populations
Philip Gerlee, Philipp M. Altrock, Cecilia Krona, Sven NelanderUtilizing gradient approximations to optimize data selection protocols for tumor growth model calibration
Allison L. Lewis, Kathleen M. Storey, Heyrim Cho, Anna C. ZittleEffects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations
Minako Izutsu, Devin M. Lake, Zachary W. D. Matson, Jack P. Dodson, Richard E. LenskiDynamic Phenotypic Switching and Group Behavior Help Non-Small Cell Lung Cancer Cells Evade Chemotherapy
Arin Nam, Atish Mohanty, Supriyo Bhattacharya, Sourabh Kotnala, …, Herbert Levine, Mohit Kumar Jolly, Prakash Kulkarni, Ravi SalgiaBranching structure of genealogies in spatially growing populations and its implications for population genetics inference
Armin Eghdami, Jayson Paulose, Diana Fusco
Tumour evolution: a tale of dispersal and interaction
Nature Eco Evo: Behind the Paper
Rob Noble: “Chance encounters at international meetings changed the course of my career and led to three recent papers.”Spatial models of tumour evolution
Nature Eco Evo: News & Views
Dakim K. Gaines & W. Kimryn Rathmell: “Spatiotemporal modelling of tumours detects at least two distinct models of cancer evolution and reveals the influence of necrosis in enhancing the metastatic potential in both models.”Share, visualize, & interrogate biological simulations online
Allen Institute for Cell Science: “The Simularium Viewer makes it easy to share and interrogate interactive 3D visualizations of biological simulation trajectories and related plots directly in a web browser. Its primary goal is to facilitate collaborations among experimental and computational biologists by removing major challenges to sharing, accessing, and comparing simulation results.”
Fields Thematic Program in Mathematical Oncology (2024)
Thomas Hillen: “We are planning to host a Thematic Program on Mathematical Oncology at the Fields Institute in Toronto. We plan for a series of workshops, conferences, long-and short term visitors, and postdocs for July-December 2024. We like to evaluate the potential interest of the community and kindly ask you to fill out this form.”
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 image shows my office whiteboard circa late 2017, superimposed on a Muller plot from the paper that grew out of the scrawling . The Venn diagram labelled "deme" and "genotype" captures a central assumption of my computational model of tumour evolution. See if you can also spot drawings related to variant allele frequencies, multiregion sampling, the distribution of mutation effects, cellular automaton rules, island models, and tree diagrams. To read more, see here.
Created by: Rob Noble
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