#MathOnco Issue 138: cancer's physical traits, clonal tracing, neoantigen heterogeneity, Moran Process, and more
This week in
Math Oncology
Nov. 5, 2020 ~ Issue 138
From the editor
Dear readers,
Today's issue contains articles on cancer's physical traits, clonal tracing, neoantigen heterogeneity, Moran Process, and more. And, there are two more new postdoctoral opportunities in the Jobs section, below.
I also encourage you to take a look at the (virtual) conference on Cancer Adaptive Therapy Models (http://catmo2020.org/) we are organizing in early December. More details below.
Enjoy,
-Jeffrey West
#MathOnco Publications
Tumour neoantigen heterogeneity thresholds provide a time window for combination immunotherapy
Authors: Guim Aguadé-Gorgorió, Ricard Solé
Physical traits of cancer
Authors: Hadi T. Nia, Lance L. Munn, Rakesh K. Jain
Clonal tracing reveals diverse patterns of response to immune checkpoint blockade
Authors: Shengqing Stan Gu, Xiaoqing Wang, Xihao Hu, Peng Jiang, ..., Henry Long, Gordon J. Freeman, Myles Brown, X. Shirley Liu
Abnormal morphology biases hematocrit distribution in tumor vasculature and contributes to heterogeneity in tissue oxygenation
Authors: Miguel O. Bernabeu, Jakub Köry, James A. Grogan, Bostjan Markelc, ..., Joe M. Pitt-Francis, Ruth J. Muschel, Tomás Alarcón, Helen M. Byrne
Combining multiple spatial statistics enhances the description of immune cell localisation within tumours
Authors: Joshua A. Bull, Philip S. Macklin, Tom Quaiser, Franziska Braun, Sarah L. Waters, Chris W. Pugh, Helen M. Byrne
Adapt or Perish: Evolutionary Rescue in a Gradually Deteriorating Environment
Authors: Loïc Marrec, Anne-Florence Bitbol
Computational models to explore the complexity of the epithelial to mesenchymal transition in cancer
Authors: Marilisa Cortesi, Chiara Liverani, Laura Mercatali, Toni Ibrahim, Emanuele Giordano
DAGBagM: Learning directed acyclic graphs of mixed variables with an application to identify prognostic protein biomarkers in ovarian cancer
Authors: Shrabanti Chowdhury, Ru Wang, Qing Yu, Catherine J. Huntoon, Larry M. Karnitz, Scott H. Kaufmann, Steven P. Gygi, Michael J. Birrer, Amanda G. Paulovich, Jie Peng, Pei Wang
Moran Pycess: a Python package to simulate Moran processes driven by game theory
Authors: Maciej Bak, Anna M. Rozlach
Time Series Data to Mathematical Model
Authors: Regina Padmanabhan, Nader Meskin, Ala-Eddin Al Moustafa
#MathOnco Preprints
Investigating epithelial-mesenchymal heterogeneity of tumors and circulating tumor cells with transcriptomic analysis and biophysical modeling
Authors: Federico Bocci, Susmita Mandal, Tanishq Tejaswi, Mohit Kumar Jolly
Topological signatures in regulatory network enable phenotypic heterogeneity in small cell lung cancer
Authors: Lakshya Chauhan, Uday Ram, Kishore Hari, Mohit Kumar Jolly
Characteristics of mathematical modeling languages that facilitate model reuse in systems biology: A software engineering perspective
Authors: Christopher Schölzel, Valeria Blesius, Gernot Ernst, Andreas Dominik
BioSimBoard
https://biosimboard.com/: "BioSimBoard is an aggregation website that provides access to the newest scientific literature on biological models and simulations. Links to each journal are autonomously updated daily. Featured write-ups, job board updates, and site clean-up is maintained by Louis Joslyn, a 5th year PhD student in Bioinformatics at University of Michigan.
Cancer Adaptive Therapy Models
Dec. 7th to 10th, 2020 (9-12 am, US Eastern / 3-6 pm European continental)
http://catmo2020.org/: "We are organizing an online workshop on Models of Adaptive Therapy. Despite the ubiquity of the evolution of resistance, the “more is better'' paradigm prevails in standard of care approaches. Over the past decade, a small group of oncologists in collaboration with evolutionary and experimental biologists have proposed an adaptive approach to cancer treatment. We aim at gathering the main groups that have been recently trying to model adaptive therapy using mathematics, or whose work could help to do so, in order to build a community, understand the state of the art, exchange on the directions the field should take, and foster collaborations."
- Co-organized by: Robert Noble, Eunjung Kim, Sandy Anderson, David Basanta, Jeffrey West, Yannick Viossat
#MathOnco Virtual Seminars
Moffitt's Integrated Mathematical Oncology Dept. Series
Mathematical Oncology Series
Dr. Hermann Frieboes
"Modulation of Immune Response to Cancer via Nanotherapy: An Integrated Experimental/Mathematical Modeling Perspective"
Dec 10, 2020 12:00pm US Eastern
#MathOnco - Featured Book
Rebel Cell: Cancer, Evolution, and the New Science of Life's Oldest Betrayal
Kat Arney: "Cancer exists in nearly every animal and has afflicted humans as long as our species has walked the earth. In Rebel Cell: Cancer, Evolution, and the New Science of Life's Oldest Betrayal, Kat Arney reveals the secrets of our most formidable medical enemy, most notably the fact that it isn’t so much a foreign invader as a double agent: cancer is hardwired into the fundamental processes of life. New evidence shows that this disease is the result of the same evolutionary changes that allowed us to thrive. Evolution helped us outsmart our environment, and it helps cancer outsmart its environment as well—alas, that environment is us."
Special Issues
"Mathematical Models of Cellular Immunotherapies in Cancer"
Guest Editors: V. Pérez-García, L. de Pillis, P. Altrock, R. RockneLatest Developments in Mathematical Oncology and Cancer Systems Biology
Guest Editors: M. Kumar Jolly, H. EnderlingFrom Ecology to Cancer Biology and Back Again
Guest Editors: Fred Adler, Sarah Amend, Chris WhelanFrontiers in quantitative cancer modeling
Guest Editors: Mohit Kumar Jolly, Heiko Enderling
Jobs
NEW: Research Fellow in Computational Systems Biology Cancer Research (Simon Mitchell)
NEW: Research Fellow in Laboratory and Computational Systems Biology Cancer Research (Simon Mitchell)
Postdoctoral Fellow in Cancer Resistance Modeling, Pfizer (Blerta Shtylla)
Principal Scientist – Oncology PK/PD Modelling (Boehringer Ingelheim)
Postdoctoral Research Position in Computational Immunology (Sylvain Cussat-Blanc)
Postdoc Position - TKI treatments in lung cancer (David Basanta)
Systems Biology Modeler Positions in Biopharma Consulting Company (Helen Moore)
Computational Approaches to Breast Cancer Evolution - Postdoc (Marc Ryser)
Math/statistical models of stem cell lineage dynamics and cancer genomics - Postdoc (Adam MacLean)
Postdoctoral Research Position in Computational Oncology (Tom Yankeelov)
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