#MathOnco Issue 129: cancer evolution: subclonal reconstruction and chromosomal instability, genomic divergence, and more.
This week in
Math Oncology
Sept 3, 2020 ~ Issue 129
From the editor
Dear readers,
Today's issue includes a flurry of activity in the broad theme of cancer evolution, including subclonal reconstruction and chromosomal instability, genomic divergence, and more.
Be sure not to miss two new blog posts: one on the "Quest for Evolutionary Control" and an interesting initiative on live code blocks embedded in publications via eLife.
Enjoy,
-Jeffrey West
#MathOnco Publications
Histoecology: Applying Ecological Principles and Approaches to Describe and Predict Tumor Ecosystem Dynamics Across Space and Time
Authors: Chandler D. Gatenbee, Emily S. Minor, Robbert J. C. Slebos, Christine H. Chung, Alexander R. A. Anderson
Subclonal reconstruction of tumors by using machine learning and population genetics
Authors: Giulio Caravagna, Timon Heide, Marc J. Williams, Luis Zapata, ..., Chris P. Barnes, Guido Sanguinetti, Trevor A. Graham & Andrea Sottoriva
Pervasive chromosomal instability and karyotype order in tumour evolution
Authors: Thomas B. K. Watkins, Emilia L. Lim, Marina Petkovic, Sergi Elizalde, ..., Samuel F. Bakhoum, Roland F. Schwarz, Nicholas McGranahan & Charles Swanton
#MathOnco Preprints
Elements and Evolutionary Determinants of Genomic Divergence Between Paired Primary and Metastatic Tumors
Authors: Ruping Sun, Athanasios N. Nikolakopoulos
Branching and extinction in evolutionary public goods games
Authors: Brian Johnson, Philipp M Altrock, Gregory J Kimmel
Gene expression has more power for predicting in vitro cancer cell vulnerabilities than genomics
Authors: Joshua M. Dempster, John M. Krill-Burger, James M. McFarland, Allison Warren, Jesse S. Boehm, Francisca Vazquez, William C. Hahn, Todd R. Golub, Aviad Tsherniak
Abnormal morphology biases haematocrit distribution in tumour 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
The Quest for Evolutionary Control
Nature Eco Evo Community Blog: Behind the Paper
Jacob Scott: "A lot of promising preliminary work suggests that we may be able to mitigate drug resistance by controlling the course of evolution in populations of bacteria and cancer cells. However, controlling the direction will be insufficient if we can't control the speed."
Welcome to a new ERA of reproducible publishing
Emmy Tsang and Giuliano Maciocci (eLife): "From today, authors with a published eLife paper can register their interest to enrich their published work with the addition of live code blocks, programmatically-generated interactive figures, and dynamically generated in-line values, using familiar tools like R Markdown and Jupyter in combination with Stencila Hub’s intuitive asset management and format conversion interface. The resulting new ERA publication will be presented as a complement to the original published paper. Very soon, a Google Docs plugin will also be made available to let authors insert executable code and data blocks into their documents using the cloud service."
Special Issue:
"Mathematical Models of Cellular Immunotherapies in Cancer"
Announcement: In this Special Issue, we plan to address cellular therapies from a mathematical and computational modeling perspective. Mathematical modeling has the potential to help in finding optimal administration protocols, provide a deeper understanding of the mechanisms and dynamics, help in the design of new clinical trials, and more. Despite the immense potential of these treatments, applied mathematicians and computational modelers have started to study these processes only very recently.
Guest Editors:
Víctor Pérez-García, Lisette de Pillis, Philipp Altrock, Russell Rockne
#MathOnco Virtual Seminars
1. Moffitt's Integrated Mathematical Oncology Dept. Series
Mathematical Oncology Series
Next talk: Dr. Kathleen (Kit) Curtius
"Computational modeling of cancer evolution to optimize screening and surveillance"
Sep 10, 2020 12:00pm US Eastern
#MathOnco - Book of the month
The Cheating Cell
Athena Aktipis: "When we think of the forces driving cancer, we don’t necessarily think of evolution. But evolution and cancer are closely linked, for the historical processes that created life also created cancer. The Cheating Cell delves into this extraordinary relationship, and shows that by understanding cancer’s evolutionary origins, researchers can come up with more effective, revolutionary treatments."
Jobs
NEW: Treating glioblastoma with immunotherapies (Morgan Craig)
Postdoctoral Research Position in Computational Immunology (Sylvain Cussat-Blanc)
Postdoc Position - TKI treatments in lung cancer (David Basanta)
Research Associate, Postdoc, and Research Faculty positions – Mathematical Oncology (Russ Rockne)
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)
Do you see something we missed? Reply to this email to send us an idea for next week's issue.
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