Somatic Phylogenomics
Alex Gavryushkin
6 July 2020
Phylogenetic inference
Image source: Wikipedia
Why is it suddenly a thing?
Molecular biology: crash course
WARNING
Next slide contains real tumour images
Alves, Joao, Sonia Prado-Lopez, Jose Manuel Cameselle-Teijeiro, David Posada. "Rapid evolution and biogeographic spread in a colorectal cancer" bioRxiv (2019).
Tumour evolution
Jahn, Katharina, Jack Kuipers, and Niko Beerenwinkel. "Tree inference for single-cell data." Genome biology 17.1 (2016): 86.
Timing tumour evolution
Lote, H., I. Spiteri, L. Ermini, A. Vatsiou, A. Roy, A. McDonald, N. Maka, et al. 2017. "Carbon Dating Cancer: Defining the Chronology of Metastatic Progression in Colorectal Cancer." Annals of Oncology 28 (6): 1243–49.
Jiří Moravec
Main computational challenge
Trees are many, very many
- Gavryushkin, Alex, and Alexei J. Drummond. "The space of ultrametric phylogenetic trees."
Journal of Theoretical Biology 403 (2016): 197-208.
- Stadler, Tanja, Timothy G. Vaughan, Alex Gavryushkin, Stephane Guindon, Denise Kühnert, Gabriel E. Leventhal, Alexei J. Drummond.
"How well can the exponential-growth coalescent approximate constant-rate birth-death population dynamics?"
Proc. R. Soc. B. Vol. 282. No. 1806. The Royal Society, 2015.
tau-space
Geodesic in time-tree space
- Gavryushkin, Alex, and Alexei J. Drummond. "The space of ultrametric phylogenetic trees."
Journal of Theoretical Biology 403 (2016): 197-208.
- Gavryushkin, Alex, and Alexei Drummond. tauGeodesic. Mar. 2015. doi: 10.5281/zenodo.47152.
https://github.com/gavruskin/tauGeodesic
- Gavryushkina, Alexandra, Tracy A. Heath, Daniel T. Ksepka, Tanja Stadler,
David Welch, and Alexei J. Drummond.
"Bayesian total-evidence dating reveals the recent crown radiation of penguins."
Systematic Biology 66.1 (2016): 57-73.
- Gavryushkin, Alex, and Alexei Drummond. tauGeodesic. Mar. 2015. doi: 10.5281/zenodo.47152.
https://github.com/gavruskin/tauGeodesic