The repos here contain some of the code I produced while working at the Wellcome Sanger Institute and MRC-Cancer Unit.
They relate to the analysis and simulation of genetic mutations in normal tissues.
See also:
https://github.com/Colorifix - Colorifix is a company producing eco-friendly textile dyes. A few of the tools we wrote have been made publicly available, e.g. a Notion API client and a framework for exchanging data between platforms
https://github.com/PHJonesGroup - further code from myself and others in the Jones group at Sanger
https://zenodo.org/record/3648706#.Yk7nyC8w3m0 - Netlogo and Java (HAL) models to accompany Colom, Bartomeu, et al. "Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium." Nature genetics 52.6 (2020): 604-614.
Python code to run various simulations of mutant clonal competition. This is also available as a package on PyPi.
It can run Moran, 2D Moran, Wright-Fisher, 2D Wright-Fisher and (non-competitive) branching processes.
The code has been used in:
Fowler, Joanna C., et al. "Selection of oncogenic mutant clones in normal human skin varies with body site." Cancer discovery 11.2 (2021): 340-361.
Abby, Emilie, et al. "Notch1 mutation drives clonal expansion in normal esophageal epithelium but impairs tumor growth." bioRxiv (2021).
(old version of this code) Michael WJ, Philip H. Jones, and Benjamin A. Hall. "Relating evolutionary selection and mutant clonal dynamics in normal epithelia." Journal of the Royal Society Interface 16.156 (2019): 20190230.
(even older version of this code) Murai, Kasumi, et al. "Epidermal tissue adapts to restrain progenitors carrying clonal p53 mutations." Cell stem cell 23.5 (2018): 687-699.
Python code for statistically analysing patterns of somatic evolutionary selection in genes or proteins.
The paper descibing this method:
Hall, M.W.J. et al. Mutations observed in somatic evolution reveal underlying gene mechanisms. Commun Biol 6, 753 (2023).
The code has also been used in Fowler, Joanna C., et al. "Selection of oncogenic mutant clones in normal human skin varies with body site." Cancer discovery 11.2 (2021): 340-361.
Code modelling the elimination of micro-tumours by highly fit mutant clones in the surrounding tissue for
Colom, B., et al. "Mutant clones in normal epithelium outcompete and eliminate emerging tumours." Nature 598.7881 (2021): 510-514.
Scripts to accompany Fowler, Joanna C., et al. "Selection of oncogenic mutant clones in normal human skin varies with body site." Cancer discovery 11.2 (2021): 340-361.
These scripts make use of the code from the clone-competition-simulation and darwinian_shift repositories.
Notebooks to generate the figures for the preprint Hall, Michael WJ, et al. "Investigating structure function relationships in the NOTCH family through large-scale somatic DNA sequencing studies." bioRxiv (2020).
Code to recreate the figures for Hall, Michael WJ, Philip H. Jones, and Benjamin A. Hall. "Relating evolutionary selection and mutant clonal dynamics in normal epithelia." Journal of the Royal Society Interface 16.156 (2019): 20190230.