Bayesian phylogenetic models for the evolution of gene expression on single-cell lineages

Objective

The PhyloCELL-EXP project is dedicated to developing and implementing robust statistical models to understand the evolutionary dynamics of gene expression in single-cell cancer lineages. We will leverage advanced Bayesian phylogenetic frameworks such as BEAST2 to systematically identify fast evolving cell lineages, reconstruct gene expression changes along cell phylogenies, and link these changes to both genetic and micro-environmental factors. Our methodological approaches will include algorithms for detecting shifts in evolutionary rates, and Brownian Motion and Ornstein-Uhlenbeck models for gene expression, that are scalable to handle thousands of genes and hundreds of cells. By making use of real multi-omics cancer datasets, PhyloCELL-EXP’s quantitative models will enable genetic inheritance and plasticity in cancer adaptation and progression to be characterized, setting new standards in statistical and computational tumor evolution research.