M. Manceau

The infinite alleles model revisited: a Gibbs sampling approach

The paper develops a Bayesian method using the infinite alleles model to infer SARS-CoV-2 population dynamics and sampling intensity from genomic data.

A skyline birth-death process for inferring the population size from a reconstructed tree with occurrences

This paper introduces a skyline birth-death process to infer population size changes over time using occurrence data and phylogenetic trees, applied to epidemiology and macroevolution.

Model-based inference of punctuated molecular evolution

The paper develops a model to detect episodes of fast divergence in molecular evolution and applies it to snake venom protein genes to identify spikes in the phylogeny.

The ancestral population size conditioned on the reconstructed phylogenetic tree with occurrence data

The paper derives the conditional probability distribution of ancestral population size given a reconstructed phylogenetic tree and occurrence data, with applications in epidemiology and macroevolution.

The probability distribution of the reconstructed phylogenetic tree with occurrence data

The paper derives a probability distribution for phylogenetic trees with occurrence data, enabling parameter estimation in epidemiology and macroevolution.

The species problem from the modeler’s point of view

The paper explores the species problem by defining three properties for species partitions and shows that any two can be satisfied while the third cannot, proposing algorithms for constructing phylogenies.