C. Colijn

Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

The paper tests whether negative frequency-dependent selection and asymmetrical recombination can explain the stability of multi-strain bacterial populations using simulations and genomic data.

Predicting the short-term success of human influenza A variants with machine learning

The paper predicts the short-term success of human influenza A variants using machine learning based on phylogenetic trees and epitope site polymorphisms.

Designing ecologically-optimised vaccines using population genomics

This paper shows that vaccines designed using population genomics and ecological models can better reduce IPD and antibiotic-resistant disease by preventing serotype replacement.

Transmission trees on a known pathogen phylogeny: enumeration and sampling

The paper calculates the number of possible transmission trees from a phylogeny and provides a method to uniformly sample them, with an R package for implementation.

Host population structure and treatment frequency maintain balancing selection on drug resistance

The paper models how host population structure and treatment frequency influence the coexistence of drug-sensitive and resistant strains of Streptococcus pneumoniae.

A metric on phylogenetic tree shapes

This paper introduces a metric for comparing phylogenetic tree shapes, distinguishing trees from different evolutionary processes and applications.