C. Colijn

Taking a BREATH (Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories) to simultaneously infer phylogenetic and transmission trees for partially sampled outbreaks

BREATH simultaneously infers phylogenetic and transmission trees for outbreaks using sequence data, improving resolution and origin timing estimates in a tuberculosis outbreak.

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.