N. F. Müller

Phylodynamics Uncovers the Transmission of Antibiotic-Resistant Escherichia coli between Canines and Humans in an Urban Environment

This study uses genomic sequencing and phylogenetics to show antibiotic-resistant E. coli is transmitted between canines and humans in urban environments.

Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference

This paper introduces a method to quantify plasmid movement in Shigella species over time, finding higher transfer rates for small plasmids and recent dissemination of a multidrug-resistant plasmid.

State-dependent evolutionary models reveal modes of solid tumor growth

This paper introduces a Bayesian state-dependent evolutionary model to infer spatially varying cell division rates in tumors using multi-region sequencing data, finding peripheral cells divide 3-6x faster than central cells.

Phylodynamic assessment of control measures for highly pathogenic avian influenza epidemics in France

This study uses phylodynamic analysis to assess the impact of control measures on H5N8 avian influenza spread in France, finding that culling reduced inter-departmental spread but transport within departments increased local transmission.

Joint inference of migration and reassortment patterns for viruses with segment genomes

This paper extends the structured coalescent to account for reassortment in segmented viruses, showing it leads to different estimates of population sizes, migration, and clock rates compared to models without reassortment.

Recombination patterns in coronaviruses

This paper introduces a method to infer recombination networks in coronaviruses and shows recombination is common and potentially beneficial in seasonal human coronaviruses.

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

The paper uses genetic sequence data and patient metadata to analyze local influenza transmission dynamics in Basel, Switzerland, finding that temperature trends correlate with transmission and that elderly and school children drive different transmission networks.

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

This study maps influenza transmission in a city at high resolution, finding socioeconomic factors like income influence infection patterns and vaccination rates, independent of population density.

Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

This study uses Bayesian inference to analyze reassortment networks in human influenza viruses, finding that reassortment events occur more frequently on fitter parts of the network.