Louis du Plessis

The paper characterizes respiratory virus genomic diversity in Switzerland using hybrid-capture sequencing and phylogenetic analysis, identifying prevalent strains and evolutionary insights.

TyCHE improves time-resolved lineage tracing by accounting for heterogeneous mutation rates, applied to memory B cells, germinal centers, gliomas, and bacterial infections.

This study analyzes the spread of H5 avian influenza in high-density poultry farms using phylogeographic tools, identifying key factors driving transmission and control thresholds.

EpiFusion improves estimation of outbreak dynamics by integrating phylodynamic and epidemiological data using particle filtering, enhancing accuracy and efficiency in large, poorly sampled epidemics.

V-pipe 3.0 is a computational pipeline for analyzing viral genomic data, enabling reproducible and scalable estimation of within-sample genetic diversity.

The paper introduces a computationally efficient birth-death model that integrates phylogenetic and epidemiological data to estimate transmission dynamics and unreported infections.

This study identifies previously unknown Treponema pallidum strains in early modern Europe, suggesting a complex history of treponemal diseases.

This paper introduces a new method to jointly estimate population size and sampling intensity dynamics from molecular sequences, showing improved accuracy over existing methods.

The paper uses ZIKV genomes to estimate the origin and spread of Zika virus in Brazil and the Americas, providing a timeframe for baseline microcephaly rates.