Guy Baele

The paper analyzes the spread of H5N1 B3.13 in U.S. dairy cattle using genomic data and movement networks, finding that cattle movement, not birds, drives the outbreak.

This study uses phylogeographic and phylodynamic methods to analyze DENV genome data, revealing asymmetric global spread patterns and the role of travel over climate in DENV transmission.

The paper reports the first detection of H5N1 clade 2.3.4.4b in mainland Australia from seabirds, tracing the viruses to Heard Island via phylogenetic analysis and highlighting the risk of mainland establishment.

The paper reports a multi-species outbreak of HPAI H5N1 on Heard Island, causing mass mortality in southern elephant seals and other seabirds, with drones used for monitoring.

This paper develops optimized RNA polymerase II-driven minigenomes for Nipah virus to enable safer research and antiviral screening.

This study uses a Bayesian mixed-effects molecular clock model to analyze HBV genomic data, revealing declining evolutionary rates and linking viral spread to human migration patterns.

The paper introduces parallel algorithms to improve the computational efficiency of structured coalescent models for phylogeographic analysis, enabling faster and larger-scale studies of pathogen spread.

The paper identifies the emergence of D1.1 reassortant H5N1 viruses in North America, which show increased transmissibility, host range, and human spillover potential.

This study tracks the spread and evolution of H5N1 in the sub-Antarctic and Antarctica, revealing long-distance dispersal and mammalian-adaptive mutations.

This study uses whole-genome sequencing and phylodynamic methods to analyze the evolutionary history and ecological dynamics of Jamestown Canyon virus, revealing its slow evolution and transmission patterns.

This paper investigates the challenges of Bayesian phylodynamic inference due to rugged tree landscapes and proposes diagnostics and strategies to improve analysis reliability.

This study models latency in Ebola virus using a novel phylogenetic approach, finding evidence of extended quiescence in the reservoir, which changes understanding of its evolutionary history and geographic spread.

This paper evaluates an adjusted Bayes factor method to reduce sampling bias in discrete phylogeographic analysis using CTMC models.

The paper introduces HIPSTR, a new consensus tree method that outperforms MCC in capturing high-support clades, and presents an updated TreeAnnotator X with faster computational routines.

This study develops and compares three novel landscape phylogeographic methods to assess environmental impacts on viral spread, providing guidelines for their use and open-source tools for viral epidemiology research.

This study reports the arrival of HPAI H5N1 clade 2.3.4.4b in sub-Antarctic Indian Ocean islands, causing mass mortality in seals and birds, and identifies independent introductions from South Georgia.

This paper introduces a Bayesian method to detect episodic evolution by comparing molecular clock models and applies it to SARS-CoV-2 data, finding strong evidence for episodic evolution.

This study reconstructs the emergence and spread of Powassan virus lineage II in the northeastern U.S. using genomic data, finding a south-to-north dispersal pattern and population growth.

This study evaluates subsampling strategies to optimize ancestral trait reconstruction in HIV-1 subtype C datasets, showing that subsampling by collection date, location, and risk group improves representativeness and reduces computational burden.

This study reports genomic surveillance in Rwanda from June to September 2021, showing the rapid spread and dominance of the Delta variant over other lineages, with implications for cross-border transmission.

This study analyzes SARS-CoV-2 genomic sequences from Rwanda to track variant evolution and regional spread, identifying emerging sub-lineages and VOCs introduced through travel.

The paper analyzes the genetic evolution and mutation patterns of SARS-CoV-2 using phylogenetic and structural analysis of 4,894 genomes, identifying potential human-adaptation related mutations.

This paper introduces BETS, a Bayesian method to evaluate temporal signal in sequence data, showing it accurately classifies datasets with or without temporal signal across various empirical examples.

This study analyzes 1600 Ebola virus genomes to show viral spread followed a gravity model, with cross-border transmission before border closures contributing to an international epidemic.