Gytis Dudas

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.

This study analyzes the evolution of Achromobacter ruhlandii over 30 years, identifying genomic features associated with epidemic potential and chronic infections.

The paper introduces baltic v1.0, a Python library for phylogenetic tree analysis and visualization, with new features for rooting, reticulate evolution, and composite figures.

This study benchmarks phylodynamic methods to analyze HIV-1 subtype C dispersal, finding robust spatial transmission patterns despite methodological variability in temporal estimates.

This study tracks the emergence and molecular evolution of H5N1 influenza viruses in U.S. dairy cattle, identifying increased mutation rates and positive selection after spillover from birds.

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 study analyzes the evolutionary history and migration patterns of Influenza D virus using phylogeographic methods, finding strong links to cattle trade and land borders.

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.

PoMeLo predicts metabolic loss in pathogen genomes by analyzing gene and pathway degradation across bacterial species.

This paper uses evolutionary genomics to identify host metabolic pathways critical for intracellular bacterial survival, validating them through in vitro assays and metabolomics.

The paper analyzes ambigrammatic narnavirus genomes to test hypotheses about functional protein coding in reverse open reading frames.

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.

This study uses phylogenetic methods and simulations to show that MERS-CoV has undergone recent recombination, suggesting frequent co-infection with distinct lineages, likely in camels.