Marc A. Suchard

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 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.

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

This study identifies ancient RNA virus genomes in Adelie penguin mummies, revealing viral sequences from specimens up to 2000 years old.

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.

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.

The paper identifies the recent origin and geographical distribution of bat viruses ancestral to SARS-CoV and SARS-CoV-2, showing they circulated in Asia before spilling over into humans.

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 evaluates dispersal metrics for viruses using simulation and compares their spread in animal populations, finding robustness to sampling effort and human-mediated dispersal signatures.

This paper introduces PIV models to estimate dispersal velocity of evolving lineages and shows improved accuracy in predicting pathogen spread using West Nile virus data.

Reanalysis of public environmental metatranscriptomes from the Huanan market links SARS-CoV-2 positivity to one wildlife stall containing raccoon dog, civet and bamboo rat genetic material.

This paper introduces a gradient-based Hamiltonian Monte Carlo sampler for efficient inference in episodic birth-death-sampling models, showing significant computational improvements over Metropolis-Hastings methods.

This study identifies novel rodent hosts of hepaciviruses, documents their diversity, and estimates the origin of the genus to be about 22 million years ago.

The paper introduces phylogenetic novelty scores to weight genetic sequences based on their evolutionary novelty, improving accuracy in character frequency estimation and other applications.

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.

January 2020 cases in Germany and Washington State were contained, while separate later introductions from China seeded the first sustained SARS-CoV-2 transmission networks in Italy and Washington State.