Alexander Fisher

Journal Article Systematic biology · November 2023 Divergence time estimation is crucial to provide temporal signals for dating biologically important events from species divergence to viral transmissions in space and time. With the advent of high-throughput sequencing, recent Bayesian phylogenetic studies ... Full text Cite

Shrinkage-based Random Local Clocks with Scalable Inference.

Journal Article Molecular biology and evolution · November 2023 Molecular clock models undergird modern methods of divergence-time estimation. Local clock models propose that the rate of molecular evolution is constant within phylogenetic subtrees. Current local clock inference procedures exhibit one or more weaknesses ... Full text Cite

Scalable Bayesian phylogenetics.

Journal Article Philosophical transactions of the Royal Society of London. Series B, Biological sciences · October 2022 Recent advances in Bayesian phylogenetics offer substantial computational savings to accommodate increased genomic sampling that challenges traditional inference methods. In this review, we begin with a brief summary of the Bayesian phylogenetic framework, ... Full text Cite

Relaxed Random Walks at Scale.

Journal Article Systematic biology · February 2021 Relaxed random walk (RRW) models of trait evolution introduce branch-specific rate multipliers to modulate the variance of a standard Brownian diffusion process along a phylogeny and more accurately model overdispersed biological data. Increased taxonomic ... Full text Cite

Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework.

Journal Article Nature communications · November 2020 Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic ... Full text Cite