Russell B Corbett-Detig

The paper introduces phastSim, a tool for efficiently simulating sequence evolution on large phylogenetic trees, particularly for SARS-CoV-2-like datasets.

The paper uses metagenomic analyses to study symbiont composition in deep-sea hydrothermal vent snails, finding that environmental factors and geographic barriers influence symbiont strain composition more than host genetics.

The paper develops a phylogenetic package to handle pandemic-scale SARS-CoV-2 genomic data, enabling real-time analysis and visualization of large mutation-annotated phylogenetic trees.

This study compares online and de novo phylogenetic methods for SARS-CoV-2, finding that maximum parsimony online approaches are more accurate and efficient than maximum likelihood or de novo methods.

The paper introduces a daily-updated database of SARS-CoV-2 mutation-annotated trees and associated tools for querying and manipulating the data.

The paper introduces UShER, a method for ultrafast phylogenetic placement of SARS-CoV-2 sequences, enabling real-time genomic contact tracing and maintaining an updated reference phylogeny.

The paper estimates changes in SARS-CoV-2 transmissibility using a phylogeny-based metric, finding that Delta is the most transmissible clade and transmissibility within clades slightly decreases over time.

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

The paper identifies lab-specific recurrent mutations in SARS-CoV-2 sequences that affect phylogenetic inference and proposes tools to improve sequence quality and phylogeny comparison.

This study investigates how positive selection affects the distribution of genomic admixture tract lengths and shows that selection can increase tract lengths on average but decrease them conditional on allele frequency.

The paper demonstrates a chromosome-scale genome assembly of a single outbred Drosophila melanogaster using a hybrid method with low input DNA.

The paper introduces mixnmatch and ancestryinfer, tools for simulating admixture scenarios and inferring local ancestry, highlighting factors affecting inference accuracy.

The paper predicts tRNA gene activity using sequence and genomic context features, finding strong correlations with G+C content and CpG density.

The paper shows tRNA genes have much higher mutation rates than the genome average, driven by transcription-associated mutagenesis and purifying selection.

The paper analyzes genomic data from passenger pigeons and their relatives to show that natural selection reduced neutral genetic diversity despite large population size, challenging previous extinction theories.