Bryan P. Thornlow

The paper identifies Introners, transposable elements driving intron gain in diverse eukaryotes, and finds they are prevalent in marine species and phylogenetically distant lineages.

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 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.

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.