Y. Turakhia

Automated Agnostic Designation of Pathogen Lineages

The paper introduces an automated method for pathogen lineage designation using phylogenetic trees, offering a consistent alternative to manual curation.

Whole-genome comparisons identify repeated regulatory changes underlying convergent appendage evolution in diverse fish lineages

The paper identifies genomic deletions associated with convergent fin reduction in multiple fish lineages by comparing whole-genome sequences of 36 wild fish species.

Mutational spectra distinguish SARS-CoV-2 replication niches

The paper analyzes SARS-CoV-2 mutational spectra to infer replication niches, finding reduced G>T mutations in Omicron linked to upper respiratory tract replication.

DecentTree: Scalable Neighbour-Joining for the Genomic Era

DecentTree improves Neighbour-Joining phylogenetic inference scalability, handling large datasets up to 64,000 SARS-CoV-2 genomes faster than existing methods.

matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2

matOptimize improves runtime and memory efficiency for SARS-CoV-2 phylogenetic tree optimization, enabling daily maintenance of large-scale phylogenies during the pandemic.

Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region

The paper develops a novel phylogenomic method to detect recombination events in SARS-CoV-2 genomes, identifying 606 recombination events across 1.6M samples with 2.7% of genomes showing recombinant ancestry, primarily in the Spike protein region.

Mutation rates and selection on synonymous mutations in SARS-CoV-2

The paper analyzes mutation rates and selection pressures in SARS-CoV-2 genomes, identifying elevated G→U and C→U mutations and challenging previous findings on synonymous site selection.

Champagne: Whole-genome phylogenomic character matrix method places Myomorpha basal in Rodentia

Champagne generates a whole-genome character matrix for phylogenomic analysis, improving resolution of mammalian phylogeny and reclassifying squirrels within Rodentia.

A novel unbiased test for molecular convergent evolution and discoveries in echolocating, aquatic and high-altitude mammals

The paper introduces a novel test to identify molecular convergent evolution in coding genes across phenotypically convergent lineages, revealing 75 novel convergences in echolocating, aquatic, and high-altitude mammals.