Russell B Corbett-Detig

The paper identifies telotrons, telomeric repeat-containing introns, in multiple eukaryotic genomes and suggests telomerase drives intron creation and remodeling.

This study shows that genome erosion in deep-sea bacterial symbionts can be reversed through horizontal gene transfer and mobile genetic elements, enabling host-switching.

The paper introduces viral_usher, a tool for scalable viral phylogenetics, and demonstrates that replication machinery explains most variance in viral mutation spectra.

This paper demonstrates the successful detection of EMS-induced mutations in Wolbachia genomes using circle sequencing, revealing a significant enrichment of C/G>T/A transitions.

The paper estimates an extreme transmission bottleneck in a deep-sea clam symbiosis using ultra-accurate sequencing, finding an effective bottleneck size of about eight symbionts per host generation.

Lorax enables real-time visualization of biobank-scale ancestral recombination graphs with integrated metadata and genomic information.

This study identifies the oldest known plague strains in Lake Baikal hunter-gatherers 5500 years ago, showing early outbreaks were lethal and challenged the idea that agriculture was necessary for plague epidemics.

Panmap efficiently aligns, genotypes, and places reads on large pangenomes using phylogenetic compression, enabling rapid analysis of up to 8 million genomes.

The paper identifies splicing deficiency in non-recombining mating-type chromosomes across phytoplankton species, showing how recombination suppression leads to transcript-level dysfunction.

This paper introduces PanMAN, a compressed pangenome data structure that captures evolutionary and mutational histories, achieving significant compression and enabling more efficient pangenomic analysis.

The paper investigates the role of the ANTSR gene in CSD across Hymenoptera, finding it conserved in Aculeata and suggesting multiple CSD loci in Formica.

The paper uses ancient metagenomics to characterize subglacial microbiomes, showing they split into two clusters based on oxygen availability and redox conditions.

The paper identifies intron-generating transposons in viral elements, suggesting dsDNA viruses may facilitate horizontal transfer of introners between species.

The paper identifies horizontal transfer of intron-containing transposons as a major source of new introns across eukaryotic lineages.

The paper introduces clam, a tool that efficiently estimates nucleotide diversity and divergence using variant-only VCFs and callable loci, improving computational performance and storage.

This study shows that genetic incompatibilities in pollen cause segregation distortion in Arabidopsis species and populations, increasing with genetic distance and contributing to reproductive isolation.

The paper identifies shifts in the mutation spectrum of SARS-CoV-2 using a phylogenetic method and finds candidate causal substitutions in the polymerase.

This study uses Drosophila melanogaster recombinant inbred lines to analyze the genetic architecture and interactions of adaptive traits, finding detectable alleles and gene-by-environment interactions but limited epistasis.

The paper introduces R2C2+UMI, a method combining concatemeric consensus sequencing with UMIs to achieve ultra-accurate sequencing of amplicons on Oxford Nanopore sequencers.

This study shows that the wMel Wolbachia strain outcompetes the promiscuous wRi strain in vitro across different host cell types, suggesting a deterministic outcome that may explain low natural mixed infections.

The paper develops a structural proteome screen to identify protein mimicry in host-microbe systems, applying it to Legionella pneumophila, Helicobacter pylori, and Wolbachia to find candidate proteins involved in host interactions.

This study compares pangoLEARN and pUShER for SARS-CoV-2 lineage assignment, finding pUShER more stable and accurate across pangolin versions.

This paper introduces snpArcher, a variant calling workflow for non-model organisms, and applies it to 26 public datasets to enable comparative population genomic analyses.

The paper develops a method to identify and quantify the effects of multiple linked selected sites in admixed populations, finding that linkage impacts selection estimates.

The paper identifies universal patterns of transposable element (TE) compartmentalization across eukaryotic genomes, linking TEs to gene families under selective pressure and adaptive functions.

The paper introduces MAPLE, a new phylogenetic analysis method that scales to large datasets by improving computational efficiency, outperforming existing tools like FastTree and RAxML-NG.

Treenome Browser allows interactive visualization of millions of genomes with large phylogenetic trees.

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 demonstrates that Illumina short-read libraries can be sequenced on the ONT MinION with high accuracy using the R2C2 method, achieving error rates comparable to Illumina MiSeq.

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