phylogenetics / evolution

MicroDUET is a genomic foundation model that provides fast, accurate representations for pathogen surveillance by distinguishing phylogeny and function.

This study shows H5N5 viruses have been repeatedly introduced across the Atlantic by high latitude seabirds, with more frequent introductions in fall and spring, and a distinct ecology from H5N1.

Serratus-guided Snakemake mining, expert curation, clustering and phylogenetic placement identify at least 32 putative novel tobamoviruses in public short-read data, mostly Amazon River metatranscriptomes; a random-forest classifier partly automates curation.

The paper analyzes IncC plasmids from Vibrio cholerae O1 El Tor isolates between 1979 and 2024, revealing their evolution and antimicrobial resistance gene diversity.

This paper examines the limits of Bayesian divergence time estimates in microbial evolution, finding that uncertainty scales with distance to calibration points rather than absolute age.

This paper develops ARG-based methods to analyze virus evolution, showing EBV coalesces predominantly inter-host and revealing gene-level selective structure.

The paper updates clade designations for H5N1 avian influenza viruses based on phylogenetic analysis of HA gene sequences from multiple regions.

This study updates the understanding of form I-related RuBisCOs by analyzing their phylogenetic relationships and identifying a form I RuBisCO gene in an archaeal MAG, highlighting uncertainties in their evolutionary history.

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

TIGRFinder annotated 6,685 TIGR arrays; cryo-EM structures show inactive RuvC domains, and E. coli reporter assays show CsTasR and MbTasA repress transcription in a guide-dependent manner.

A >50,000-element viral smORF library screened by growth, MHC-I, ER stress, Perturb-seq and mass spectrometry yields >2,000 active microproteins and shows EBV BNLF2b inhibits PKA by mimicry.

This paper develops a digital microfluidic platform that enables simultaneous short- and long-read viral genomic surveillance with improved efficiency and accuracy.

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

The paper develops a method to detect recombination breakpoints and signs of human-made manipulation in viral sequences, finding no evidence of such manipulation in SARS-CoV-1, MERS-CoV, or SARS-CoV-2.

This paper introduces a site-specific mutation model (SSM) for pandemic-scale phylogenetics, showing it better captures mutation patterns in SARS-CoV-2 genomes than classical models.

biomeStat automates genomic epidemiology analysis of 1,000 Dengue virus genomes, revealing immune escape sites and conserved drug targets in under 24 hours.

The paper presents tools to harmonize viral genomic data across repositories and mask lab-specific artifacts, improving phylogenetic analysis accuracy.

CMAPLE 2 improves phylogenetic inference speed and memory efficiency for large pathogen genome datasets, enabling analysis of nearly four million SARS-CoV-2 genomes in 12 days.

The paper compares the evolutionary changes in the central complex and mushroom bodies across Heliconiini butterflies, finding conservation in the central complex and expansion in the mushroom bodies linked to foraging behavior.

LucaPhylo infers phylogenetic trees from unaligned protein sequences using hyperbolic geometry and protein language models, achieving accuracy comparable to alignment-based methods for divergent RNA viruses.

The paper analyzes SARS-CoV-2 spike evolution in Canada, finding that variant emergence, not vaccine deployment, drove episodic positive selection at the provincial level.

The paper investigates the genetic diversity of Tomato brown rugose fruit virus in Morocco using viral gene analysis and haplotype networks, finding low diversity and geographic structure.

Omni2Tree directly analyzes raw sequencing reads to reconstruct viral phylogenies and identify diversification, outperforming assembly and reference-based methods in low-coverage scenarios.

This study investigates the origin and evolution of grapevines through phylogenomic analysis of 29 genome assemblies, revealing evolutionary relationships and genomic features contributing to their adaptation.

The paper improves phylogenetic inference by incorporating lineage abundance into maximum likelihood methods, showing significant accuracy gains in SARS-CoV-2 data.

Sequenced HBV from wild Amazonian primates in a deforested, densely settled region matched human genotypes A and D, while pristine-forest monkeys were all negative, consistent with human-to-primate spillover.

The paper identifies a rapidly expanding multidrug-resistant M. tuberculosis clade originating from Russia and circulating in Moldova, posing a threat to MDR-TB control.

The paper shows that mutations increasing ORF9b expression are common in SARS-CoV-2 variants and PCI sequences, suggesting ORF9b's role in viral evolution and immune evasion.

Splicer performs phylogenetic placement in sub-linear time, enabling efficient classification of large-scale genetic sequences with high accuracy.

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.