George Spyro Bouras

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

The paper identifies mutations in the mfd gene in S. aureus isolates from a CRS patient, linking them to a mucoid hyper-biofilm phenotype and increased enterotoxin production.

The paper shows bacterial strain identity is the main factor determining phage infectivity in Achromobacter, with lineage and strain identity explaining 90% of variation in infection efficiency.

The paper improves viral protein clustering by combining diversified sequence profiles with structural information, revealing a more accurate picture of viral protein diversity.

The paper predicts homooligomeric phage protein structures using a computational framework, confirming predictions for dimers and trimers and showing high accuracy in classifying homooligomeric states.

Baktfold improves protein functional annotation for microbial genomes using structural information, achieving higher annotation rates than existing tools for bacteria and archaea.

agtools provides a Python framework to manipulate assembly graphs across formats, enabling analysis and integration into bioinformatics workflows.

Phold pairs ProstT5-predicted 3Di tokens with Foldseek searches against 1,363,704 curated phage structures, annotating 49.4% of CDS in 1,419 INPHARED genomes versus 34.7% for Pharokka MMseqs2.

The paper identifies three novel phages targeting vancomycin-resistant E. faecalis and shows that LicD-mediated cell wall decoration influences phage sensitivity and biofilm formation.

Phynteny combines ESM2 protein embeddings, a BiLSTM, and circular-attention transformer layers to exploit phage gene order, assigning one of nine PHROG functional categories to unannotated genes.

This study uses structure-informed methods to annotate hypothetical proteins from Pseudomonas phages, showing that combining structural and sequence-based approaches can annotate up to 43% of previously unannotated proteins.

ProtSpace visualizes protein embeddings in 2D/3D to reveal functional patterns and challenges existing classifications in phage and venom protein analyses.

Sphae is a bioinformatics pipeline that rapidly assesses phage therapeutic potential by analyzing genomic markers for safety and efficacy in under ten minutes.

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

Hybracter improves bacterial genome assembly accuracy and speed, outperforming existing tools in hybrid and long-read-only modes, especially for small plasmids.

This study compares full-length 16S rRNA sequencing using Oxford Nanopore Technology (FL-ONT) with Illumina V3-V4 short-read sequencing in head and neck cancer tissues, finding FL-ONT provides better resolution at lower taxonomic levels.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

The paper predicts stop codon reassignment in bacteriophage genomes to improve functional annotation, showing significant increases in gene length and coding density.

Phables improves phage genome recovery from fragmented viral metagenome assemblies, recovering more high-quality genomes and resolving variants with high nucleotide identity.

This study isolates and characterizes three novel Crassvirales phages infecting Bacteroides cellulosilyticus WH2, revealing they do not co-evolve with their hosts and share a conserved tail spike protein involved in host interaction.