George Spyro Bouras

Second-site capsule-locus mutations, not Ade efflux disruption, determine phage susceptibility across an Acinetobacter baumannii transposon mutant panel

First community challenge for automated virus taxonomy

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.

Mutations in mfd cause Staphylococcus aureus mucoid hyper-biofilm phenotype in chronic rhinosinusitis

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.

Host species background, defence systems, and phage tail gene architecture shape phage infectivity in cystic fibrosis-associated Achromobacter

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.

Improving viral protein clustering using both diversified protein profiles and structural information

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

Computational prediction resolves thousands of homooligomeric phage protein structures

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: Sensitive protein functional annotation across the microbial tree of life using structural information

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

agtools: a software framework to manipulate assembly graphs

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

Protein Structure Informed Bacteriophage Genome Annotation with Phold

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.

LicD-Mediated Cell Wall Decoration Governs Phage Sensitivity in Enterococcus faecalis Clinical Isolates

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.

Synteny-aware functional annotation of bacteriophage genomes with Phynteny

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.

Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins

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: a tool for visualizing protein space

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

Sphae: An automated toolkit for predicting phage therapy candidates from sequencing data

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

How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies

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: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies

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

A comparison between full-length 16S rRNA Oxford Nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues

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.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

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.

Predicting stop codon reassignment improves functional annotation of bacteriophages

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

Phables: from fragmented assemblies to high-quality bacteriophage genomes

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

Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

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.