Susanna R. Grigson

VHAMSTeR predicts viral host associations across five categories using genomic language models and biological features, outperforming existing methods and uncovering new RNA bacteriophages.

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

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.

The paper analyzes 15,000 bacterial genomes to investigate the presence of antimicrobial resistance (AMR) genes in prophages across human body sites and regions, finding diverse AMR genes associated with prophages.

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

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.