Przemysław Decewicz

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.

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.

The paper quantifies the benefits and costs of prophages in bacterial genomes, showing uniform prophage density and estimating their energetic contribution.

The paper presents a gold-standard dataset of manually curated bacterial genomes and a framework to evaluate prophage prediction algorithms, showing their performance metrics across seven tools.