Author

A. Arkin

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Open access Sep 2026

Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.

Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by challenges related to selection of phages infecting specific bacterial strains. Here we present a phylogeny-agnostic machine-learning framework predicting strain...

A. Noonan, Lucas Morinière, E. O. Rivera-Lopez et al. · Nature Microbiology · 0 citations

Open access Sep 2026

Genome-wide characterization of host factors involved in single-stranded RNA and DNA phage infection pathways

Single stranded RNA (ssRNA) and single stranded DNA (ssDNA) bacteriophages represent a key component of the global virome, yet the host genetic networks supporting their infection cycles remain poorly understood. Here, we present a comprehensive, genome-wide mapping of the genetic landscape regulating infection cycles...

Isabella Murray, Roniya Thapa Magar, Denish Piya et al. · bioRxiv · 0 citations

Open access Jul 2026

Surface architecture of the bacterial envelope determines phage adsorption route in pathogenic Escherichia coli O157:H7

This study provides the first genome-scale, functional genetic map of phage susceptibility determinants in O157:H7 and demonstrates that the state of the outer surface layers, specifically the O-antigen and the gfc-etk capsule, determines whether phages can reach conserved terminal receptors.

E. O. Rivera-Lopez, Lucas Morinière, A. Kazakov et al. · bioRxiv · 0 citations

Open access Mar 2026

The WalRK two-component system in Streptococcus pneumoniae ensures robustness of secondary wall polymer attachment

This study shows that the conserved capsule gene CpsA is not strictly required for capsule attachment but instead works together with other LytRIZCpsAIZPsr (LCP) ligases, however, it requires the essential WalRK signaling system to maintain cell envelope integrity.

J. Zik, Zeyu Fu, M. Price et al. · bioRxiv · 0 citations

Open access Jul 2026

The WalRK two-component system in Streptococcus pneumoniae ensures robustness of secondary wall polymer attachment

A strong negative genetic interaction is identified between the genes encoding the putative capsule ligase CpsA and the WalRK histidine kinase, a component of the WalRK two-component system regulating cell wall homeostasis, showing that the conserved capsule gene CpsA is not strictly required for capsule attachment but...

J. Zik, Zeyu Fu, M. Price et al. · mBio · 0 citations