Alexey I. Fomenkov

A virion protein of an archaeal virus inhibits a Type V BREX defense system in Haloarcula hispanica

This study characterizes a Type V BREX defense system in Haloarcula hispanica and shows that two archaeal viruses evade it via a virion protein.

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Domainator identifies proteins involved in antiviral systems by clustering and analyzing domain-based gene neighborhoods and integrating a protein language model.

Matching Excellence: ONT's Rise to Parity with PacBio in Genome Reconstruction of Non-Model Bacterium with High GC Content

This study compares ONT and PacBio sequencing for genome reconstruction of high GC content bacteria, finding ONT can achieve high-quality genomes without hybridization.

Reassembling a cannon in the DNA defense arsenal: genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

The paper investigates the BREX phage exclusion system in Salmonella, showing that mutations in flanking genes affect methylation and restriction despite intact modification genes.

Rapid Identification of Methylase Specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

RIMS-seq identifies methylase specificities and sequences bacterial genomes using a simple protocol, revealing new methylase targets in bacteria and synthetic communities.

Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium

The paper presents the genome sequences of two laboratory Salmonella strains and traces their ancestry, revealing hybridization events and their historical use in research.

Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments

The paper introduces MFRE-Seq, a method to identify 5-methylcytosine sites in bacterial genomes using restriction enzyme digestion and sequencing, confirming known motifs and discovering novel ones.