Andrea Telatin

This paper uses ICA to analyze TraDIS-Xpress data from E. coli, identifying functional modules of antimicrobial resistance genes across multiple stress conditions.

The paper introduces PHORAGER, a pipeline for identifying prophages in bacterial genomes, and reports the discovery of 23,132 putative prophages in ESKAPE pathogens.

This study uses shotgun metagenomics to show that the gut microbiome of insectivorous bats remains stable during temporary managed care, with minimal changes in microbial composition.

This study examines the impact of a bacteriophage cocktail on healthy gut microbiota using an in vitro human colon model, finding minimal disruption with specific effects on Escherichia coli.

The paper compares INPHARED database snapshots from 2021 to 2026, showing growth in phage genomes but reduced novel species diversity and persistent host bias.

This study benchmarks five ARG detection tools on simulated metagenomic datasets, showing coverage and community complexity impact accuracy, with ARGprofiler leading in F1-score and computational efficiency.

The paper develops a framework to improve functional annotation in metagenomics by integrating gene families and metabolic reactions, significantly increasing detectable reactions and data prevalence in human gut microbiome studies.

The paper identifies a novel gene cluster in Bifidobacterium pseudolongum that enables resistant starch utilization, linking CAZyme profiles to niche adaptation in infant and adult microbiomes.

This study analyzes prophages and defense systems in Bifidobacterium genomes to reveal co-evolutionary 'arms race' dynamics between bacteria and phages.

The paper examines bacteriophage diversity in COPD patients and finds it declines with disease severity, showing disrupted viral-bacterial relationships in those with frequent exacerbations.

This study shows that a low protein diet reduces liver damage from Salmonella infection by altering macrophage metabolism and autophagy.

The paper compares Illumina and Oxford Nanopore sequencing for viral genome recovery from human gut samples, finding Illumina better for resolved genomes and hybrid approaches better for diversity.

The paper classifies Lak megaphages into a new viral order, Grandevirales, based on protein and nucleotide analyses, revealing their unique genetic code and evolutionary relationships.

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

MetaPhage is a pipeline that automates the analysis, annotation, and classification of bacteriophages in metagenomics data, providing a comprehensive report and interactive visualization.

BamToCov provides efficient tools for calculating sequence coverage from BAM/CRAM files, with memory optimization and support for strand-specific analysis.