Val F. Lanza

The paper develops a rules-based classifier to predict ciprofloxacin resistance in Klebsiella pneumoniae from genotype data and demonstrates its global distribution association with quinolone consumption.

The paper investigates mercury resistance in gut microbiota of children, finding high prevalence of Hg-resistant bacteria and strong taxonomic structuring of resistance genes.

The paper characterizes microbial communities in hospital sinks, showing they are stable, multi-kingdom reservoirs harboring MDROs and shaped by environmental factors.

BacTaxID provides a universal framework for bacterial classification using whole-genome k-mer sketches, achieving concordance with species and sub-species systems and capturing strain-level diversity.

This study identifies multireplicon plasmids in bacterial genomes, showing they are common, gene-rich, and shaped by predictable fusion rules that influence AMR spread.

The paper shows plasmid mutation rates increase logarithmically with copy number, outpacing segregational drift, enhancing bacterial evolvability.

The paper analyzes plasmid copy numbers across bacterial species and identifies a universal scaling law linking copy number and plasmid size.

The study analyzes the gut resistome of the Wayampi, revealing similar antibiotic resistance gene richness to Europeans but higher metal resistance gene diversity, highlighting shared and distinct resistance patterns.

This study shows that scRNA-seq on FFPE tissue is suitable for analyzing breast cancer, identifying a subpopulation of multi-ciliated cells in invasive ductal carcinomas.

The paper presents a comprehensive multi-omics dataset of healthy individuals, revealing sex and age influences and providing reference ranges for omics features.

The paper identifies bacteriocin distribution patterns in Enterococcus faecium and Enterococcus lactis genomes using a tailored database and reveals associations with antibiotic resistance and mobile genetic elements.

The paper investigates the long-term dynamics of Serratia marcescens complex in hospital sinks, identifying persistent strains linked to outbreaks and revealing new insights into their ecology and resistance gene acquisition.

The paper introduces a computational pipeline for consistent plasmid typing using long-read sequencing data, enabling classification of novel and known plasmid types.

This study analyzes the phylogenetic structure and evolution of Klebsiella pneumoniae clonal groups 14 and 15 using genomic data, revealing independent evolutionary trajectories and the role of plasmids and accessory genomes in their diversification.

PATO is a toolkit for pangenome analysis that efficiently handles thousands of genomes, offering fast and accurate methods for core-genome definition, population structure, and gene sharedness networks.

The paper analyzes optrA-carrying Enterococcus faecalis genomes to identify common genetic features and a chromosomal hotspot for optrA acquisition across diverse hosts and regions.

The paper develops a 3D-based method to predict antibiotic resistance determinants in the human intestinal microbiota and identifies resistotypes in a cohort.