Sergio Arredondo-Alonso

The paper uses long-read sequencing to analyze plasmids and chromosomes in E. coli over two decades, revealing long-term plasmid-lineage associations and success strategies.

gplasCC classifies and reconstructs plasmids from short-read sequencing data across multiple bacterial species using simplified plasmidEC and species-specific databases.

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

This paper introduces plasmidEC and gplas2 to accurately predict and reconstruct antibiotic resistance plasmids in E. coli using short-read sequencing data, outperforming existing methods.

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 benchmarks six plasmid prediction tools for E. coli short-read data, finding that none reliably reconstruct all plasmids, especially those carrying antibiotic resistance genes.

This study quantifies the modes of vanA-type vancomycin resistance dissemination in Dutch hospitals, finding clonal spread as the dominant mechanism with significant contributions from horizontal gene transfer.

This paper uses genome-wide co-evolution analysis to identify genomic rearrangements in Enterococcus faecium, linking them to adaptation to hospital environments.

gplas separates plasmid contigs from bacterial genomes using short-read data to enable plasmid epidemiology analysis.

This study analyzes the genomes of Enterococcus faecium strains to understand their adaptive evolution, identifying plasmids as key indicators of host specificity through population-wide genomic analysis.