Jukka Corander

The paper identifies invasion-associated genetic variants in pneumococcal lineages by separating serotype and lineage effects, highlighting candidate determinants for experimental investigation.

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.

This study traces the evolutionary path from ST131-B to ST131-C clades in E. coli by analyzing genomic data from ST131-B0 isolates, revealing genetic changes associated with antibiotic resistance and host adaptation.

The paper develops a model to analyze pangenome dynamics and finds that differences in bacterial pangenomes are mainly due to variation in the number of rapidly exchanged genes.

This study tracks the 28-year evolution of a Burkholderia pseudomallei strain in sterile water, identifying genetic changes and metabolic adaptations to nutrient-depletion.

This paper uses machine learning to predict the prevalence of ST131-C in UTIs and BSIs using antimicrobial susceptibility data, finding a link between UTI prevalence and BSI burden.

This study investigates the translocation of Pseudomonas aeruginosa between body sites in hospitalized patients, finding that clones often move from the respiratory tract to the gut.

The paper investigates the evolutionary dynamics of colibactin production and resistance in E. coli, showing clonal expansions linked to co-evolution between production and immunity.

The paper estimates the basic reproduction number (R0) for pandemic E. coli clones and finds that ST131-A has an R0 comparable to pandemic influenza viruses.

This study sequenced 4,475 H. influenzae isolates from Thailand and combined them with global data to show pervasive recombination and purifying selection, with MDR lineages widespread and not restricted to disease-causing subpopulations.

The paper identifies megaplasmids in Enterobacteriaceae species, showing they are self-transmissible, encode drug resistance, and may enhance bacterial competitiveness.

The paper characterizes a persistent, azole-resistant C. parapsilosis strain responsible for a hospital outbreak, identifying genetic mutations linked to antifungal resistance.

This paper reclassifies SHV β-lactamase alleles in K. pneumoniae genomes based on mutations, improving genotype-phenotype understanding and updating the Kleborate tool.

TRACS improves transmission inference by accurately estimating SNP-level genetic distances, outperforming existing methods in multiple datasets and revealing species-specific transmission rates between mothers and infants.

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

This paper develops a genomic autogenous vaccine for poultry to reduce Campylobacter, showing reduced extra-intestinal survival genes and meat surface survival in vaccinated flocks.

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.

The paper characterizes iuc3-carrying plasmids in Klebsiella pneumoniae isolates, identifying convergent plasmids with resistance and virulence genes and highlighting their global epidemiology.

The paper introduces a self-supervised deep learning framework for DNA sequence analysis that improves variant effect prediction and open chromatin region prediction across human and plant genomes.

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.

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 SINCOPA, a phylogeny-based method for detecting locus-specific selective sweeps in bacterial strains, and applies it to over 500 microbial genomes to identify sweeps in genes related to biofilm formation and environmental adaptation.

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

Mandrake reduces the dimensionality of large microbial genome datasets to visualize population structure, using both a pipeline and an interactive web application.

This study uses deep sequencing to analyze pneumococcal genetic diversity in infants and mothers, revealing transmission patterns and treatment impacts on resistant strains.

The paper introduces a pipeline for genomic epidemiology using mixed samples, showing comparable results to colony picks in a nosocomial setting.

This paper applies genome-wide association, prediction, and heritability analyses to bacterial data, identifying genetic factors influencing antibiotic resistance and within-host survival in Streptococcus pneumoniae.

The paper presents a population structure-aware method to classify genes in a bacterial pan-genome, revealing distinct evolutionary dynamics in 7,500 E. coli genomes.

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.