Jukka Corander

Integrating bacterial genomics and host transcriptomics links Burkholderia pseudomallei variation to melioidosis mortality and neutrophil responses

Identifying candidate genetic determinants associated with invasion in pneumococcal lineages

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

Ciprofloxacin resistance in Klebsiella pneumoniae: phenotype prediction from genotype and global distribution of resistance determinants

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.

Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage

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.

Rapid gene exchange explains differences in bacterial pangenome structure

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.

A 28-year evolution experiment on Burkholderia pseudomallei survival in nutrient-depleted sterile water

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

Machine learning based lineage prediction from AMR phenotypes for Escherichia coli ST131 clade C surveillance across infection types

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.

High frequency body site translocation of nosocomial Pseudomonas aeruginosa

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.

Co-evolution between colibactin production and resistance is linked to clonal expansions in Escherichia coli

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.

Basic reproduction number for pandemic Escherichia coli clones varies markedly and can be comparable to pandemic influenza viruses

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.

The major pathogen Haemophilus influenzae experiences pervasive recombination and purifying selection at local and global scales

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.

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

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

Genomic characterization of a persistent, azole-resistant C. parapsilosis strain responsible for a hospital outbreak during the first COVID-19 wave

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

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae

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

Enhanced metagenomics-enabled transmission inference with TRACS

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: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs

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

Detecting co-selection through excess linkage disequilibrium in bacterial genomes

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.

Convergence and global epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus.

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

Self-supervised learning for DNA sequences with circular dilated convolutional networks

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.

PlasmidEC and gplas2: An optimised short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli

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.

Identification of selective sweeps in bacteria

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.

Consistent typing of plasmids with the mge-cluster pipeline

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

Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation

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

Pneumococcal within-host diversity during colonisation, transmission and treatment

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

Genomic Epidemiology with Mixed Samples

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

Genome-wide association, prediction and heritability in bacteria

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.

Different evolutionary trends form the twilight zone of the bacterial pan-genome

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.

Mode and dynamics of vanA-type vancomycin-resistancedissemination in Dutch hospitals

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.

A comprehensive and high-quality collection of E. coli genomes and their genes

This paper curates a high-quality collection of over 10,000 E. coli and Shigella genomes to facilitate analysis of genetic diversity and lineage differences.

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

The paper estimates molecular clock rates in Campylobacter using a birthday problem analogy to quantify lineage turnover and diversification in environmental bacteria.