Tommi Mäklin

This paper introduces a Bayesian ordered logistic regression GWAS model for bacterial antimicrobial resistance phenotypes, showing improved variant discovery and MIC prediction by accounting for threshold-dependent effects.

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 paper introduces a novel algorithm for approximate local alignment search using k-bounded matching statistics, showing it is as fast and accurate as state-of-the-art tools in bacterial genomics tasks.

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.

This paper introduces SKA2, a method for rapid and accurate genotyping of bacterial populations, showing superior variant recall and no false positives in outbreak simulations.

Themisto is a scalable k-mer index for pseudoalignment against bacterial genomes, outperforming existing tools in speed, memory use, and recall.

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

The paper introduces mSWEEP, a method for high-resolution bacterial lineage quantification from plate sweeps, showing improved accuracy in detecting and estimating abundances of bacterial lineages.