V. Mustonen

Quantifying massively parallel microbial growth with spatially mediated interactions

The paper quantifies microbial growth variability across spatial locations using machine learning and develops a spatial consumer-resource model to explain growth patterns and infer intrinsic growth parameters.

Turnover shapes evolution of birth and death rates

This paper reformulates population genetics by incorporating turnover rates, showing their evolutionary importance and how they influence fixation, substitution, and demographic transitions.

Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes

This study characterizes intra-tumor heterogeneity across 2,658 human cancer genomes, identifying subclonal mutations and evolutionary patterns across 38 cancer types.

Machine-learning prediction of resistance to sub-inhibitory antimicrobial concentrations from Escherichia coli genomes

This paper uses machine learning to predict E. coli growth under sub-inhibitory antimicrobial concentrations from genomic data, finding moderate to strong correlations but highlighting remaining missing heritability.

Genomic epidemiology and evolution of Escherichia coli in wild animals

This study analyzes whole genome sequencing data of commensal E. coli from wild animals to explore population structure, host associations, and the presence of virulence and antibiotic resistance genes.

Strong selective environments determine evolutionary outcome in time-dependent fitness seascapes

This study shows that strong selective agents drive evolutionary outcomes in time-dependent fitness seascapes, with implications for predicting and mitigating drug resistance.

Drug-induced resistance evolution necessitates less aggressive treatment

This paper shows that aggressive drug treatments can increase resistance evolution by altering mutation rates, and proposes an optimal treatment strategy that minimizes resistance risk.

Repeatable ecological dynamics govern response of experimental community to antibiotic pulse perturbation

The paper studies how antibiotic pulses affect microbial communities, finding repeatable responses driven by species traits and immigration, alongside rapid within-species evolution.

Eco-evolutionary control of pathogens

The paper develops a fitness model to analyze eco-evolutionary control of pathogens, showing how control strategies depend on mutation rates and population size.

The Repertoire of Mutational Signatures in Human Cancer

The paper characterizes 49 mutational signatures in human cancer using a large dataset of somatic mutations, revealing associations with exposures and DNA repair mechanisms and identifying signatures of unknown origin.

The evolutionary history of 2,658 cancers

This study uses whole-genome sequencing of cancer samples to reconstruct the evolutionary history of 39 cancer types, identifying early and late-stage mutational patterns and driver genes.