Dennis D. Krutkin

Co-occurrence network multicollinearity artefacts using centered log-ratio transformation

The paper shows that zero substitution before clr transformation creates multicollinearity artefacts in co-occurrence networks and demonstrates that rclr eliminates these artefacts.

ARGus: A Co-assembly workflow for MAG generation, ARG detection, and virulence analysis

ARGus co-assembles metagenomes to generate MAGs, detect ARGs, and analyze virulence factors in environmental samples.

Moisture and material shape microbial communities in the built environment through disturbance-productivity relationships

The paper tests how moisture and building materials affect microbial diversity in the built environment, finding that disturbances reduce diversity in some cases and vary by material and microbe type.

To impute or not to impute in untargeted metabolomics - that is the compositional question

This study evaluates imputation methods for untargeted metabolomics data, finding that kNN and RF imputation perform poorly with missing data, especially MNAR, and that missing data proportion significantly affects accuracy.

Genetic hypogonadal (Gnrh1 hpg) mouse model uncovers influence of reproductive axis on maturation of the gut microbiome during puberty

This study uses a genetic hypogonadal mouse model to show that the HPG axis influences gut microbiome maturation during puberty, with some sex differences independent of the HPG axis and age also playing a role.