Fernando de la Cruz

This study identifies metabolic signatures in MASLD using stool metagenomes, showing shifts in butyrate and alcohol-producing pathways linked to microbial gene content and plasmid exchange.

The paper uses experimental evolution to show that circadian clock mutations in cyanobacteria enhance growth under continuous light by altering transcriptomic and metabolic responses.

JINA is a workflow that integrates existing tools to analyze bacterial genomes via a network approach, enabling visualization and identification of genomic patterns and associations.

This study identifies Pantoea as a core endophytic bacterium vertically transmitted through wheat seeds, demonstrating its intergenerational transfer and specificity.

The paper introduces a method to measure pangenome relatedness using Jaccard Index and a novel distance metric to capture both vertical and horizontal gene transfer in Salmonella Typhi, enhancing genomic surveillance.

COPLA assigns plasmids to existing PTUs and identifies potential new PTUs, with 41% of samples assigned and 4% suggesting new classifications.

This paper describes a method for task switching in engineered bacteria using plasmid copy number manipulation and presents computational simulations of the model.