Juan D. Tibocha‐Bonilla

Genome-scale mapping of plant transcription factor effector domains reveals conserved regulatory principles across eukaryotes

The paper maps transcription factor effector domains in plants and compares their function across eukaryotes, revealing conserved and lineage-specific regulatory principles.

Human Genome-Scale Models of Metabolism and Gene Expression Reveal Resource Constraints of Cancer Cell Lines

The paper develops human ME-Models that integrate gene expression and metabolism, showing improved growth-rate predictions and biological plausibility in cancer cell lines.

Multi-strain Analysis of Pseudomonas putida Reveals the Metabolic and Genetic Diversity of the Species.

This study analyzes 164 Pseudomonas putida strains to reveal metabolic and genetic diversity, curating GEMs and identifying strain-specific adaptations for biotechnology applications.

Proteome allocation of the microbiome reveals how diet and metabolic dysbiosis impact disease

The paper uses ME-models to predict proteome allocation in the gut microbiome and identifies taxa associated with metabolic changes in IBD patients.