Matthew L. Jenior

The paper develops a systems biology pipeline to design bacterial consortia that protect against severe Clostridioides difficile infection by targeting amino acid cross-feeding.

Reconstructor is a user-friendly COBRApy tool for automated genome-scale metabolic network reconstruction with gap-filling, generating high-quality models for further biological analysis.

The paper introduces a method to quantify genomic, biochemical, and phenotypic evidence for metabolic network reconstructions, improving accuracy by integrating continuous evidence.

RIPTiDe improves metabolic predictions by integrating transcriptomic data with flux minimization to identify cost-effective metabolic pathways in bacteria without requiring knowledge of growth conditions.

This study introduces PROTEAN, a method to analyze metabolic capabilities of Lactobacillus strains, revealing site-specific differences in predicted metabolic production.