Transcriptome-guided parsimonious flux analysis improves predictions with metabolic networks in complex environments. - Matthew L. Jenior; Thomas J. Moutinho Jr.; Bonnie V. Dougherty; Jason A. Papin (PLoS Comput. Biol., 2020)

Medusa: Software to build and analyze ensembles of genome-scale metabolic network reconstructions. - Gregory L. Medlock; Thomas J. Moutinho Jr.; Jason A. Papin (PLoS Comput. Biol., 2020)

Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions. - Thomas J. Moutinho Jr.; Benjamin C. Neubert; Matthew L. Jenior; Jason A. Papin (PLoS Comput. Biol., 2022)