Chen, Jin, Jose A. Gomez, Kai Hoeffner, Paul I. Barton, and Michael A. Henson. "Metabolic modeling of synthesis gas fermentation in bubble column reactors." Biotechnology for biofuels 8, no. 1 (2015): 89.
[Link]
Code can be downloaded here: Syngas bubble column model
Chen, Jin, Jose A. Gomez, Kai Hoeffner, Poonam Phalak, Paul I. Barton, and Michael A. Henson. "Spatiotemporal modeling of microbial metabolism." BMC systems biology 10, no. 1 (2016): 21.
[PDF]
Code can be downloaded here: Syngas bubble column model; Pseudomonas aeruginosa biofilm model
Phalak, Poonam, Jin Chen, Ross P. Carlson, and Michael A. Henson. "Metabolic modeling of a chronic wound biofilm consortium predicts spatial partitioning of bacterial species." BMC systems biology 10, no. 1 (2016): 90.
[PDF]
Code can be downloaded here: Pseudomonas aeruginosa/Staphylococcus Aureus biofilm model
Chen, Jin, James Daniell, Derek Griffin, Xueliang Li, and Michael A. Henson. "Experimental testing of a spatiotemporal metabolic model for carbon monoxide fermentation with Clostridium autoethanogenum." Biochemical Engineering Journal (2017).
[Link]
Code can be downloaded here: Gas fermentation simulation with a published GEM of Clostridium autoethanogenum
Xiangan Li and Michael A. Henson. "Metabolic modeling of bacterial co-culture systems predicts enhanced carbon monoxide-to-butyrate conversion compared to monoculture systems." Biochemical Engineering Journal (2019). [Link]
Code can be downloaded here: Bacterial co-culture model
Michael A. Henson. “Computational Modeling of the Gut Microbiota Reveals Putative Metabolic Mechanisms of Recurrent Clostridioides difficile Infection.” PLOS Computational Biology (2021).
[Link]
Code can be downloaded here: C. difficile gut microbiota models