1. 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
  2. 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
  3. 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
  4. Henson, Michael A., and Poonam Phalak. "Byproduct Cross Feeding and Community Stability in an In Silico Biofilm Model of the Gut Microbiome." Processes 5, no. 1 (2017): 13. [Link]
    Code can be downloaded here: Bacteroides thetaiotaomicron/Faecalibacterium prausnitzii/Escherichiacoli gut microbiome model
  5. 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
  6. Xiangan Li, Derek Griffin, Xueliang Li, and Michael A. Henson. "Incorporating hydrodynamics into spatiotemporal metabolic models of bubble column gas fermentation." Biotechnology and Bioengineering (2018). [Link]
    Code can be downloaded here: Bubble column gas fermentation model with gas phase hydrodynamics and published GEM of C. ljungdahlii (updated)