Computational Framework of the Human and Animal Gut Microbiota
  • Global metabolic interaction network of the mammalian gut microbiota
  • Click for download (linked to SymBio.info)
  • References:
  • R. Lim, J. J. T. Cabatbat, T. L. P. Martin, H. Kim, S. Kim, J. Sung, C.-M. Ghim, P.-J. Kim, “Large-scale metabolic interaction network of the mouse and human gut microbiota”, Sci. Data 7, 204 (2020), Link
    J. Sung, S. Kim, J. J. T. Cabatbat, S. Jang, Y.-S. Jin, G. Y. Jung, N. Chia, P.-J. Kim, “Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis”, Nat. Commun. 8, 15393 (2017), Link
Mathematical Model of the Plant Circadian System
  • MF2015: Circadian clock model of plant Arabidopsis thaliana
  • Click for download (MF2015 and the kernel in MATLAB format)
  • Reference: M. Foo, D. E. Somers, P.-J. Kim, “Kernel architecture of the genetic circuitry of the Arabidopsis circadian system”, PLOS Comput. Biol. 12, e1004748 (2016), Link
Large-scale Analysis of Food and Nutrients
  • Recommendable foods for omnivorous and vegetarian diets of a physically active 20-year-old male with standard height and weight
  • Click for download
  • Source code for generating irreducible food sets to calculate nutritional fitness
  • Click for download
  • Visualization App from an NIH Codeathon Project led by Adam Thomas (NIH)
  • Click for app
  • References:
  • S. Kim, M. F. Fenech, P.-J. Kim, “Nutritionally recommended food for semi- to strict vegetarian diets based on large-scale nutrient composition data”, Sci. Rep. 8, 4344 (2018), Link
    S. Kim, J. Sung, M. Foo, Y.-S. Jin, P.-J. Kim, “Uncovering the nutritional landscape of food”, PLOS ONE 10, e0118697 (2015), Link
    (Visualization App) T. Antar, L. Chan, E. Jason, D. Moraczewski, K. Pu, E. Ruan, A. G. Thomas, “Visualizing the nutritional landscape of food: an NIH Codeathon Project” (2021), Link