Computational Framework of the Human and Animal Gut Microbiota
  • Global metabolic interaction network of the mammalian gut microbiota
  • Click for download (linked to
  • 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
  • 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