Papers - RENCI/fuse-dashboard-immcellfie Wiki

  1. Thiele I, Palsson BØ. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc. 5:93–121. 2010. doi: 10.1016/j.crmeth.2021.100040
  2. Norsigian CJ, Fang X, Seif Y, Monk JM, Palsson BØ. A workflow for generating multi-strain genome-scale metabolic models of prokaryotes. Nat Protoc. 15:1–14. 2020. doi: 10.1016/j.crmeth.2021.100040
  3. Price ND, Reed JL, Palsson BØ. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol. 2:886–897. 2004. doi: 10.1016/j.crmeth.2021.100040
  4. Lewis NE, Nagarajan H, Palsson BØ. Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods. Nature Reviews Microbiology. pp. 291–305. 2012. doi: 10.1016/j.crmeth.2021.100040
  5. O’Brien EJ, Monk JM, Palsson BØ. Using genome-scale models to predict biological capabilities. Cell. 161:971–987. 2015. doi: 10.1016/j.crmeth.2021.100040
  6. Richelle A, Kellman BP, Wenzel AT, Chiang AWT, Reagan T, Gutierrez JM, Joshi C, Li S, Liu JK, Masson H, Lee J, Li Z, Heirendt L, Trefois C, Juarez EF, Bath T, Borland D, Mesirov JP, Robasky K, Lewis NE. Model-based assessment of mammalian cell metabolic functionalities using omics data. Cell Rep Methods. 5:93–121. 2021. doi: 10.1016/j.crmeth.2021.100040
  7. Richelle A, Chiang AWT, Kuo C-C, Lewis NE. Increasing consensus of context-specific metabolic models by integrating data-inferred cell functions. PLoS Comput Biol. 15:e1006867. 2019. doi: 10.1016/j.crmeth.2021.100040