Papers - RENCI/fuse-dashboard-immcellfie GitHub Wiki
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
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
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
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
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
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
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