Table 1.
Overview of some recent literature papers on the modeling and computational analysis of metabolism.
| Pathway/Aim ofthe Model | Cell Type/Organ | Organism | Modeling Approach &Methodology | ExperimentalData | Reference |
|---|---|---|---|---|---|
| Glycolysis | - | T. brucei | CM, ODE | L | Achcar et al. [159] |
| GW metabolic network and succinic acid production | - | S. cerevisiae | GW, FBA | M | Agren et al. [58] |
| GW metabolic network | - | A. niger | GW, FBA | L | Andersen et al. [173] |
| Mitochondrial energy metabolism, Na+/Ca2+ cycle, K+ cycle | Heart, liver | B. taurus, S. scrofa, R. norvegicus | CM, DAE, PE, SA | L, M | Bazil et al. [80] |
| OXPHOS | Cardiomyocytes | R. norvegicus | CM, ODE | L | Beard [156] |
| Electron transport chain | Heart homogenates | R. norvegicus | CM, ODE, CRL | L, M | Chang et al. [154] |
| Glycolysis, OXPHOS | Not specified | Eukaryotic, H. sapiens | CM, Control theory | L | Cloutier et al. [200] |
| Bow-tie architecture of metabolism | Not specified | H. sapiens | GW, Topological analysis | L | Csete et al. [118] |
| Central metabolism | - | Yeast | CM, FBA | L | Damiani et al. [65] |
| Energy metabolism | Skeletal muscle cell | Mammal | CM, PDE | L | Dasika et al. [165] |
| Glycolysis and pentose phosphate pathway | - | E. coli | CM, ODE, SA | L | Degenring et al. [179] |
| Glycolysis and pentose phosphate pathway | - | E. coli | CM, ODE, SA | L | Degenring et al. [179] |
| Biosynthesis of valine and leucine | - | C. glutaminicum | CM, ODE, SDE | M | Dräger et al. [76] |
| Anabolic, catabolic, chemiosmosis pathways | - | E. coli | GW, Control theory | M | Federowicw et al. [202] |
| Small world behavior of metabolism | Not specified | H. sapiens | GW, Topological analysis | L | Fell et al. [116] |
| GW metabolic network | Not specified | H. sapiens | GW, FBA | L | Duarte et al. [39] |
| GW metabolic network | - | E. coli MG1655 | GW, FBA | M | Edwards and Palsson [175] |
| GW metabolic network | - | H. influenzae | GW, FBA | L | Edwards et al. [36] |
| Cancer metabolic networks | Various (NCI-60 collection) | H. sapiens | Network reconstruction, FBA, gene (pair) analysis | L | Folger et al. [208] |
| GW metabolic network HepatoNet1 | Hepatocytes | H. sapiens | GW. Network reconstruction | L | Gille et al. [220] |
| Cytochrome bc1 complex, ROS production | Muscle, heart, liver, kidney, brain | R. norvegicus | CM, ODE | L | Guillaud et al. [153] |
| GW metabolic network EHMN | Not specified | H. sapiens | GW, Network reconstruction | L | Hao et al. [221] |
| GW metabolic network | - | S. cerevisiae S288c | GW, Network reconstruction, FBA | L | Heavner et al. [3] |
| GW metabolic network | - | S. cerevisiae | Network reconstruction | L | Herrgård et al. [43] |
| Topological properties of metabolism | - | 43 different organisms | GW, Topological analysis | L | Jeong et al. [27] |
| Glycolysis, OXPHOS | - | Not specified | CM, ODE, Game theory | - | Kareva [189] |
| Whole-cell life cycle model | - | M. genitalium | GW, FBA, ODE | L, M | Karr et al. [204] |
| Glycolysis, pentose phosphate pathway | - | T. brucei | CM, ODE | L | Kerkhoven et al. [64] |
| Energy metabolism | Colorectal cells | H. sapiens | CM, FBA, EM | M | Khazaei et al. [214] |
| GW metabolic network | - | Synechocystis sp. PCC 6803 | GW, FBA | L | Knoop et al. [37] |
| Glycolysis, gluconeogenesys, glycogen metabolism | Hepatocytes | H. sapiens | CM, ODE | L | König et al. [157] |
| Adenine nucleotide translocase | Heart mitochondria | B. taurus | CM, ODE, PE, SA | L | Metelkin et al. [152] |
| GW metabolic network | - | Z. mays L. subsp. mays | GW, Network reconstruction | L | Monaco et al. [40] |
| Xylose metabolism | - | L. lactis IO-1 | CM, ODE, SA | M | Oshiro et al. [183] |
| GW metabolic network | - | S. cerevisiae | GW, Network reconstruction, FBA | L | Österlund et al. [222] |
| GW metabolic network and succinic acid production | - | S. cerevisiae | GW, FBA | M | Otero et al. [57] |
| Topological properties of metabolism | - | 43 different organisms, E. coli | GW, Topological analysis | L | Ravasz et al. [122] |
| One-carbon metabolism, trans-sulfuration pathway, synthesis of glutathione | Hepatocyte | H. sapiens | CM, ODE | L | Reed et al. [158] |
| Glycolysis, TCA cycle, pentose phosphate pathway, glutaminolysis, OXPHOS | HeLa cell | H. sapiens | CM, FBA | M | Resendis-Antonio et al. [67] |
| Modularity of metabolism | Not specified | H. sapiens | GW, Topological analysis | L | Resendis-Antonio et al. [120] |
| GW metabolic network | Not specified | H. sapiens | GW, Network reconstruction | L | Sahoo et al. [223] |
| Acetone, butanol and ethanol production | - | C. acetobutylicum | CM, ODE, SA | M | Shinto et al. [184] |
| Cancer metabolic networks | Various (NCI-60 collection) | H. sapiens | FBA | L | Shlomi et al. [206] |
| GW metabolic network | - | S. cerevisiae | GW, FBA | L | Simeonidis et al. [130] |
| Glycolysis | - | S. cerevisiae | CM, ODE | M | Teusink et al. [62] |
| GW metabolic network | Not specified | H. sapiens | GW, FBA | L | Thiele et al. [4] |
| Primary metabolism | - | E. coli | CM, ODE, EM | - | Tran et al. [101] |
| Fueling reaction network | - | E. coli W3110 | CM, FBA | M | Varma et al. [174] |
| Reduced model of cell metabolism | - | - | CM, FBA | L | Vazquez et al. [61] |
| Small-world property of metabolism | - | E. coli | GW. Topological analysis | L | Wagner et al. [117] |
| GW metabolic network | - | C. glabrata | GW, FBA | L | Xu et al. [38] |
| Erythrocyte metabolism | Red blood cell | H. sapiens | Hybrid: ODE + MFA | - | Yugi et al. [166] |
| Mitochondrial energy metabolism | Various tissues | Mammal | CM, ODE | - | Yugi [224] |
| Modularity of metabolism | Not specified | H. sapiens | GW, Topological analysis | L | Zhao et al. [119] |
| ROS-induced ROS release in mitochondria network | Cardiomyocytes | C. porcellus | CM, ODE, PDE, RD, Finite Difference Method | M | Zhou et al. [164] |
Abbreviations. CM: Core model; CRL: Chemiosmotic Rate Law; DAE: Differential Algebraic Equations; EM: Ensemble modeling; FBA: Flux Balance Analysis; GW: Genome-wide model; L: experimental data obtained from literature; M: experimental data measured with ad hoc experiments; MFA: Metabolic Flux Analysis; ODE: Ordinary Differential Equations; PDE: Partial Differential Equations; PE: Parameter Estimation; SA: Sensitivity Analysis; SDE: Stochastic Differential Equations.