Other Organisms

Supplementary Table 1: Available predictive genome-scale metabolic network reconstructions

Adam M. Feist, Markus J. Herrgard, Ines Thiele, Jennie L. Reed, Bernhard Ø. Palsson "Reconstruction of Biochemical Networks in Microbial Organisms", Nat. Rev. Microbiol. 2009 Feb;7(2):129-43.

Supplementary Table 2 - Common issues encountered during metabolic network reconstruction

This list includes genome-scale metabolic network reconstructions that have been converted into predictive genome-scale models and whose predictive power has been validated against experimental data.

This table is managed and updated by Jonathan Monk (jmonk@ucsd.edu). Please send me an email with any missing information.

[Bacteria] [Archaea] [Eukaryotes]

Reconstruction status: 

P = In progress, D = draft, F = Finish

Compartment abbreviations:

* a: acidocalcisome * c: cytoplasm * e: extra-organism/extracellular * f: flagellum * g: golgi * h: chloroplast * i: apicoplast * l: lysosome * m: mitochondrion * n: nucleus * o: glyoxysomes * p: periplasm * r: ER * s: plastid *u: thykaloid lumen * v: vacuole * x: peroxisome * y: glycosome * gm: golgi membrane * mm: mitochondrial membrane * nm: nuclear membrane * pm: plasma membrane * rm: ER membrane * vm: vacuolar membrane * xm: peroxisomal membrane

Multiple cell type interaction models

Human alveolar macrophage and M. tuburculosis: Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N. *Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions*. Mol Syst Biol. 2010 Oct 19;6:422. PMID: [20959820]
Mesophyll and bundle sheath cells in C4 plants: de Oliveira Dal'molin CG, Quek LE, Palfreyman RW, Brumbley SM, Nielsen LK. C4GEM, *a Genome-Scale Metabolic Model to Study C4 Plant Metabolism*. Plant Physiol. 2010 Dec;154(4):1871-85. PMID: [20974891] 
Human brain cells: Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, König R, Palsson BØ. *Large-scale in silico modeling of metabolic interactions between cell types in the human brain*. Nat Biotechnol. 2010 Dec;28(12):1279-85. PMID: [21102456]

Smaller scale reconstructions/models

Aspergillus niger: David H, Akesson M, Nielsen J, "Reconstruction of the central metabolism of Aspergillus niger", European Journal of Biochemistry, 270(21):4243-4253 (2003). PMID: [14622289].
Chlamydomonas rheinhardtii: Boyle NR, Morgan JA. "Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii.",BMC Syst Biol. 2009 Jan 7;3(1):4. PMID: [19128495].
Desulfovibrio vulgaris/Methanococcus maripaludis: Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, Leigh JA, Stahl DA. "Metabolic modeling of a mutualistic microbial community" Mol Syst Biol. 2007;3:92. PMID: [17353934] 
Pichia pastoris: Tortajada M, Llaneras F, Pico J. "Validation of a constraint-based model of Pichia pastors metabolism under data scarcity", BMC Syst Biol, 4:115 (2010). PMID: [20716335] 
Synechocystis sp PCC 6803: Shastri AA, Morgan JA, “Flux balance analysis of photoautotrophic metabolism”, Biotechnol Prog, 21(6):1617-1626 (2005). PMID: [16321043].
Synechocystis sp PCC 6803: Hong SJ, Lee CG. “Evaluation of Central Metabolism Based on a Genomic Database of Synechocystis PCC6803”, Biotechnol Bioprocess Eng, 12:165-173 (2007). 
Trypanosoma cruzi: Roberts SB, Robichaux JL, Chavali AK, Manque PA, Lee V, Lara AM, Papin JA, Buck GA. "Proteomic and network analysis characterize stage-specific metabolism in Trypanosoma cruzi". BMC Syst Biol. 2009 May 16;3:52. PMID: [19445715]. 
Zymomonas mobilis: Tsantili IC, Karim MN, Klapa MI. “Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis.” Microb. Cell Fact. 6:8 (2007). PMID: [17349037].

Metabolic reconstructions with no modeling:

Mannheimia succiniproducens: Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ, "The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens" Nature Biotechnology, 22:1275-1281 (2004). PMID: [15378067]
Plasmodium falciparum: Yeh I, Hanekamp T, Tsoka S, Karp PD, Altman RB, "Computational analysis of Plasmodium falciparum metabolism: organizing genomic information to facilitate drug discovery" Genome Research, 14:917-924 (2004). PMID: [15078855]
Human: Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD, "Computational prediction of human metabolic pathways from the complete human genome" Genome Biology, 6:R2.1-R2.17 (2004). PMID: [15642094]
Methanococcus jannaschii: Tsoka S, Simon D, Ouzounis CA, "Automated metabolic reconstruction for Methanococcus jannaschii" Archaea, 1:223-229 (2004). PMID: [15810431]
Bos taurus: Soh S, Lewin HA, *Reconstruction of metabolic pathways for the cattle genome BMC Systems Biology*. 2009 Mar 12;3:33. PMID: [19284618]
Fish (5 species: Zebrafish, Medaka, Takifugu, Tetraodon, Stickleback) Li S, Pozhitkov A, Ryan RA, Manning CS, Brown-Peterson N, Brouwer M. *Constructing a fish metabolic network model*. Genome Biol. 2010 Nov 29;11(11):R115. PMID: [21114829]

Reconstructions and models of other cellular networks:

Jak-Stat signaling network: Papin, J.A. and Palsson, B.Ø., "The JAK-STAT Signaling Network in the Human B-Cell: An Extreme Signaling Pathway Analysis ", Biophysical Journal, 87: 37-46(2004). PMID: [15240442]
Toll-like receptor signaling network: Li, F., Thiele, I., Jamshidi, N., and Palsson, B.Ø.,"Identification of Potential Pathway Mediation Targets in Toll-Like Receptor Signaling", PLoS Comp Biol. PMID:[19229310]
Transcriptional and translational machinery: Thiele, I., Jamshidi, N., Fleming, M.T., Palsson, B.Ø., "Genome-scale reconstruction of E. coli 's transcriptional and translational machinery: A knowledge-base, its mathematical formulation, and its functional characterization.", PLoS Comp Biol. PMID: [19282977]

Integrated networks and models:

Metabolism and transcriptional regulation

• Covert MW, Knight EM, Reed JL, Herrgård MJ, Palsson BØ. "Integrating high-throughput and computational data elucidates bacterial networks." Nature. 2004. 429(6987): 92-6. PMID: [15129285]
• Goelzer A, Bekkal Brikci F, Martin-Verstraete I, Noirot P, Bessières P, Aymerich S, Fromion V. "Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis." BMC Syst Biol. 2008 Feb 26;2:20. PMID: [18302748]
• Chandrasekaran S, Price ND. "Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis." Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17845-50. PMID: [20876091]
• Barua D, Kim J, Reed JL. "An automated phenotype-driven approach (GeneForce) for refining metabolic and regulatory models." PLoS Comput Biol. 2010 Oct 28;6(10):e1000970. PMID: [21060853]

Metabolism, signaling, transcriptional regulation 

• Covert MW, Xiao N, Chen TJ, and Karr JR. "Integrated Flux Balance Analysis Model of Escherichia coli" Bioinformatics. 2008. 24(18): 2044-2050. PMID: [18621757]
• Min Lee J, Gianchandani EP, Eddy JA, Papin JA. " Dynamic analysis of integrated signaling, metabolic, and regulatory networks." PLoS Comput Biol. 2008 May 23;4(5):e1000086. [18483615]

Additional Review Articles on Metabolic Reconstructions and Methods

Computational Modeling Software and Tools

• Grafahrend-Belau E, Klukas C, Junker BH, Schreiber F. "FBA-SimVis Interactive visualisation of constraint-based metabolic models." Bioinformatics. 2009 Jul 3 [19578041]
• Le Fèvre F, Smidtas S, Combe C, Durot M, d'Alché-Buc F, Schachter V. "CycSim-an online tool for exploring and experimenting with genome-scale metabolic models." Bioinformatics. 2009 Aug 1;25(15):1987-8. [19420054]