Whole-genome metabolic network reconstruction and constraint-based modeling

Methods in Enzymology

Volumn 500, Issue , 2011, Pages 411-433

  Haggart, Charles R ^a,b   Bartell, Jennifer A ^a   Saucerman, Jeffrey J ^a,b   Papin, Jason A ^a  

^a University of Virginia   (United States)

^b UNIVERSITY OF VIRGINIA   (United States)

Author keywords

Constraint based modeling; Flux balance analysis; Metabolic genome scale network reconstruction; Minimization of metabolic adjustment

Indexed keywords

PROTEIN;

ANALYTIC METHOD; ARTICLE; AUTOMATION; BAYES THEOREM; BIOMASS; COMPUTER MODEL; COMPUTER PROGRAM; CONSTRAINT BASED MODELING; DYNAMIC FLUX BALANCE ANALYSIS; EXPERIMENTAL DESIGN; FLUX BALANCE ANALYSIS; FLUX VARIABILITY ANALYSIS; GENOME; GENOME SCALE NETWORK RECONSTRUCTION; GENOMICS; IN VITRO STUDY; METABOLITE; METABOLOMICS; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEOMICS; SEQUENCE ALIGNMENT; STOICHIOMETRY; TRANSCRIPTOMICS; VALIDATION PROCESS;

EID: 80053069269     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385118-5.00021-9     Document Type: Chapter

References (56)

1. M.R. Andersen, M.L. Nielsen, and J. Nielsen Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger Mol. Syst. Biol. 4 2008 178 (Pubitemid 351441042)
2. S.A. Becker, and B.O. Palsson Context-specific metabolic networks are consistent with experiments PLoS Comput. Biol. 4 5 2008 e1000082
3. S.A. Becker, A.M. Feist, M.L. Mo, G. Hannum, and B.O. Palsson Quantitative prediction of cellular metabolism with constraint-based models: The COBRA toolbox Nat. Protoc. 2 3 2007 727 738 (Pubitemid 47040034)
4. A.P. Burgard, and C.D. Maranas Optimization-based framework for inferring and testing hypothesized metabolic objective functions Biotechnol. Bioeng. 82 6 2003 670 677 (Pubitemid 36576230)
5. A.P. Burgard, P. Pharkya, and C.D. Maranas Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Biotechnol. Bioeng. 84 6 2003 647 657 (Pubitemid 37420336)
6. D.E. Cameron, J.M. Urbach, and J.J. Mekalanos A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae Proc. Natl. Acad. Sci. USA 105 25 2008 8736 8741 (Pubitemid 351987749)
7. M. DeJongh, K. Formsma, P. Boillot, J. Gould, and M. Rycenga Toward the automated generation of genome-scale metabolic networks in the SEED BMC Bioinformatics 8 2007 139
8. N.C. Duarte, S.A. Becker, N. Jamshidi, I. Thiele, and M.L. Mo Global reconstruction of the human metabolic network based on genomic and bibliomic data Proc. Natl. Acad. Sci. USA 104 6 2007 1777 1782 (Pubitemid 46239855)
9. M. Durot, P.Y. Bourguignon, and V. Schachter Genome-scale models of bacterial metabolism: Reconstruction and applications FEMS Microbiol. Rev. 33 1 2009 164 190
10. A.M. Feist, and B.O. Palsson The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli Nat. Biotechnol. 26 6 2008 659 667 (Pubitemid 351824691)
11. A.M. Feist, M.J. Herrgard, I. Thiele, J.L. Reed, and B.O. Palsson Reconstruction of biochemical networks in microorganisms Nat. Rev. Microbiol. 7 2 2009 129 143
12. L.A. Gallagher, E. Ramage, M.A. Jacobs, R. Kaul, and M. Brittnacher A comprehensive transposon mutant library of Francisella novicida, a bioweapon surrogate Proc. Natl. Acad. Sci. USA 104 3 2007 1009 1014 (Pubitemid 46154727)
13. E.P. Gianchandani, M.A. Oberhardt, A.P. Burgard, C.D. Maranas, and J.A. Papin Predicting biological system objectives de novo from internal state measurements BMC Bioinformatics 9 2008 43
14. M.G. Giglio, C.W. Collmer, J. Lomax, and A. Ireland Applying the Gene Ontology in microbial annotation Trends Microbiol. 17 7 2009 262 268
15. O. Gonzalez, T. Oberwinkler, L. Mansueto, F. Pfeiffer, and E. Mendoza Characterization of growth and metabolism of the haloalkaliphile Natronomonas pharaonis PLoS Comput. Biol. 6 6 2010 e1000799
16. T. Hao, H.W. Ma, X.M. Zhao, and I. Goryanin Compartmentalization of the Edinburgh Human Metabolic Network BMC Bioinformatics 11 2010 393
17. C.S. Henry, J.F. Zinner, M.P. Cohoon, and R.L. Stevens iBsu1103: A new genome-scale metabolic model of Bacillus subtilis based on SEED annotations Genome Biol. 10 6 2009 R69
18. M.J. Herrgard, N. Swainston, P. Dobson, W.B. Dunn, and K.Y. Arga A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology Nat. Biotechnol. 26 10 2008 1155 1160
19. M.A. Jacobs, A. Alwood, I. Thaipisuttikul, D. Spencer, and E. Haugen Comprehensive transposon mutant library of Pseudomonas aeruginosa Proc. Natl. Acad. Sci. USA 100 24 2003 14339 14344 (Pubitemid 37499238)
20. M.D. Jankowski, C.S. Henry, L.J. Broadbelt, and V. Hatzimanikatis Group contribution method for thermodynamic analysis of complex metabolic networks Biophys. J. 95 3 2008 1487 1499
21. L. Jerby, T. Shlomi, and E. Ruppin Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism Mol. Syst. Biol. 6 2010 401
22. P.D. Karp, S.M. Paley, M. Krummenacker, M. Latendresse, and J.M. Dale Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology Brief. Bioinform. 11 1 2010 40 79
23. K.J. Kauffman, P. Prakash, and J.S. Edwards Advances in flux balance analysis Curr. Opin. Biotechnol. 14 5 2003 491 496 (Pubitemid 37298033)
24. M. Kircher, and J. Kelso High-throughput DNA sequencing - Concepts and limitations Bioessays 32 6 2010 524 536
25. A.L. Knorr, R. Jain, and R. Srivastava Bayesian-based selection of metabolic objective functions Bioinformatics 23 3 2007 351 357 (Pubitemid 46323158)
26. A. Kuzniar, R.C. van Ham, S. Pongor, and J.A. Leunissen The quest for orthologs: Finding the corresponding gene across genomes Trends Genet. 24 11 2008 539 551
27. J.M. Lee, E.P. Gianchandani, and J.A. Papin Flux balance analysis in the era of metabolomics Brief. Bioinform. 7 2 2006 140 150 (Pubitemid 44404880)
28. D.S. Lun, G. Rockwell, N.J. Guido, M. Baym, and J.A. Kelner Large-scale identification of genetic design strategies using local search Mol. Syst. Biol. 5 2009 296
29. R. Mahadevan, and C.H. Schilling The effects of alternate optimal solutions in constraint-based genome-scale metabolic models Metab. Eng. 5 4 2003 264 276 (Pubitemid 38122488)
30. R. Mahadevan, J.S. Edwards, and F.J. Doyle 3rd Dynamic flux balance analysis of diauxic growth in Escherichia coli Biophys. J. 83 3 2002 1331 1340 (Pubitemid 34977706)
31. T. Niittylae, B. Chaudhuri, U. Sauer, and W.B. Frommer Comparison of quantitative metabolite imaging tools and carbon-13 techniques for fluxomics Methods Mol. Biol. 553 2009 355 372
32. M.A. Oberhardt, J. Puchalka, K.E. Fryer, V.A. Martins dos Santos, and J.A. Papin Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1 J. Bacteriol. 190 8 2008 2790 2803 (Pubitemid 351508178)
33. M.A. Oberhardt, A.K. Chavali, and J.A. Papin Flux balance analysis: Interrogating genome-scale metabolic networks Methods Mol. Biol. 500 2009 61 80
34. M.A. Oberhardt, J.B. Goldberg, M. Hogardt, and J.A. Papin Metabolic network analysis of Pseudomonas aeruginosa during chronic cystic fibrosis lung infection J. Bacteriol. 192 20 2010 5534 5548
35. J.D. Orth, I. Thiele, and B.O. Palsson What is flux balance analysis? Nat. Biotechnol. 28 3 2010 245 248
36. J.A. Papin, N.D. Price, S.J. Wiback, D.A. Fell, and B.O. Palsson Metabolic pathways in the post-genome era Trends Biochem. Sci. 28 5 2003 250 258 (Pubitemid 36588667)
37. K.R. Patil, I. Rocha, J. Forster, and J. Nielsen Evolutionary programming as a platform for in silico metabolic engineering BMC Bioinformatics 6 2005 308
38. P. Pharkya, and C.D. Maranas An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems Metab. Eng. 8 1 2006 1 13 (Pubitemid 43017837)
39. P. Pharkya, A.P. Burgard, and C.D. Maranas OptStrain: A computational framework for redesign of microbial production systems Genome Res. 14 11 2004 2367 2376 (Pubitemid 39517344)
40. N.D. Price, J.A. Papin, and B.O. Palsson Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis Genome Res. 12 5 2002 760 769 (Pubitemid 34546463)
41. N.D. Price, J.L. Reed, and B.O. Palsson Genome-scale models of microbial cells: Evaluating the consequences of constraints Nat. Rev. Microbiol. 2 11 2004 886 897 (Pubitemid 39567269)
42. K. Raman, and N. Chandra Flux balance analysis of biological systems: Applications and challenges Brief. Bioinform. 10 4 2009 435 449
43. I. Rocha, J. Forster, and J. Nielsen Design and application of genome-scale reconstructed metabolic models Methods Mol. Biol. 416 2008 409 431
44. I. Rocha, P. Maia, P. Evangelista, P. Vilaca, and S. Soares OptFlux: An open-source software platform for in silico metabolic engineering BMC Syst. Biol. 4 2010 45
45. J.M. Savinell, and B.O. Palsson Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods J. Theor. Biol. 155 2 1992 201 214
46. R. Schuetz, L. Kuepfer, and U. Sauer Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Mol. Syst. Biol. 3 2007 119
47. D. Segre, D. Vitkup, and G.M. Church Analysis of optimality in natural and perturbed metabolic networks Proc. Natl. Acad. Sci. USA 99 23 2002 15112 15117 (Pubitemid 35334618)
48. R.S. Senger Biofuel production improvement with genome-scale models: The role of cell composition Biotechnol. J. 5 7 2010 671 685
49. T. Shlomi, O. Berkman, and E. Ruppin Regulatory on/off minimization of metabolic flux changes after genetic perturbations Proc. Natl. Acad. Sci. USA 102 21 2005 7695 7700 (Pubitemid 40741033)
50. T. Shlomi, M.N. Cabili, M.J. Herrgard, B.O. Palsson, and E. Ruppin Network-based prediction of human tissue-specific metabolism Nat. Biotechnol. 26 9 2008 1003 1010
51. K. Smallbone, and E. Simeonidis Flux balance analysis: A geometric perspective J. Theor. Biol. 258 2 2009 311 315
52. P.F. Suthers, M.S. Dasika, V.S. Kumar, G. Denisov, and J.I. Glass A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189 PLoS Comput. Biol. 5 2 2009 e1000285
53. I. Thiele, and B.O. Palsson A protocol for generating a high-quality genome-scale metabolic reconstruction Nat. Protoc. 5 1 2010 93 121
54. C.J. Van Noorden Imaging enzymes at work: Metabolic mapping by enzyme histochemistry J. Histochem. Cytochem. 58 6 2010 481 497
55. A. Varma, and B.O. Palsson Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 Appl. Environ. Microbiol. 60 10 1994 3724 3731 (Pubitemid 24298868)
56. Y. Yang, D. Gilbert, and S. Kim Annotation confidence score for genome annotation: A genome comparison approach Bioinformatics 26 1 2010 22 29