Ll-ACHRB: A scalable algorithm for sampling the feasible solution space of metabolic networks

Bioinformatics

Volumn 32, Issue 15, 2016, Pages 2330-2337

  Saa, Pedro A ^a   Nielsen, Lars K ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; METABOLISM; METHODOLOGY; SOFTWARE; THEORETICAL MODEL;

ALGORITHMS; METABOLIC NETWORKS AND PATHWAYS; MODELS, THEORETICAL; RESEARCH DESIGN; SOFTWARE;

EID: 84991475919     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw132     Document Type: Article

References (38)

1. Almaas, E. et al. (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature, 427, 839-843.
2. Beard, D. et al. (2002) Energy balance for analysis of complex metabolic networks. Biophys. J., 83, 79-86.
3. Bordbar, A. et al. (2010) Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular systems biology, 6, 422.
4. Bordbar, A. et al. (2011) iAB-RBC-283: a proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states. BMC Syst. Biol., 5, 110.
5. Bordbar, A. et al. (2014) Minimal metabolic pathway structure is consistent with associated biomolecular interactions. Mol. Syst. Biol., 10, 737.
6. Bordel, S. et al. (2010) Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLOS Comput. Biol., 6., e1000859
7. Dal'Molin, C.G.D. et al. (2015) A multi-tissue genome-scale metabolic modeling framework for the analysis of whole plant systems. Front. Plant Sci., 6, 4.
8. De Martino, D. et al. (2015) Uniform sampling of steady states in metabolic networks: heterogeneous scales and rounding. Plos One, 10, e0122670.
9. Dyer, M. and Frieze, A. (1988) On the complexity of computing the volume of a polyhedron. SIAM J. Comput., 17, 967-974.
10. Feist, A.M. et al. (2014) Constraint-based modeling of carbon fixation and the energetics of electron transfer in geobacter metallireducens. PLOS Comput. Biol., 10, e1003575.
11. Givens, G. and Hoeting, J. (2012) Computational Statistics. 2nd edition. John Wiley & Sons Inc, Hoboken, NJ.
12. Kass, R. et al. (1998) Markov Chain Monte Carlo in Practice: a roundtable discussion. Am. Stat., 52, 93-100.
13. Kaufman, D.E. and Smith, R.L. (1998) Direction choice for accelerated convergence in hit-and-run sampling. Oper. Res., 46, 84-95.
14. Kiatsupaibul, S. et al. (2011) An analysis of a variation of hit-and-run for uniform sampling from general regions. ACM Trans. Model. Comput. Simul., 21, 3.
15. Lewis, N.E. et al. (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol., 10, 291-305.
16. Lewis, N.E. et al. (2010) Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nat. Biotechnol., 28, 1279. U1291.
17. Lovasz, L. (1999) Hit-and-run mixes fast. Math. Prog., 86, 443-461.
18. Megchelenbrink, W. et al. (2014) optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks. Plos One, 9, e86587.
19. Mo, M.L. et al. (2009) Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol., 3, 37.
20. Neal, R.M. (2003) Slice sampling. Ann. Stat., 31, 705-741.
21. Nigam, R. and Liang, S. (2007) Algorithm for perturbing thermodynamically infeasible metabolic networks. Comput. Biol. Med., 37, 126-133.
22. Orth, J.D. et al. (2011) A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol. Syst. Biol., 7, 535.
23. Price, N.D. et al. (2004) Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies. Biophys. J., 87, 2172-2186.
24. Price, N.D. et al. (2006) Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. Biophys. J., 90, 3919-3928.
25. Reed, J.L. and Palsson, B.O. (2004) Genome-scale in silico models of E.coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res., 14, 1797-1805.
26. Reimers, A. (2015) Obstructions to sampling qualitative properties. Plos One, 10, e0135636.
27. Schellenberger, J. et al. (2011) Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys. J., 100, 544-553.
28. Schellenberger, J. and Palsson, B.O. (2009) Use of randomized sampling for analysis of metabolic networks. J. Biol. Chem., 284, 5457-5461.
29. Schellenberger, J. et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc., 6, 1290-1307.
30. Shoaie, S. et al. (2013) Understanding the interactions between bacteria in the human gut through metabolic modeling. Sci. Rep. UK, 3, 2532.
31. Simonovits, M. (2003) How to compute the volume in high dimension? Math. Prog., 97, 337-374.
32. Smith, R.L. (1984) Efficient Monte-Carlo procedures for generating points uniformly distributed over bounded regions. Oper. Res., 32, 1296-1308.
33. Thiele, I. et al. (2005) Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants. J. Bacteriol., 187, 5818-5830.
34. Thomas, A. et al. (2014) Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance. Sci. Rep., 4, 3925.
35. Unden, G. and Bongaerts, J. (1997) Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors. Biochim. Biophys. Acta Bioenerg., 1320, 217-234.
36. Wiback, S.J. et al. (2004) Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J. Theor. Biol., 228, 437-447.
37. Xi, Y.P. et al. (2011) Comparative study of computational methods to detect the correlated reaction sets in biochemical networks. Brief. Bioinf., 12, 132-150.
38. Zhang, Y. et al. (2009) Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Science, 325, 1544-1549.