NetCmpt: A network-based tool for calculating the metabolic competition between bacterial species

Bioinformatics

Volumn 28, Issue 16, 2012, Pages 2195-2197

  Kreimer, Anat ^a   Doron Faigenboim, Adi ^b   Borenstein, Elhanan ^c,d,e   Freilich, Shiri ^d  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b VOLCANI CENTER   (Israel)

^c UNIVERSITY OF WASHINGTON   (United States)

^d University of Washington   (United States)

^e SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BACTERIUM; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; INTERNET; METABOLISM; METHODOLOGY; SPECIES DIFFERENCE;

ALGORITHMS; BACTERIA; COMPUTATIONAL BIOLOGY; INTERNET; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SOFTWARE; SPECIES SPECIFICITY;

EID: 84865067157     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts323     Document Type: Article

References (31)

1. Alon, U. (2003) Biological networks: the tinkerer as an engineer. Science, 301, 1866-1867.
2. Becker, S.A. and Palsson, B.O. (2005) Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation. BMC Microbiol., 5, 8.
3. Borenstein, E. and Feldman, M.W. (2009) Topological signatures of species interactions in metabolic networks. J. Comput. Biol., 16, 191-200.
4. Borenstein, E. et al. (2008) Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc. Natl. Acad. Sci. USA, 105, 14482-14487.
5. Carr, R. and Borenstein, E. (2012) NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment. Bioinformatics, 28, 734-735.
6. Chaffron, S. et al. (2010) A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res., 20, 947-959.
7. Dutilh, B.E. et al. (2009) Increasing the coverage of ametapopulation consensus genome by iterative read mapping and assembly. Bioinformatics, 25, 2878-2881.
8. Ebenhoh, O. et al. (2004) Structural analysis of expanding metabolic networks. Genome Inform., 15, 35-45.
9. Feist, A.M. et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol., 3, 121.
10. Feist, A.M. et al. (2009) Reconstruction of biochemical networks in microorganisms. Nat. Rev. Microbiol., 7, 129-143.
11. Freilich, S. et al. (2008) Metabolic innovations towards the human lineage. BMC Evol. Biol., 8, 247.
12. Freilich, S. et al. (2010a) Decoupling environment-dependent and independent genetic robustness across bacterial species. PLoS Comput. Biol., 6, e1000690.
13. Freilich, S. et al. (2010b) The large-scale organization of the bacterial network of ecological co-occurrence interactions. Nucleic Acids Res., 38, 3857-3868.
14. Freilich, S. et al. (2011) Competitive and cooperative metabolic interactions in bacterial communities. Nat. Commun., 2, 589.
15. Handorf, T. et al. (2008) An environmental perspective on metabolism. J. Theor. Biol., 252, 530-537.
16. Handorf, T. et al. (2005) Expanding metabolic networks: scopes of compounds, robustness, and evolution. J. Mol. Evol., 61, 498-512.
17. Janga, S.C. and Babu, M.M. (2008) Network-based approaches for linking metabolism with environment. Genome Biol., 9, 239.
18. Jeong, H. et al. (2000) The large-scale organization of metabolic networks. Nature, 407, 651-654.
19. Kanehisa, M. and Goto, S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
20. Kharchenko, P. et al. (2005) Expression dynamics of a cellular metabolic network. Mol. Syst. Biol., 1, 0016.
21. Klitgord, N. and Segre, D. (2010) Environments that induce synthetic microbial ecosystems. PLoS Comput. Biol., 6, e1001002.
22. Klitgord, N. and Segre, D. (2011) Ecosystems biology of microbial metabolism. Curr. Opin. Biotechnol., 22, 541-546.
23. Kreimer, A. et al. (2008) The evolution of modularity in bacterial metabolic networks. Proc. Natl. Acad. Sci. USA, 105, 6976-6981.
24. Ma, H. and Zeng, A.P. (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics, 19, 270-277.
25. Oberhardt, M.A. et al. (2009) Applications of genome-scale metabolic reconstructions. Mol. Syst. Biol., 5, 320.
26. Oh, Y.K. et al. (2007) Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J. Biol. Chem., 282, 28791-28799.
27. Papp, B. et al. (2011) Systems-biology approaches for predicting genomic evolution. Nat. Rev. Genet., 12, 591-602.
28. Pignatelli, M. et al. (2008) Metagenomics reveals our incomplete knowledge of global diversity. Bioinformatics, 24, 2124-2125.
29. Raymond, J. and Segre, D. (2006) The effect of oxygen on biochemical networks and the evolution of complex life. Science, 311, 1764-1767.
30. Stolyar, S. et al. (2007) Metabolic modeling of a mutualistic microbial community. Mol. Syst. Biol., 3, 92.
31. Wintermute, E.H. and Silver, P.A. (2010) Emergent cooperation in microbial metabolism. Mol. Syst. Biol., 6, 407.