Functional molecular ecological networks

mBio

Volumn 1, Issue 4, 2010, Pages

  Zhou, Jizhong ^a,b,c   Deng, Ye ^a,e   Luo, Feng ^d   He, Zhili ^a   Tu, Qichao ^a   Zhi, Xiaoyang ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c TSINGHUA UNIVERSITY   (China)

^d AMRL   (United States)

^e Glomics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIODIVERSITY; BIOGEOCHEMISTRY; BIOSPHERE; CONCEPTUAL FRAMEWORK; CONTROLLED STUDY; ECOSYSTEM; GENE REGULATORY NETWORK; GEOCHEMISTRY; HIGH THROUGHPUT SCREENING; METAGENOMICS; MOLECULAR ECOLOGY; MOLECULAR HYBRIDIZATION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SOCIAL INTERACTION;

EID: 79952136790     PISSN: None     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00169-10     Document Type: Article

References (58)

1. Montoya, J. M., S. L. Pimm, and R. V. Sole. 2006. Ecological networks and their fragility. Nature 442:259-264.
2. Bascompte, J., P. Jordano, C. J. Melian, and J. M. Olesen. 2003. The nested assembly of plant-animal mutualistic networks. Proc. Natl. Acad. Sci. U. S. A. 100:9383-9387.
3. Bastolla, U., M. A. Fortuna, A. Pascual-Garcia, A. Ferrera, B. Luque, and J. Bascompte. 2009. The architecture of mutualistic networks minimizes competition and increases biodiversity. Nature 458:1018-1020.
4. Cattin, M. F., L. F. Bersier, C. Banasek-Richter, R. Baltensperger, and J. P. Gabriel. 2004. Phylogenetic constraints and adaptation explain foodweb structure. Nature 427:835-839.
5. Holland, M. D., and A. Hastings. 2008. Strong effect of dispersal network structure on ecological dynamics. Nature 456:792-794.
6. Raes, J., and P. Bork. 2008. Molecular eco-systems biology: towards an understanding of community function. Nat. Rev. Microbiol. 6:693-699.
7. Ruan, Q. S., D. Dutta, M. S. Schwalbach, J. A. Steele, J. A. Fuhrman, and F. Z. Sun. 2006. Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors. Bioinformatics 22:2532-2538.
8. Fuhrman, J. A. 2009. Microbial community structure and its functional implications. Nature 459:193-199.
9. Handelsman, J., J. M. Tiedje, L. Alvarez-Cohen, M. Ashburner, I. K. O. Cann, E. F. DeLong, W. F. Doolittle, C. M. Fraser-Liggett, A. Godzik, J. I. Gordon, M. Riley, M. B. Schmid, and A. H. Reid. 2007. Committee on metagenomics: challenges and functional applications. The National Academies Press, Washington, DC.
10. He, Z., T. J. Gentry, C. W. Schadt, L. Wu, J. Liebich, S. C. Chong, Z. Huang, W. Wu, B. Gu, P. Jardine, C. Criddle, and J. Zhou. 2007. GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J. 1:67-77.
11. Wang, F., H. Zhou, J. Meng, X. Peng, L. Jiang, P. Sun, C. Zhang, J. D. Van Nostrand, Y. Deng, Z. He, L. Wu, J. Zhou, and X. Xiao. 2009. GeoChip-based analysis of metabolic diversity of microbial communities at the Juan de Fuca Ridge hydrothermal vent. Proc. Natl. Acad. Sci. U. S. A. 106:4840-4845.
12. Zhou, J., S. Kang, C. W. Schadt, and C. T. Garten, Jr. 2008. Spatial scaling of functional gene diversity across various microbial taxa. Proc. Natl. Acad. Sci. U. S. A. 105:7768-7773.
13. Gardner, T. S., and J. J. Faith. 2005. Reverse-engineering transcription control networks. Phys. Life Rev. 2:65-88.
14. Zhang, B., and S. Horvath. 2005. A general framework for weighted gene co-expression network analysis. Stat. Appl. Genet. Mol. Biol. 4:Article17.
15. Barabasi, A. L., and Z. N. Oltvai. 2004. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5:101-115.
16. Luo, F., Y. Yang, J. Zhong, H. Gao, L. Khan, D. K. Thompson, and J. Zhou. 2007. Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinform. 8:299.
17. Luo, F., J. X. Zhong, Y. F. Yang, R. H. Scheuermann, and J. Z. Zhou. 2006. Application of random matrix theory to biological networks. Phys. Lett. A 357:420-423.
18. Yang, Y., D. P. Harris, F. Luo, W. Xiong, M. Joachimiak, L. Wu, P. Dehal, J. Jacobsen, Z. Yang, A. V. Palumbo, A. P. Arkin, and J. Zhou. 2009. Snapshot of iron response in Shewanella oneidensis by gene network reconstruction. BMC Genomics 10:131.
19. Zhou, A., Z. He, A. M. Redding-Johanson, A. Mukhopadhyay, C. L. Hemme, M. Joachimiak, F. Luo, Y. Deng, K. S. Bender, Q. He, J. D. Keasling, D. A. Stahl, M. W. Fields, T. C. Hazen, A. P. Arkin, J. D. Wall, and J. Zhou. May 2010, posting date. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. Environ. Microbiol. [Epub ahead of print.] doi: 10.1111/j.1462-2920.2010.02234.x.
20. Reich, P. B., S. E. Hobbie, T. Lee, D. S. Ellsworth, J. B. West, D. Tilman, J. M. Knops, S. Naeem, and J. Trost. 2006. Nitrogen limitation constrains sustainability of ecosystem response to CO2. Nature 440:922-925.
21. Fuhrman, J. A., and J. A. Steele. 2008. Community structure of marine bacterioplankton: patterns, networks, and relationships to function. Aquat. Microb. Ecol. 53:69-81.
22. Mehta, M. L. 1990. Random matrices, 2nd ed. Academic Press, Inc., New York, NY.
23. Luo, F., J. Zhong, Y. Yang, and J. Zhou. 2006. Application of random matrix theory to microarray data for discovering functional gene modules. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 73:031924.
24. Alon, U. 2003. Biological networks: the tinkerer as an engineer. Science 301:1866-1867.
25. Barabasi, A. L. 2009. Scale-free networks: a decade and beyond. Science 325:412-413.
26. Muller-Linow, M., C. C. Hilgetag, and M. T. Hutt. 2008. Organization of excitable dynamics in hierarchical biological networks. PLoS Comput. Biol. 4:e1000190.
27. Guimera, R., M. Sales-Pardo, and L. A. Amaral. 2007. Classes of complex networks defined by role-to-role connectivity profiles. Nat. Phys. 3:63-69.
28. Kitano, H. 2004. Biological robustness. Nat. Rev. Genet. 5:826-837.
29. He, Z., M. Xu, Y. Deng, S. Kang, L. Kellogg, L. Wu, J. D. van Nostrand, S. E. Hobbie, P. Reich, and J. Zhou. 2010. Metagenomic analysis reveals a marked divergence in the structure of belowground microbial communities at elevated CO2. Ecol. Lett. 13:564-575.
30. Horvath, S., and J. Dong. 2008. Geometric interpretation of gene coexpression network analysis. PLoS Comput. Biol. 4:e1000117.
31. Fitter, A. H., C. A. Gilligan, K. Hollingworth, A. Kleczkowski, R. M. Twyman, J. W. Pitchford, and N. S. B. Programme. 2005. Biodiversity and ecosystem function in soil. Funct. Ecol. 19:369-377.
32. Curtis, D., B. V. North, and P. C. Sham. 2001. Use of an artificial neural network to detect association between a disease and multiple marker genotypes. Ann. Hum. Genet. 65:95-107.
33. Berlow, E. L., J. A. Dunne, N. D. Martinez, P. B. Stark, R. J. Williams, and U. Brose. 2009. Simple prediction of interaction strengths in complex food webs. Proc. Natl. Acad. Sci. U. S. A. 106:187-191.
34. Dunne, J. A., R. J. Williams, and N. D. Martinez. 2002. Food-web structure and network theory: the role of connectance and size. Proc. Natl. Acad. Sci. U. S. A. 99:12917-12922.
35. Fortuna, M. A., and J. Bascompte. 2006. Habitat loss and the structure of plant-animal mutualistic networks. Ecol. Lett. 9:278-283.
36. Olesen, J. M., J. Bascompte, Y. L. Dupont, and P. Jordano. 2007. The modularity of pollination networks. Proc. Natl. Acad. Sci. U. S. A. 104:19891-19896.
37. Bascompte, J., and D. B. Stouffer. 2009. The assembly and disassembly of ecological networks. Philos. Trans. R. Soc. Lond. B Biol. Sci. 364:1781-1787.
38. Tylianakis, J. M., T. Tscharntke, and O. T. Lewis. 2007. Habitat modification alters the structure of tropical host-parasitoid food webs. Nature 445:202-205.
39. Heimann, M., and M. Reichstein. 2008. Terrestrial ecosystem carbon dynamics and climate feedbacks. Nature 451:289-292.
40. Gruber, N., and J. N. Galloway. 2008. An Earth-system perspective of the global nitrogen cycle. Nature 451:293-296.
41. Reich, P. B., J. Knops, D. Tilman, J. Craine, D. Ellsworth, M. Tjoelker, T. Lee, D. Wedin, S. Naeem, D. Bahauddin, G. Hendrey, S. Jose, K. Wrage, J. Goth, and W. Bengston. 2001. Plant diversity enhances ecosystem responses to elevated CO2 and nitrogen deposition. Nature 410:809-812.
42. Lewin, G. R., E. Mckintosh, and S. B. Mcmahon. 1994. Nmda receptors and activity-dependent tuning of the receptive-fields of spinal-cord neurons. Nature 369:482-485.
43. Horvath, S., B. Zhang, M. Carlson, K. V. Lu, S. Zhu, R. M. Felciano, M. F. Laurance, W. Zhao, S. Qi, Z. Chen, Y. Lee, A. C. Scheck, L. M. Liau, H. Wu, D. H. Geschwind, P. G. Febbo, H. I. Kornblum, T. F. Cloughesy, S. F. Nelson, and P. S. Mischel. 2006. Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target. Proc. Natl. Acad. Sci. U. S. A. 103:17402-17407.
44. Cline, M. S., M. Smoot, E. Cerami, A. Kuchinsky, N. Landys, C. Workman, R. Christmas, I. Avila-Campilo, M. Creech, B. Gross, K. Hanspers, R. Isserlin, R. Kelley, S. Killcoyne, S. Lotia, S. Maere, J. Morris, K. Ono, V. Pavlovic, A. R. Pico, A. Vailaya, P. L. Wang, A. Adler, B. R. Conklin, L. Hood, M. Kuiper, C. Sander, I. Schmulevich, B. Schwikowski, G. J. Warner, T. Ideker, and G. D. Bader. 2007. Integration of biological networks and gene expression data using cytoscape. Nat. Protoc. 2:2366-2382.
45. West, D. B. 1996. Introduction to graph theory. Prentice Hall, Upper Saddle River, NJ.
46. Brandes, U., and T. Erlebach. 2005. Network analysis: methodological foundations. Springer-Verlag, Berlin, Germany.
47. Watts, D. J., and S. H. Strogatz. 1998. Collective dynamics of "smallworld" networks. Nature 393:440-442.
48. Ravasz, E., A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabasi. 2002. Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
49. Costa, L. D., F. A. Rodrigues, G. Travieso, and P. R. V. Boas. 2007. Characterization of complex networks: a survey of measurements. Adv. Phys. 56:167-242.
50. Latora, V., and M. Marchiori. 2001. Efficient behavior of small-world networks. Phys. Rev. Lett. 87:198701.
51. Wasserman, S., and K. Faust. 1994. Social network analysis: methods and applications. Cambridge University Press, Cambridge, United Kingdom.
52. Krackhardt, D. 1994. Graph theoretical dimensions of informal organizations. Lawrence Erlbaum, Hillsdale, NJ.
53. Butts, C. T. 2008. Social network analysis with sna. J. Stat. Softw. 24:1-51.
54. Csardi, G. 2006. The Igraph library. http://cneurocvs.rmki.kfki.hu/igraph/.
55. Newman, M. E. J. 2006. Modularity and community structure in networks. Proc. Natl. Acad. Sci. U. S. A. 103:8577-8582.
56. Clauset, A., M. E. Newman, and C. Moore. 2004. Finding community structure in very large networks. Phys. Rev. E 70:066111.
57. Maslov, S., and K. Sneppen. 2002. Specificity and stability in topology of protein networks. Science 296:910-913.
58. Dixon, P. 2003. VEGAN, a package of R functions for community ecology. J. Veg. Sci. 14:927-930.