Genetic network inference as a series of discrimination tasks

Bioinformatics

Volumn 25, Issue 7, 2009, Pages 918-925

  Kimura, Shuhei ^a   Nakayama, Satoshi ^a   Hatakeyama, Mariko ^b  

^a TOTTORI UNIVERSITY   (Japan)

^b RIKEN   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA;

ACCURACY; ALGORITHM; ARTICLE; BIOINFORMATICS; DISCRIMINANT ANALYSIS; DNA REPAIR; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; MATHEMATICAL COMPUTING; NONHUMAN; PRIORITY JOURNAL; SYSTEM ANALYSIS; SYSTEMS BIOLOGY;

BACTERIA (MICROORGANISMS);

EID: 63549084899     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp072     Document Type: Article

References (34)

1. Akutsu,T. et al. (2000) Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics, 16, 727-734.
2. Bansal,M. and di Bernardo,D. (2007) Inference of gene networks from temporal gene expression profiles. IET Syst. Biol., 5, 306-312.
3. Burges,C.J.C. (1998) A tutorial on support vector machines for pattern recognition. Data Min. Knowl. Discov., 2, 121-167.
4. Cho,D.Y. et al. (2006) Identification of biochemical networks by S-tree based genetic programming. Bioinformatics, 22, 1631-1640.
5. Chou,I.C. et al. (2006) Parameter estimation in biochemical systems models with alternating regression. Theor. Biol. and Med. Model., 3, 25.
6. Cleveland,W.S. (1979) Robust locally weight regression and smoothing scatterplots. J. Am. Stat. Assoc., 79, 829-836.
7. D'haeseleer,P. et al. (2000) Genetic network inference: From co-expression clustering to reverse engineering. Bioinformatics, 16, 707-726.
8. Ergün,A., Lawrence,C.A. et al. (2007) A network biology approach to prostate cancer. Mol. Syst. Biol., 3, 82.
9. Faith,J.J. et al. (2007) Large-scale mapping and validation of Escherichia Coli transcriptional regulation from a compendium of expression profiles. PLoS Biol., 5, e8.
10. Gardner,T.S. et al. (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301, 102-105.
11. Gonzalez,O.R. et al. (2006) Parameter estimation using simulated annealing for S-system Models of biochemical networks. Bioinformatics 23, 480-486.
12. Graepel,T. et al. (1999) Classification on proximity data with LP-machines. In Proceedings of International Conference on Artificial Neural Networks'99, Edinburgh, UK, pp. 304-309.
13. Hlavacek,E.S. and Savageau,M.A. (1996) Rules for coupled expression of regulator and effector genes in inducible circuits. J. Mol. Biol., 255, 121-139.
14. Imoto,S. et al. (2002) Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression. Pac. Symp. Biocomput., 7, 175-186.
15. Kikuchi,S. et al. (2003) Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics, 19, 643-650.
16. Kimura,S. et al. (2005) Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinformatics 21, 1154-1163.
17. Kimura,S. et al. (2008) Function approximation approach to the inference of reduced NGnet models of genetic networks. BMC Bioinformatics, 9, 23.
18. Liu,P.K. and Wang,F.S. (2008) Inference of biochemical network models in S-system using multiobjective optimization approach. Bioinformatics 24, 1085-1092.
19. Maki,Y. et al. (2001) Development of a system for the inference of large scale genetic networks. Pac. Symp. Biocomput., 6, 446-458.
20. Margolin,A.A. et al. (2006) ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics, 7, S7.
21. Mehrotra,S. (1992). On the implementation of a primal-dual interior point method, SIAM J. Optim., 2, 575-601.
22. Ronen,M. et al. (2002) Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl Acad. Sci. USA, 99, 10555-10560.
23. Sakamoto,E. and Iba,H. (2001) Inferring a System of Differential Equations for a Gene Regulatory Network by using Genetic Programming, In Proceedings of 2001 Congress on Evolutionary Computation,Seoul, Korea, pp. 720-726.
24. Savageau,M.A. (1969) Biochemical SystemsAnalysis I. Some mathematical properties of the rate law for the component enzymatic reactions. J. Theor. Biol., 25, 365-369.
25. Sutton,M.D. et al. (2000) The SOS response: Recent insights into umuDC-dependent mutagenesis and DNA damage tolerance. Ann. Rev. Genet., 34, 479-497.
26. Thieffry,D. et al. (1998) From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia Coli. BioEssays, 20, 433-440.
27. Tsai,K.Y. and Wang,F.S. (2005) Evolutionary optimization with data collocation for reverse engineering of biological networks. Bioinformatics, 21, 1180-1188.
28. Vance,W. et al. (2002) Determination of causal connectivities of species in reaction networks. Proc. Natil Acad. Sci. USA, 99 5816-5821.
29. Veflingstad,S.R. et al. (2004) Priming nonlinear searches for pathway identification. Theor. Biol. Med. Model., 1, 8.
30. Vilela,M. et al. (2007) Automated smoother for the numerical decoupling of dynamics models. BMC Bioinformatics, 8, 305.
31. Voit,E.O. (2000) Computational Analysis of Biochemical Systems. Cambridge University Press, Cambridge.
32. Voit,E.O. and Almeida,J. (2004) Decoupling dynamical systems for pathway identification from metabolic profiles. Bioinformatics, 20, 1670-1681.
33. Yeung,M.K.S. et al. (2002) Reverse Engineering Gene Networks using Singular Value Decomposition and Robust Regression, Proc. Natl Acad. Sci. USA, 99, 6163-6168.
34. Yu,J. et al. (2004) Advances to Bayesian network inference for generating causal networks from observational biological data, Bioinformatics, 20, 3594-3603.