Combination of Neuro-Fuzzy Network Models with Biological Knowledge for Reconstructing Gene Regulatory Networks

Journal of Bionic Engineering

Volumn 8, Issue 1, 2011, Pages 98-106

  Liu, Guixia ^a   Liu, Lei ^a   Liu, Chunyu ^b   Zheng, Ming ^a   Su, Lanying ^a   Zhou, Chunguang ^a  

^a JILIN UNIVERSITY   (China)

^b CHANGCHUN UNIVERSITY OF CHINESE MEDICINE   (China)

Author keywords

Biological knowledge; Gene regulatory networks; Neuro fuzzy network; Regulators

Indexed keywords

BIOLOGICAL KNOWLEDGE; CELLULAR SYSTEM; COMPUTATIONAL BIOLOGY; CORE FACTORS; GENE REGULATORY NETWORKS; LARGE-SCALE EXPRESSION; NEURO-FUZZY ARCHITECTURES; NEURO-FUZZY NETWORK; REGULATORS; REGULATORY CONDITIONS; REGULATORY NETWORK; WEIGHT VALUES;

BIOINFORMATICS; FUZZY RULES; GENE EXPRESSION;

FUZZY NEURAL NETWORKS;

EID: 79952996247     PISSN: 16726529     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-6529(11)60008-5     Document Type: Article

References (22)

1. Shen X, Vikalo H Inferring parameters of gene regulatory networks via particle filtering. EURASIP Journal on Advances in Signal Processing 2010, 2010:204612.
2. Loomis WF, Sternberg PW Genetic networks. Science 1995, 269:649.
3. Albert R Boolean modeling of genetic regulatory networks. Complex Networks 2004, Springer, New York, USA. E. Ben-naim, H. Frauenfelder, Z. Toroczkai (Eds.).
4. Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Favera RD, Califano A ARACNE: An algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. BMC Bioinformatics 2006, 7(Suppl 1):S7.
5. Liu GX, Feng W, Wang H, Liu L, Zhou CG Reconstruction of gene regulatory networks based on two-stage Bayesian network structure learning algorithm. Journal of Bionic Engineering 2009, 6:86-92.
6. Akutsu T, Miyano S, Kuhara S Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pacific Symposium on Biocomputing 1999, 4:17-28.
7. Chen KC, Wang TY, Tseng HH, Huang CYF, Kao CY A stochastic differential equation model for quantifying transcriptional regulatory network in Saccharomyces cerevisiae. Bioinformatics 2005, 21:2883-2990.
8. van Someren EP, Wessels LF, Reinders MJ Linear modeling of genetic networks from experimental data. Proceedings of International Conference on Intelligent System for Molecular Biology 2000, 8:355-366.
9. Friedman N, Linial M, Nachman I, Pe'er D Using Bayesian networks to analyze expression data. Journal of Computational Biology 2000, 7:601-620.
10. Maraziotis I, Dragomir A, Bezerianos A Recurrent neuro-fuzzy network models for reverse engineering gene regulatory interactions. Lecture Notes in Computer Science 2005, 3695:24-34.
11. Datta D, Choudhuri S S, Konar A, Nagar A, Das S. A recurrent fuzzy neural model of a gene regulatory network for knowledge extraction using differential evolution. Proceedings of the Eleventh conference on Congress on Evolutionary Computation, Trondheim, Norway, 2009, 2900-2906.
12. Floares A G. A neural networks algorithm for inferring drug gene regulatory networks from microarray time-series with missing transcription factors information. Proceedings of the International Joint Conference on Neural Networks, Atlanta, GA, USA, 2009, 848-854.
13. Knott S, Mostafavi S, Mousavi P A neural network based modeling and validation approach for identifying gene regulatory networks. Neurocomputing 2010, 73:2419-2429.
14. Ao SI, Palade V Ensemble of Elman neural networks and support vector machines for reverse engineering of gene regulatory networks. Applied Soft Computing 2011, 11:1718-1726.
15. Echanobe J, del Campo I, Bosque G An adaptive neuro-fuzzy system for efficient implementations. Information Sciences 2008, 178:2150-2162.
16. Lin CJ, Lee CY A self-organizing recurrent fuzzy CMAC model for dynamic system identification. International Journal of Intelligent Systems 2008, 23:384-396.
17. Salgado P Rule generation for hierarchical collaborative fuzzy system. Applied Mathematical Modelling 2008, 32:1159-1178.
18. Zadeh LA Fuzzy sets. Information and Control 1965, 8:338-353.
19. Cell Cycle Analysis Cell Cycle Gene Expression Data in Saccharomyces cerevisiae, [2011-2-24] http://genome-www.stanford.edu/cellcycle/.
20. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 1998, 9:3273-3297.
21. Saccharomyces Genome Database, [2011-2-24] http://www.yeastgenome.org.
22. Predicted Regulatory Module Saccharomyces Genome Database, [2011-2-24] http://db.yeastgenome.org/exp_modules/cellcycle/cluster_293.html.