Inference of Boolean networks under constraint on bidirectional gene relationships

IET Systems Biology

Volumn 3, Issue 3, 2009, Pages 191-202

  Vahedi, G ^a   Ivanov, I V ^b   Dougherty, E R ^a,c  

^a Texas A and M University   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c TRANSLATIONAL GENOMICS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM PERFORMANCE; ATTRACTOR STRUCTURE; BOOLEAN NETWORKS; CHARACTERISATION; COEFFICIENT OF DETERMINATION; DATA DISTRIBUTION; DESIGN METHOD; GRAPH TOPOLOGY; INFERENCE ALGORITHM; INFERRED NETWORKS; NETWORK-BASED; PREDICTIVE RELATIONSHIPS; STEADY STATE DATA; STEADY STATE PROBABILITIES; TARGET GENES; TEMPORAL DATA;

GENES; PROBABILITY DISTRIBUTIONS;

INFERENCE ENGINES;

ANALYTIC METHOD; ARTICLE; CANCER GENETICS; GENE REGULATORY NETWORK; GENE TARGETING; GENETIC ALGORITHM; GENETIC ASSOCIATION; INFORMATION SCIENCE; MELANOMA; PREDICTION; PROBABILITY; STEADY STATE;

ALGORITHMS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE REGULATORY NETWORKS; MELANOMA; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 66249116679     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2007.0070     Document Type: Article

References (26)

1. De Jong, H.: 'Modeling and simulation of genetic rAgulatory systems: a literature review', J. Comput. Biol., 2002, 9, (1), p. 67-103
2. Ivanov, I., and Dougherty, E.R.: 'Modeling genetic regulatory networks: continuous or discrete?', J. Biol. Syst., 2006, 14, (2), p. 219-229
3. van Someren, E.P., Wessels, L.F.A., Backer, E., and Reinders, M.J.T.: 'Multi-criterion optimization for genetic network modeling', Signal Process., 2003, 83, (4), p. 763-775 10.1016/S0165-1684(02)00473-5 0165-1684
4. Liang, S., Fuhrman, S., and Somogyi, R.: 'REVEAL, a general reverse engineering algorithm for inference of genetic network architectures', Pac. Symp. Biocomput., 1998, 3, p. 18-29
5. Akutsu, T.: 'Identification of genetic networks from a small number of gene expression patterns under the Boolean network model', Pac. Symp. Biocomput., 1999, p. 17-28
6. Shmulevich, I., Saarinen, A., Yli-Harja, O., and Astola, J.: 'Inference of genetic regulatory networks under the best-fit extension paradigm', Computational and Statistical Approaches To Genomics, 2002
7. Lahdesmaki, H., Shmulevich, I., and Yli-Harja, O.: 'On learning gene regulatory networks under the boolean network model', Mach. Learn., 2003, 52, (1, 2), p. 147-167 10.1023/A:1023905711304 0885-6125
8. Yu, J., Smith, V.A., Wang, P.P., Hartemink, A.J., and Jarvis, E.D.: 'Advances to bayesian network inference for generating causal networks from observational biological data', Bioinformatics, 2004, 20, (18), p. 3594-3603
9. Kauffman, S.A.: 'Metabolic stability and epigenesis in randomly constructed genetic nets', J. Theor. Biol., 1969, 22, (3), p. 437-467
10. Kauffman, S.: 'ThS origins of order: self-organization and selection in evolution', (Oxford University Press, New York 1993)
11. Dougherty, E.R., Kim, S., and Chen, Y.D.: 'Coefficient of determination in nonlinear signal processing', Signal Process., 2000, 80, (10), p. 2219-2235 10.1016/S0165-1684(00)00079-7 0165-1684
12. Shmulevich, I., Dougherty, E.R., Kim, S., and Zhang, W.: 'Probabilistic boolean networks: A rule-based uncertainty model for gene regulatory networks', Bioinformatics, 2002, 18, (2), p. 261-274
13. Pal, R., Ivanov, I., Datta, A., Bittner, M.L., and Dougherty, E.R.: 'Generating boolean networks with a prescribed attractor structure', Bioinformatics, 2005, 21, (21), p. 4021-4025
14. Dougherty, E.R., and Xiao, Y.: 'Design of probabilistic boolean networks under the requirement of contextual data consistency', IEEE Trans. Signal Process., 2006, 54, (9), p. 3603-3613 10.1109/TSP.2006.877641 1053-587X
15. Zhao, W., Serpedin, E., and Dougherty, E.R.: 'Inferring connectivity of genetic networks using information theoretic criteria', IEEE/ACM Trans. Comput. Biol. Bioinf., 2008, 5, (2), p. 262-274
16. Dougherty, E.R.: 'Validation of inference procedures for gene regulatory networks', Curr. Genom., 2008, 8, (6), p. 351-359
17. Kaufman, V., Mihaljev, T., and Drossel, B.: 'Scaling in critical random Boolean networks', Phys. Rev. E, 2005, 72, (4), p. 1-9 part 2, article no. 046124
18. Kaufman, V., and Drossel, B.: 'On the properties of cycles of simple Boolean networks', Eur. Phys. J. B, 2005, 43, (1), p. 115-124 10.1140/ epjb/e2005-00034-6 1434-6028
19. B. Drossel: 'Random boolean networks', http://arxiv.org/abs/0706.3351, 2008
20. Kaufman, V., and Drossel, B.: 'Relevant components in critical random Boolean networks', New J. Phys., 2006, 8, p. 1-16 article no. 228 1367-2630
21. Kim, S.C., Dougherty, E.R., and Chen, Y.D.: Et al. 'Multivariate measurement of gene expression relationships', Genomics, 2000, 67, (2), p. 201-209
22. Bittner, M., Meitzer, P., and Chen, Y.: Et al. 'Molecular classification of cutaneous malignant melanoma by gene expression profiling', Nature, 2000, 406, (6795), p. 536-540 0028-0836
23. Kim, S., Li, H., and Dougherty, E.R.: Et al. 'Can markov chain models mimic biological regulation?', J. Biol. Syst., 2002, 10, (4), p. 337-357
24. Datta, A., Choudhary, A., Bittner, M.L., and Dougherty, E.: 'External control in markovian genetic regulatory networks: The imperfect information case', Bioinformatics, 2004, 20, p. 924-930
25. Chen, Y., Kamat, V., Dougherty, E.R., Bittner, M.L., Meltzer, P., and Trent, J.: 'Ratio statistics of gene expression levels and applications to microarray data analysis', Bioinformatics, 2002, 18, (9), p. 207-1215
26. Paul, U., Kaufman, V., and Drossel, B.: 'Properties of attractors of canalyzing random Boolean networks', Phys. Rev. E, 2006, 73, (2), p. 1-9 part 2, article no. 026118