Optimization-based inference for temporally evolving Boolean networks with applications in biology

Proceedings of the American Control Conference

Volumn , Issue , 2011, Pages 4129-4134

  Chang, Young Hwan ^a   Gray, Joe ^b   Tomlin, Claire ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL DATA; BOOLEAN NETWORKS; GENETIC NETWORKS; OPTIMIZATION PROBLEMS; OPTIMIZATION SCHEME; PRIORI INFORMATION; ROBUST NETWORK; SIMULATION STUDIES; STRUCTURE AND DYNAMICS; SYSTEMS BIOLOGY; TIME INTERVAL;

BOOLEAN ALGEBRA; OPTIMIZATION;

COMPUTER SIMULATION;

EID: 80053158755     PISSN: 07431619     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (19)

1. K. Sachs, D. Gifford, T. Jaakkola, P. Sorger, and D. A. Lauffenburger. Bayesian Network Approach to Cell Signaling Pathway Modeling, Sci. STKE, Vol. 2002, Issue 148, p. pe38, 3 September 2002
2. N. Friedman and D. Koller. Being Bayesian About Network Structure. A Bayesian Approach to Structure Discovery in Bayesian Networks, MACHINE LEARNING, Vol. 50, Numbers 1-2, pp 95-125
3. J. Yu, V. A. Smith, P. P. Wang, A. J. Hartemink, and E. D. Jarvis. Advances to Bayesian network inference for generating causal networks from observational biological data, Bioinformatics (2004) Vol. 20 (18), 3594-3603, July 29, 2004
4. H. Schmidt, K.H. Cho, and E. W. Jacobsen. Identification of small scale biochemical networks based on general type system perturbations, FEBS J. 272, Vol. 272, Issue 9, pp 21412151, May 2005
5. M. Bansal, G. D. Gatta, and D. di Bernardo. Inference of gene regulatory networks and compound mode of action from time course gene expression profiles, Bioinformatics (2006) Vol. 22 (7), pp 815-822
6. H. Schmidt and E.W. Jacobsen. Linear systems approach to analysis of complex dynamic behaviors in biochemical networks, Systems Biology, IEE Proceeding, Vol. 1, Issue 1, pp 149-158, June 2004.
7. E. Sontag, A. Veliz-Cuba, R. Laubenbacher, and A. S. Jarrahy. The effect of negative feedback loops on the dynamics of boolean networks, Biophysical Journal, Vol 95 (2), pp 518-526, July 2008
8. Y. M. Zou, Modeling and analyzing complex biological networks incooperating experimental information on both network topology and stable states, Bioinformatics, Vol 26 (16), pp 2037-2041, July 2, 2010
9. U. Alon. Network motifs: theory and experimental approaches, Nature Review Genetics, Vol 8, pp 450-461
10. S. Han, Y. Yoon, and K. H. Cho, Inferring biomolecular interaction networks based on convex optimization, Computational Biology and Chemistry, Vol 31, pp 347-354
11. H. Y. Chang, B. H. Lawrence, and J. C. Diane. Learning Patterns in the Dynamics of Biological Networks, International Conference on Knowledge Discovery and Data Mining archive, Proceedings of the 15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 2009, pp 977-986
12. M. S. Kim, J. R. Kim and K. H. Cho. Dynamic network rewiring determines temporal regulatory functions in Drosophila melanogaster development processes, Bioessays, Vol 32, pp 505-513
13. B.B. Marc, B. Alfredo, P. Andrea, W. Martin and Z. Riccardo. Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach, BMC Bioinformatics 2010, Vol 11, pp 355
14. S. Boyd and L. Vandenberghe. 2004. Convex Optimization (Cambridge University Press)
15. A. Aswani, N. Boyd, and C. Tomlin, Graph-Theoretic Topological Control of Biological Genetic Networks, American Control Conference St. Louis, MO, USA June 10-12, 2009
16. N. V. Sergina, M. Rausch, D. Wang, J. Blair, H. Byron, K. M. Shokat, and M. M. Moasser. Escape from HER family tyrosine kinase inhibitor therapy by the kinase-inactive HER3, Nature Vol 445, 2007
17. D. Kim, Y.K. Kwon, and K.H. Cho, Coupled positive and negative feedback circuits form an essential building block of cellular signaling pathways, BioEssays, Vol 29, Issue 1, pp 8590, January 2007
18. D. N. Amin, N. Sergina, D. Ahuja, M. McMahon, J. A. Blair, D. Wang, B. Hann, K. M. Koch, K. M. Shokat, and M. M. Moasser, Resiliency and Vulnerability in the HER2-Her3 Tumorigenic Driver. Sci Transl Med Vol 2, Issue 16, 2010
19. S. Itani, J. Gray, and C. Tomlin, An ODE Model for the HER2/3-AKT Signaling pathway in cancers that overexpress HER2, American Control Conference, St. Louis, MO, USA, June 10-12, 2009