Necessary and sufficient conditions for dynamical structure reconstruction of LTI networks

IEEE Transactions on Automatic Control

Volumn 53, Issue 7, 2008, Pages 1670-1674

  Gonçalves, Jorge ^a   Warnick, Sean ^b  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b 3361 TMCB   (United States)

Author keywords

Network reconstruction; Networked systems; Systems biology

Indexed keywords

CHEMICAL REACTIONS; CONTROL THEORY; INVARIANCE; RESTORATION; TIME VARYING CONTROL SYSTEMS; TRANSFER FUNCTIONS;

CHEMICAL REACTION NETWORKS; DYNAMICAL STRUCTURES; INPUT-OUTPUT DATA; LINEAR-TIME-INVARIANT SYSTEMS; MINIMALITY; NECESSARY AND SUFFICIENT CONDITIONS; NETWORK RECONSTRUCTION; NETWORKED SYSTEMS; SYSTEMS BIOLOGY;

REPAIR;

EID: 52249116064     PISSN: 00189286     EISSN: None     Source Type: Journal    
DOI: 10.1109/TAC.2008.928114     Document Type: Article

References (15)

1. M. Andrec, B. M. Kholodenko, R. M. Levy, and E. D. Sontag, "Inference of signaling and gene regulatory networks by steady-state perturbation experiments: Structure and accuracy," J. Theor. Biol., vol. 232, no. 3, pp. 427-441, 2005.
2. P. Berman, B. Dasgupta, and E. D. Sontag, "Randomized approximation algorithms for set multicover problems with applications to reverse engineering of protein and gene networks," Discrete Appl. Math. Special Ser. Comput. Molec. Biol., vol. 155, pp. 733-749, 2007.
3. C. Cosentino, W. Curatola, F. Montefusco, M. Bansal, D. di Bernardo, and F. Amato, "Linear matrix inequalities approach to reconstruction of biological networks," Inst. Eng. Technol. Syst. Biol., vol. 1, no. 3, 2007.
4. T. Gardner, D. Bernardo, D. Lorenz, and J. Collins, "Inferring genetic networks and identifying compound mode of action via expression profiling," Science, vol. 301, pp. 102-105, Jul. 2003.
5. J. Gonçalves, R. Howes, and S. Warnick, "Dynamical structure functions for the reverse engineering of LTI networks," presented at the Conf. Decision Control, New Orleans, LA, 2007.
6. N. Guelzim, S. Bottani, P. Bourgine, and F. Kepes, "Topological and causal structure of the yeast transcriptional regulatory network," Nature Gen., vol. 31, pp. 60-63, 2002.
7. R. Howes, N. Dalchau, J. Gonçalves, and S. Warnick, "Reconstruction of biological networks through gene silencing and overexpression," presented at the 8th Int. Conf. Systems Biology, Long Beach, CA, 2007.
8. A. Julius, M. Zavlanos, S. Boyd, and G. J. Pappas, "Genetic network identification using convex programming," presented at the 8th Int. Conf. Systems Biology, Long Beach, CA, 2007.
9. B. N. Kholodenko, A. Kiyatkin, F. Bruggeman, E. D. Sontag, H. Westerhoff, and J. Hoek, "Untangling the wires: A novel strategy to trace functional interactions in signaling and gene networks," Proc. National Academy Sciences USA, vol. 99, pp. 12841-12846, 2002.
10. L. Ljung, System Identification-Theory for the User. Upper Saddle River, NJ: Prentice-Hall, 1999.
11. S. Maslov and K. Sneppen, "Specificity and stability in topology of protein networks," Science, vol. 296, pp. 910-913, 2002.
12. A. Papachristodoulou and H. El-samad, "Algorithms for discriminating between biochemical reaction network models: Towards systematic experimental design," presented at the American Controls Conf., New York, 2007.
13. E. Sontag, A. Kiyatkin, and B. N. Kholodenko, "Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data," Bioinform., vol. 20, no. 12, pp. 1877-1886, 2004.
14. J. Stelling, S. Klamt, K. Bettenbrock, S. Schuster, and E. D. Gilles, "Metabolic network structure determines key aspects of functionality and regulation," Nature, vol. 420, pp. 190-193, 2002.
15. P. Uetz, L. Giot, G. Cagney, T. A. Mansfield, R. S. Judson, J. R. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, B. Godwin, D. Conover, T. Kalbfleisch, G. Vijayadamodar, M. Yang, M. Johnston, S. Fields, and J. M. Rothberg, "A comprehensive analysis of protein-protein interactions in saccharomyces cerevisiae," Nature, vol. 403, pp. 623-627, 2000.