Dynamical structure analysis of sparsity and minimality heuristics for reconstruction of biochemical networks

Proceedings of the IEEE Conference on Decision and Control

Volumn , Issue , 2008, Pages 173-178

  Howes, Russell ^a   Eccleston, Lee ^b   Goncalves, Jorge ^b   Stan, Guy Bart ^b   Warnick, Sean ^a  

^a 3361 TMCB   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

INVARIANCE; LINEAR SYSTEMS; RELIGIOUS BUILDINGS; TIME VARYING CONTROL SYSTEMS;

BIOCHEMICAL NETWORK; DYNAMICAL STRUCTURE; LINEAR TIME INVARIANT SYSTEMS; MINIMAL REALIZATIONS; NETWORK RECONSTRUCTION; NETWORK STRUCTURES; OVER-EXPRESSION; STRUCTURAL INFORMATION;

TRANSFER FUNCTIONS;

EID: 62949208926     PISSN: 07431546     EISSN: 25762370     Source Type: Conference Proceeding    
DOI: 10.1109/CDC.2008.4739364     Document Type: Conference Paper

References (13)

1. E. Sontag, A. Kiyatkin, B. Kholodenko, "Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data," IEEE Bioinformatics, Vol. 20, Issue 12, pp. 1877-1886, 2004.
2. N. Soranzo, G. Bianconi, C. Altafini, "Comparing association network algorithms for reverse engineering of large-scale gene regulatory networks: synthetic versus real data," Bioinformatics Vol. 23, Issue 13, pp. 1640-1647, 2007.
3. N. Barker, C. Myers, H. Kuwahara, "Learning Genetic Regulatory Network Connectivity from Time Series Data," Advances in Applied Artificial Intelligence, Lecture Notes in Computer Science, Vol. 4031, pp. 962-971, 2006.
4. N. Friedman. "Inferring Cellular Networks Using Probabilistic Graphical Models," Science, Vol. 303, Issue 5659, pp. 799-805, 2004.
5. K. Basso, A. A. Margolin, G. Stolovitzky, U. Klein, R. Dalla-Favera, "Reverse engineering of regulatory networks in human B cells," Nature Genetics, Vol. 37, pp. 382-390, 2005.
6. A. Papachristodoulou, B. Recht, "Determining Interconnections in Chemical Reaction Networks," Proceedings of the 2007 American Control Conference, pp. 4872-4877, 2007.
7. M. Bansal, V. Belcastro, A. Ambesi-Impiombato, and D. Di Bernardo, "How to infer gene networks from expression profiles," Molecular Systems Biology Vol. 3, Issue 78, 2007.
8. J. Goncalves, R. Howes, S. Warnick, "Dynamical Structure Functions for the Reverse Engineering of LTI Networks," Proceedings of the 2007 Conference on Decision and Control, pp. 1516-1522, 2007.
9. J. Goncalves, S. Warnick. "Necessary and Sufficient Conditions for Dynamical Structure Reconstruction of LTI Networks", IEEE Transactions of Automatic Control, 2008 (to appear).
10. E. Sontag, "Network reconstruction based on steady-state data". Essays in Biochemistry, 45, 2008 (to appear).
11. C. T. Chen, Linear System Theory and Design, Revised. Saunders College Publishing, Orlando, 1984.
12. D. Di Bernardo, T. Gardner, J. Collins, "Robust Identification of large genetic networks," Pac. Symp. Biocomput, Vol. 9, pp. 486-497, 2004.
13. B. Bamieh, L. Giarré, "On Discovering Low Order Models in Biochemical Reaction Kinetics," Proceedings of the 2007 American Control Conference, pp. 2702-2707, 2007.