Automatic reconstruction of molecular and genetic networks from discrete time series data

BioSystems

Volumn 93, Issue 3, 2008, Pages 181-190

  Durzinsky, Markus ^a   Wagler, Annegret ^a   Weismantel, Robert ^a   Marwan, Wolfgang ^a  

^a OTTO VON GUERICKE UNIVERSITY   (Germany)

Author keywords

Discrete time series data; Molecular network; Network reconstruction; Petri net; Signal transduction; Synthetic biology

Indexed keywords

RHODOPSIN;

ALGORITHM; AUTOMATION; DATA SET; NUMERICAL METHOD; RECONSTRUCTION; TIME SERIES;

ALGORITHM; ARTICLE; ARTIFICIAL NEURAL NETWORK; MATHEMATICAL ANALYSIS; PHOTORECEPTOR; SIGNAL TRANSDUCTION; SPOROGENESIS; TIME SERIES ANALYSIS;

EID: 48049101174     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2008.04.001     Document Type: Article

References (23)

1. Baumgarten, B., 1996. Petri-Netze-Grundlagen und Anwendungen. Spektrum Akademischer Verlag.
2. Goss P.J.E., and Peccoud J. Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 6750-6755
3. Hardy S., and Robillard P.N. Phenomenological and molecular-level Petri net modeling and simulation of long-term potentiation. BioSystems 82 (2005) 26-38
4. Heiner, M., Koch, I., 2004. Petri net based model validation in systems biology. Paper presented at: Proceedings of the 25th International Conference on Application and Theory of Petri Nets, ICATPN 2004, Bologna, Italy, Springer Verlag Berlin.
5. Hoff W.D., Jung K.-H., and Spudich J.L. Molecular mechanism of photosignaling by archaeal sensory rhodopsins. Annu. Rev. Biophys. Biomol. Struct. 26 (1997) 223-258
6. Kholodenko B.N., Kiyatkin A., Bruggeman F.J., Sontag E., Westerhoff H.V., and Hoek J.B. Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 12841-12846
7. Koch, I., Heiner, M., 2008. Petri nets. In: Junker, B.H., Schreiber, F. (Eds.), Biological Network Analysis. Wiley Book Series on Bioinformatics (Series Eds. Yi Pan, Albert Y. Zomaya), pp. 139-179 (Chapter 7).
8. fr. Photochem. Photobiol. 73 (2001) 697-702
9. Marwan W., and Starostzik C. The sequence of regulatory events in the sporulation control network of Physarum polycephalum analysed by time-resolved somatic complementation of mutants. Protist 153 (2002) 391-400
10. Marwan W. Detecting functional interactions in a gene and signaling network by time-resolved somatic complementation analysis. BioEssays 25 (2003) 950-960
11. Marwan W., Sujatha A., and Starostzik C. Reconstructing the regulatory network controling commitment and sporulation in Physarum polycephalum based on hierarchical Petri net modeling and simulation. J. Theor. Biol. 236 (2005) 349-365
12. Marwan W., Wagler A., and Weismantel R. A mathematical approach to solve the network reconstruction problem. Math. Methods Oper. Res. 67 (2008) 117-132
13. Matsuno H., Tanaka Y., Aoshima H., Doi A., Matsui M., and Miyano S. Biopathways representation and simulation on hybrid functional Petri net. In Silico Biol. 3 (2003) 389-404
14. Mayo M. Learning Petri net models of non-linear gene interactions. BioSystems 82 (2005) 74-82
15. Otomo J., Marwan W., Oesterhelt D., Desel H., and Uhl R. Biosynthesis of the two halobacterial light sensors P480 and SR and variation in gain of their signal transduction chains. J. Bacteriol. 171 (1989) 2155-2159
16. Papin J.A., Hunter T., Palsson B.O., and Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nat. Rev. Mol. Cell Biol. 6 (2005) 99-111
17. Pinney J.W., Westhead R.D., and McConkey G.A. Petri net representations in systems biology. Biochem. Soc. Trans. 31 (2003) 1513-1515
18. Rosenstengel B., and Winand U. Petri-Netze: Eine Anwendungsorientierte Einführung, 4. Auflage (1991), Vieweg, Braunschweig
19. Sontag E., Kiyatkin A., and Kholodenko B.N. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 20 (2004) 1877-1886
20. Stark J., Callard R., and Hubank M. From the top down: towards a predictive biology of signalling networks. Trends Biotechnol. 21 (2003) 290-293
21. Starostzik C., and Marwan W. A photoreceptor with characteristics of phytochrome triggers sporulation in the true slime mould Physarum polycephalum. FEBS Lett. 370 (1995) 146-148
22. Starostzik C., and Marwan W. Functional mapping of the branched signal transduction pathway that controls sporulation in Physarum polycephalum. Photochem. Photobiol. 62 (1995) 930-933
23. Starostzik C., and Marwan W. Kinetic analysis of a signal transduction pathway by time-resolved somatic complementation of mutants. J. Exp. Biol. 201 (1998) 1991-1999