An algorithmic framework for network reconstruction

Theoretical Computer Science

Volumn 412, Issue 26, 2011, Pages 2800-2815

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

^a OTTO VON GUERICKE UNIVERSITY   (Germany)

Author keywords

Computational biology; Integer decomposition; Petri nets; Reverse engineering

Indexed keywords

ALGORITHMIC FRAMEWORK; COMPUTATIONAL BIOLOGY; EXPERIMENTAL DATA; INHERENT COMPLEXITY; INTEGER DECOMPOSITION; NETWORK RECONSTRUCTION; REGULATORY MECHANISM; SYSTEMS BIOLOGY;

ALGORITHMS; BIOINFORMATICS; GRAPH THEORY; PETRI NETS; REVERSE ENGINEERING;

BIOLOGICAL SYSTEMS;

EID: 79955732248     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tcs.2010.08.016     Document Type: Conference Paper

References (22)

1. W. Marwan, A. Wagler, and R. Weismantel A mathematical approach to solve the Network Reconstruction Problem Math. Methods Oper. Res. 67 2008 117 132
2. M. Durzinsky, A. Wagler, and R. Weismantel A combinatorial approach to reconstruct Petri nets from experimental data Computational Methods in Systems Biology LNCS vol. 5307 2008 328 346
3. B.N. Kholodenko, A. Kiyatkin, F.J. Bruggeman, E. Sontag, H.V. Westerhoff, and J.B. Hoek Untangling the wires: a strategy to trace functional interactions in signaling and gene networks Proceedings of the National Academy of Sciences of the United States of America 99 20 2002 12841 12846
4. R. Laubenbacher, and B. Stigler A computational algebra approach to reverse engineering of gene regulatory networks J. Theor. Biol. 229 2005 523 537
5. R. Krishna, and S. Guo A partial granger causality approach to explode causal networks derived from multi-parameter data Computational Methods in Systems Biology LNCS vol. 5307 2008 9 27
6. W. Marwan, A. Wagler, R. Weismantel, Petri nets as a framework for the reconstruction and analysis of signaling transduction pathways and regulatory networks, Natural Computing (2009) in press, (doi:10.1007/s11047-009-9152-x ).
7. M. Chen, and W. Hofestdt Quantitative Petri net model fo gene regulated metabolic networks in the cell In Silico Biology 3 2003 347 365 (Pubitemid 37493056)
8. M. Chen, and W. Hofestdt A Petri net application of metabolic processes J. Syst. Anal. Modell. Simul. 16 1994 113 122
9. I. Koch, M. Heiner, Petri nets, in: B.H. Junker, F. Schreiber (Eds.), Biological Network Analysis, in: Wiley Book Series on Bioinformatics, 2008, pp. 139179.
10. J.W. Pinney, R.D. Westhead, and G.A. McConkey Petri net representations in systems biology Biochem. Soc. Tarns. 31 2003 1513 1515 (Pubitemid 38031013)
11. M. Durzinsky, W. Marwan, A. Wagler, and R. Weismantel Automatic reconstruction of molecular and genetic networks from experimental time series data BioSystems 93 2008 181 190
12. W. Marwan Detecting functional interactions in a gene and signalling network by time-resolved somatic complementation analysis BioEssays 25 2003 950 960 (Pubitemid 37221519)
13. W.D. Hoff, K.-H. Jung, and J.L. Spudich Molecular mechanism of photosignaling by archaeal sensory rhodopsins Annu. Rev. Biophys. Biomol. Struct. 26 1997 223 258 (Pubitemid 27255373)
14. W. Marwan, A. Sujatha, and C. Starostzik Reconstructing the regulatory network controlling commitment and sporulation in physarum polycephalum based on hierarchical petri net modeling and simulation J. Theoret. Biol. 236 2005 349 365 (Pubitemid 41140440)
15. M. Heiner, and I. Koch Petri net based model validation in systems biology 25th International Conference on Application and Theory of Petri Nets, Bologna 2004 Springer Verlag Berlin
16. H. Matsuno, Y. Tanaka, H. Aoshima, A. Doi, M. Matsui, and S. Miyano Biopathways representation and simulation on hybrid functional petri net In Silico Biol. 3 2003 389 404 (Pubitemid 37493057)
17. J.W. Pinney, R.D. Westhead, and G.A. McConkey Petri net representations in systems biology Biochem. Soc. Trans. 31 2003 1513 1515 (Pubitemid 38031013)
18. C.A. Petri, Kommunikation mit Automaten, Bonn: Institut fr Instrumentelle Mathematik, Schriften des IIM Nr. 2, 1962.
19. A. Wagler, R. Weismantel, The combinatorics of modeling and analysing biological systems, Natural Comput. (2009) in press, (doi:10.1007/s11047-009- 9165-5 ).
20. A.J. Hartemink, Principled computational methods for the validation and discovery of genetic regulatory networks, Dissertation, Massachusetts Institute of Technology, 2001.
21. fr Photochem. Photobiol. 73 2001 697 702
22. C. Starostzik, and W. Marwan A photoreceptor with characteristics of phytochrome triggers sporulation in the true slime mould Physarum polycephalum FEBS Lett. 370 1995 146 148