Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

BMC Systems Biology

Volumn 5, Issue , 2011, Pages

  Durzinsky, Markus ^a   Wagler, Annegret ^b   Marwan, Wolfgang ^a  

^a OTTO VON GUERICKE UNIVERSITY   (Germany)

^b UNIVERSITÉ CLERMONT AUVERGNE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ENTEROBACTERIACEAE;

PHOSPHATE;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; ENTEROBACTERIACEAE; GENE REGULATORY NETWORK; METABOLISM; METHODOLOGY; PHYSIOLOGY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ALGORITHMS; ENTEROBACTERIACEAE; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL; PHOSPHATES; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

EID: 79960555561     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-113     Document Type: Article

References (23)

1. Marbach D, Prill RJ, Schaffter T, Mattiussi C, Floreano D, Stolovitzky G. Revealing strengths and weaknesses of methods for gene network inference. Proceedings of the National Academy of Sciences of the United States of America 2010, 107(14):6286-6291. 10.1073/pnas.0913357107, 2851985, 20308593.
2. Papin JA, Hunter T, Palsson BO, Subramaniam S. Reconstruction of cellular signalling networks and analysis of their properties. Nat Rev Mol Cell Biol 2005, 6(2):99-111. 10.1038/nrm1570, 15654321.
3. Sontag E, Kiyatkin A, Kholodenko BN. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics 2004, 20(12):1877-1886. 10.1093/bioinformatics/bth173, 15037511.
4. Stark J, Brewer D, Barenco M, Tomescu D, Callard R, Hubank M. Reconstructing gene networks: what are the limits?. Biochem Soc Trans 2003, 31(Pt 6):1519-1525.
5. Stark J, Callard R, Hubank M. From the top down: towards a predictive biology of signalling networks. Trends in Biotechnology 2003, 21(7):290-293. 10.1016/S0167-7799(03)00140-9, 12837611.
6. Durzinsky M, Wagler A, Weismantel R, Marwan W. Automatic reconstruction of molecular and genetic networks from discrete time series data. BioSystems 2008, 93(3):181-190. 10.1016/j.biosystems.2008.04.001, 18524471.
7. Marwan W, Wagler A, Weismantel R. A mathematical approach to solve the network reconstruction problem. Mathematical Methods of Operations Research 2008, 67(1):117-132.
8. Rosenstengel B, Winand U. Petri-Netze: eine anwendungsorientierte Einführung. 1991, Braunschweig: Vieweg, 4.
9. Heiner M, Lehrack S, Gilbert D, Marwan W. Extended stochastic Petri nets for model-based design of wetlab experiments. Transactions on Computational Systems Biology XI 2009, 138-163.
10. Marwan W, Wagler A, Weismantel R. Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks. Nat Comput 2009, 1-16.
11. Pinney JW, Westhead RD, McConkey GA. Petri Net representations in systems biology. Biochem Soc Trans 2003, 31:1513-1515. 10.1042/BST0311513, 14641101.
12. Durzinsky M, Wagler A, Weismantel R. A combinatorial approach to reconstruct Petri nets from experimental data. Computational Methods in Systems Biology: 2008 2008, 328-346. Rostock: Springer-Verlag Berlin.
13. Durzinsky M, Marwan W, Wagler A. Reconstructing extended Petri nets. University of Magdeburg., http://www.fma.ovgu.de/forschung/forschung_inhalt/veroeffentlichungen/preprints__technical_reports-p-942/preprints/2010/10_19.html
14. Hsieh Y-J, Wanner BL. Global regulation by the seven-component Pi signaling system. Current Opinion in Microbiology 2010, 13(2):198-203. 10.1016/j.mib.2010.01.014, 2847643, 20171928.
15. Neidhardt FC, Ingraham JL, Schaechter M. Physiology of the Bacterial Cell. A Molecular Approach. 1990, Sunderland, Massachusetts: Sinauer Associates.
16. Marwan W, Rohr C, Heiner M. Petri nets in Snoopy: A unifying framework for the graphical?display, computational modelling, simulation, and bioinformatic annotation of bacterial regulatory networks. Bacterial Molecular Networks Humana Press, Thieffry D, .
17. Rohr C, Marwan W, Heiner M. Snoopy--a unifying Petri net framework to investigate biomolecular networks. Bioinformatics 2010, 26(7):974-975. 10.1093/bioinformatics/btq050, 20139470.
18. Heiner M. Snoopy. 2010, , http://www-dssz.informatik.tu-cottbus.de/index.html?/~wwwdssz/software/snoopy.html
19. Wagler A. Prediction of network structure. Modeling in Systems Biology The Petri Net Approach 2011, 307-336. London: Springer, Koch I, Reisig W, Schreiber F.
20. Torres LM, Wagler AK. Model reconstruction for discrete deterministic systems. Electronic Notes in Discrete Mathematics 2010, 36(C):175-182.
21. Wagler A, Weismantel R. The combinatorics of modeling and analyzing biological systems. Natural Computing 2009,
22. Durzinsky M, Marwan W, Ostrowski M, Schaub T, Wagler A. Automatic network reconstruction using ASP. Theory and Practice of Logic Programming 2011,
23. McCluskey EJ. Minimization of boolean functions. Bell Systems Technical Journal 1956, 35:1417-1444.