Biology Reference
In-Depth Information
Genrich, H., K?ffner, R. and Voss, K. (2001). Executable Petri net models for the analysis of metabolic pathways. Int. J.
STTT 3 , 394-404.
Heiner, M., Koch, I. and Schuster, S. (2000). Using time-dependent petri nets for the analysis of metabolic networks. In:
Modellierung und Simulation Metabolischer Netzwerke, Preprint No. 10, Hofestadt R., Lautenbach, K. and Lange, M.
(eds), Faculty of Computer Science, University of Magdeburg, pp. 15-21.
Heiner, M., Koch, I. and Voss, K. (2001). Analysis and simulation of steady states in metabolic pathways with Petri nets.
In: CPN '01 - Third Workshop and Tutorial on Practical Use of Coloured Petri Nets and the CPN Tools, Jensen, K. (ed),
University of Aarhus, Denmark, pp. 15-34.
Heinrich, R. and Schuster, S. (1996). The Regulation of Cellular Systems. Chapman and Hall, New York.
Helfert, S., Estevez, A. M., Bakker, B., Michels, P. and Clayton, C. (2001). Roles of triosephosphate isomerase and aerobic
metabolism in Trypanosoma brucei . Biochem. J. 357 , 117-125.
Hofestadt, R. (1994). A petri net application to model metabolic processes. Syst. Anal. Mod. Simul.
16 , 113-122.
Horn, F. and Jackson, R. (1972). General mass action kinetics. Arch. Rational Mech. Anal.
47 , 81-116.
Huang, Y., Jeng, M. D., Xie, Z. and Chung, S. (2001).
Deadlock prevention policy based on Petri nets and siphons.
International Journal of Production Research 39 , 283-305.
Iordache, M. V., Moody, J. O. and Antsaklis, P. J. (2000). Automated synthesis of liveness enforcing supervisors using
Petri nets, Technical Report isis-00-004, Dept. of Electrical Engr., Univ. of Notre Dame.
Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N. and Barabasi, A. L. (2000). The large-scale organization of metabolic
networks. Nature 407 , 651-654.
Kanehisa, M. and Goto, S. (2000). KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res.
28 , 27-30.
Kemper, P. (1993). Linear time algorithm to find a minimal deadlock in a strongly connected free-choice net, In : Proc.
14th International Conference Application and Theory of Petri Nets, Chicago, M. Ajmone-Marsan (ed.), Springer, LNCS
691 , 319-338.
Klamt, S. and Stelling, J. (2003). Two approaches for metabolic pathway analysis? Trends Biotechn. 21 , 64-69.
Kuffner, R., Zimmer, R. and Lengauer, T. (2000).
Pathway analysis in metabolic databases via differential metabolic
display (DMD). Bioinformatics 16 , 825-836.
Leiser, J. and Blum, J. J. (1987).
On the analysis of substrate cycles in large metabolic systems.
Cell Biophys.
11 ,
123-138.
Liao, J. C., Hou, S.-Y. and Chao, Y.-P. (1996). Pathway analysis, engineering and physiological considerations for
redirecting central metabolism. Biotechnol. Bioeng. 52 , 129-140.
Matsuno, H., Doi, A., Nagasaki, M. and Miyano, S. (2000). Hybrid Petri net representation of gene regulatory network.
Pac. Symp. Biocomput. 5 , 341-352.
Mendes, P. (1997). Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci.
22 , 361-363.
Moody, J. O. and Antsaklis, P. J. (1998). Deadlock avoidance in Petri nets with uncontrollable transitions. Proceedings of
1998 American Control Conference, Philadelphia, pp. 24-26.
Oliveira, J. S., Bailey, C. G., Jones-Oliveira, J. B., Dixon, D. A., Gull, D. W. and Chandler, M. L. (2003). A computational
model for the identification of biochemical pathways in the Krebs cycle. J. Comput. Biol. 10 , 57-82.
Othmer, H. G. (1981).
The interaction of structure and dynamics in chemical reaction networks.
In:
Modelling of
Chemical Reaction Systems, Ebert, K. H., Deuflhard, P. and Jager, W. (eds), Springer, Berlin, p. 2.
Overkamp, K. M., Bakker, B. M., Kotter, P., Luttik, M. A. H., van Dijken, J. P. and Pronk, J. T. (2002).
Metabolic
Engineering of glycerol production in Saccharomyces cerevisiae . Appl. Environm. Microbiol.
68 , 2814-2821.
Peleg, M., Yeh, I. and Altman, R. (2002). Modeling biological processes using workflow and Petri net models. Bioinfor-
matics 18 , 825-837.
Pfeiffer, T., S anchez-Valdenebro, I., Nuno, J. C., Montero, F. and Schuster, S. (1999). METATOOL: For studying metabolic
networks. Bioinformatics 15 , 251-257.
Price, N. D., Papin, J. A. and Palsson, B. O. (2002). Determination of redundancy and systems properties of the metabolic
network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res.
12 , 760-769.
Reddy, V. N., Liebmann, M. N. and Mavrovouniotis, M. L. (1996). Qualitative analysis of biochemical reaction systems.
Comput. Biol. Med. 26 , 9-24.
Reisig, W. (1985). Petri Nets: An Introduction. Springer, Berlin.
Rohwer, J. M. and Botha, F. C. (2001). Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro
kinetic data. Biochem. J. 358 , 437-445.
Schmidt, K. (1996a). How to calculate symbolically siphons and traps of algebraic Petri nets. Technical Report, Helsinki
University of Technology, A39 , 1-40.
Schmidt, K. (1996b). Siphons and traps for algebraic Petri nets. Proc. Workshop CS&P, Berlin, 157-168.
Schuster, S. and Hilgetag, C. (1994). On elementary flux modes in biochemical reaction systems at steady state. J. Biol.
Syst. 2 , 165-182.
Search WWH ::




Custom Search