Durzinsky Markus, Marwan Wolfgang, Wagler Annegret
Magdeburg Centre for Systems Biology, Otto-von-Guericke Universität Magdeburg,Universitätsplatz 2, 39106 Magdeburg, Germany.
J Math Biol. 2013 Jan;66(1-2):203-23. doi: 10.1007/s00285-012-0511-3.
The aim of this work is to extend a previously presented algorithm (Durzinsky et al. 2008b in Computational methods in systems biology, LNCS, vol 5307. Springer, Heidelberg, pp 328–346; Marwan et al. 2008 in Math Methods Oper Res 67:117–132) for the reconstruction of standard place/transition Petri nets from time-series of experimental data sets. This previously reported method finds provably all networks capable to reproduce the experimental observations. In this paper we enhance this approach to generate extended Petri nets involving mechanisms formally corresponding to catalytic or inhibitory dependencies that mediate the involved reactions. The new algorithm delivers the set of all extended Petri nets being consistent with the time-series data used for reconstruction. It is illustrated using the phosphate regulatory network of enterobacteria as a case study.
这项工作的目的是扩展先前提出的一种算法（Durzinsky等人，2008b，《系统生物学中的计算方法》，LNCS，第5307卷。施普林格出版社，海德堡，第328 - 346页；Marwan等人，2008，《数学方法与运筹学》67:117 - 132），用于从实验数据集的时间序列重建标准位置/变迁Petri网。这种先前报道的方法能够证明找到所有能够重现实验观测结果的网络。在本文中，我们改进了这种方法，以生成扩展的Petri网，其中涉及形式上对应于介导相关反应的催化或抑制依赖性的机制。新算法给出了与用于重建的时间序列数据一致的所有扩展Petri网的集合。以肠道细菌的磷酸盐调节网络为例进行了说明。
