Abstract: This thesis proposes a new model for the shoot apical meristem in the plant Arabidopsis that captures the spatial organization of the stem cells and the WUSCHEL domain, which has been shown to play an important regulatory function. A reduction of the parameter space is carried out to allow for an application of a simulated annealing algorithm to find good parameter sets. The accepted dynamical systems are analyzed and the results indicate that WUSCHEL does not directly contribute to the spatial positioning of the stem cells. Instead the regulation acts via genes in the peripheral zone. It is still an open question which these regulatory genes are and that is the motivation for presenting a list of candidates based on collected experimental data. A new microarray analysis algorithm based on previously developed weighted permutation tests is proposed and evaluated on data generated by a gene expression model. The algorithm performs well under such conditions and is therefore applied to the real microarray data with the purpose of listing candidates for the gene in the peripheral zone regulating the spatial organization of the stem cells.