Henrik Jönsson, Marcus Heisler, G. Venugopala Reddy, Vikas Agrwal, Victoria Gor, Bruce E. Shapiro, Eric Mjolsness, Elliot M. Meyerowitz Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem to appear in Bioinformatics (special issue for ISMB2005) Abstract: Motivation: The above ground tissues of higher plants are generated from a small region of cells situated at the plant apex called the shoot apical meristem. An important genetic control circuit modulating the size of the {\em Arabidopsis thaliana} meristem is a feed-back network between the CLAVATA3 and WUSCHEL genes. Although the expression patterns for these genes do not overlap, WUSCHEL activity is both necessary and sufficient (when expressed ectopically) for the induction of CLAVATA3 expression. However, upregulation of CLAVATA3 in conjunction with the receptor kinase CLAVATA1 results in the down regulation of WUSCHEL. Despite much work, experimental data for this network is incomplete and additional hypotheses are needed to explain the spatial locations and dynamics of these expression domains. Predictive mathematical models describing the system should provide a useful tool for investigating and discriminating among possible hypotheses, by determining which hypotheses best explain observed gene expression dynamics. Results: We are developing a method using {\em in vivo} live confocal microscopy to capture quantitative gene expression data and create templates for computational models. We present two models accounting for the organization of the WUSCHEL expression domain. Our preferred model uses a reaction-diffusion mechanism, in which an activator induces WUSCHEL expression. This model is able to organize the WUSCHEL expression domain. In addition, the model predicts the dynamical reorganization seen in experiments where cells, including the WUSCHEL domain, are ablated, and also predicts the spatial expansion of the WUSCHEL domain resulting from removal of the CLAVATA3 signal. Availability: An extended description of the model framework and image processing algorithms can be found at http://www.computableplant.org, together with additional results and simulation movies. LU TP 05-02