Our research focuses on the biophysical and genetic bases of pattern formation and morphogenesis. How is gene expression regulation coordinated in space and time during embryo development? How are gene expression patterns reliably shaped in the presence of molecular fluctuations, genetic variability and environmental perturbations? We address these questions using a multilevel modelling approach, capturing key quantitative aspects of the interplay between the biophysical mechanisms underlying cell and tissue morphogenesis and the regulation of gene expression. Our theoretical models are developed in close relation with experimental data and are mainly used to formulate organised hypotheses and make testable predictions. As the models’ validation is strongly dependent on quantifying and estimating the biological parameters involved, we also work on the development of quantitative image analysis methods, databases and parameter optimisation algorithms.