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SyBiL: Systems Biology in Leipzig

Levels of modelling complexity.

Systems biology is an emerging fascinating new field of science, covering the complexity of biology from molecular scales to ecosystems. Within this broad spectrum we focus specifically onto models of complex cell and tissue organisation and function directed gene regulation. Our focus is biomedical and we address both, the understanding of basic mechanisms of tissue self-organisation and the potential practical use of the models in tissue engineering and drug testing. We will concentrate our attention on understanding how cells organise their function in terms of cell differentiation, lineage commitment, cell-cell and cell-environment interaction. Hence, we are interested in the processes linking regulation on the molecular and genomic level (regulomic level) to the functional capacity of self-organizing tissues.
Our approach is comparative considering different growth conditions, different genetic / molecular perturbations of selected cell-biological systems (progenitor cells, retina, skin) on which we have particular experimental and modelling expertise and where we can pursue different strategies in a paradigmatic way.
The experimental set-up is supported by a comprehensive modelling program addressing four layers of complexity:

  1. We elaborate our models to detect regulatory elements on the genetic and molecular level (promoter prediction, prediction for non-coding regulatory RNA, protein-protein interaction, protein-RNA-interaction).
  2. We will extend our current modelling approaches to dynamic intracellular gene networks and to characterise the mechanisms involved in switching and locking cell function, e.g. lineage differentiation cascades, and the impact of genetic or drug manipulations.
  3. We plan to extend and elaborate our generic family of 3D-models of tissue formation and functioning, integrating tissue biomechanics of cell-cell and cell-environment interactions. This will involve tissue-specific combined pharmacokinetic-pharmacodynamic models, which can be used for tissue engineering.
  4. We will develop models which can be used to optimise medical treatment strategies, testable in clinical trials. To integrate models acting on different scales (in time or space), we will provide generic methods of constructing integrative models using rigorous mathematical methods on how to adapt to different scales while maintaining essential system properties.

Publications concerning Systems Biology: IZBI, IMISE