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Master‘s Thesis: Mathematical Modeling of a Sea Urchin Gene Regulatory Network

By Clemens Kühn and Departmet Vertebrate Genomic


The recent sequencing of the genome of the sea urchin Strongylocentrotus purpuratus opens up exciting perspectives for scientists. One of the most exciting and also most challenging goals is to fully understand the mechanisms driving the development of a fertilized egg to an adult organism. This understanding is achieved by combining experimental and computational methods to establish and validate hypotheses about the developmental process. In this work, I describe the design of mathematical models of the Sea Urchin gene regulatory network that controls endoderm and mesoderm formation, a key step in embryonic development. The models are loosely based on a network proposed by Davidson et al. and the associated data. They are validated by comparison to various data. Validation of the constructed models clearly shows that the models suffer from a lack of data. Especially the model based on the proposed network is unable to reproduce the experimental data. The validation of the models employs a novel approach using sampled parameters to infer features of large ODE models with unknown kinetic parameters. The present thesis was prepared in th

Year: 2013
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