After the finishing of the first large genomics initiatives it became more and more apparent that the knowledge of the genomes is not sufficient to achieve significant advances in molecular medicine in the near future. Indeed, the acquired genomic data is rather a fundament to the interpretation of data stemming from transcriptomics and proteomics experiments. This requires a close collaboration of researchers from different fields, biology, medical sciences, biochemistry, analytical chemistry and computer science. The high-throughput settings of many of these experiments need advanced algorithmic techniques and data analysis capabilities which are only now being developed.

The goal of this seminar is to bring together experts from both fields: life science and computer science/computational biology. Together they should present recent advances in their field and identify relevant problems that ought to be solved in order to advance science in the field. We plan to address the following topics

• Strategies for differential analysis of complex protein and peptide mixtures
• Algorithms for peptide identification
• Models and algorithms for protein interaction networks
• Novel experimental and computational methods of interest to proteomics

The expected outcome or the seminar is a better understanding of the expectations, needs, and possibilities both of experimental and bioinformatic tools for proteome analysis. Computer scientists should understand how the data for proteome analysis are generated and what their implications are, while experimental scientists need to know how the data can be evaluated and validated. The seminar is intended to set off new initiatives for collaborations between experimental and computational sciences that will result in novel, rugged and fully automatable total analysis systems for proteome characterization. We intend to publish extended abstracts or papers presented at this workshop as a book.

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