Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn

Seminar

Speaker: Kai Kruse, AG Bioinformatics

Title: Towards the identification of (regulatory) motifs/modules in metabolic networks

Time: Wed, Aug 4, 2010, 10:00am

Place: MPI für Molekulare Pflanzenphysiologie, Room 0.21 in The Box

Abstract:
Biological systems consist of a multitude of diverse, interacting components from which directed and robust behavior emerges. The ambition to uncover structure and design principles in an ever-growing amount of experimental data has made pattern identification algorithms an indispensable tool for biological analysis. This study presents a novel approach for finding motifs in metabolic pathways, considering both the structure and underlying dynamics of a system to obtain concise and interpretable results.

The method is based on `structural kinetic modeling' (SKM), allowing the analysis of system dynamics without having explicit knowledge of kinetic parameters. A set of randomly generated SKM models serves as input for a decision tree classification algorithm, which derives dynamic motifs of system components with specific attributes essential for the preservation of a steady state.

Two major biochemical pathways were investigated: The energy and redox metabolism of human erythrocytes and the tricarboxylic acid cycle of mammalian mitochondria. Results provide insight into elementary combinations of enzymes contributing to system robustness and the significance of defined enzymatic properties. The importance and functionality of allosteric regulation and the difference of motifs for distinct metabolic states is also highlighted.

This work can fundamentally contribute to a system-level understanding of biological processes with respect to stability and robustness. It demonstrates the importance of considering the fine-tuned interplay of pathway components in addition to structural aspects of a system and is applicable to large scale networks, where an explicit kinetic model is unavailable.

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Past NLD Seminars (1994-2007) & (2008 ...)

Students' seminar: Theoretical Physics, PIK, Modeling & TSA Berlin-Potsdam-Colloquia: PhysGesellschaft Berlin, TU Berlin, Pro Physik, AIP, AEI, MPI-KGF, GFZ, HMI, PIK, AWI, Max Planck Institute for the History of Science, Mathematik, DPG Disputationen, & Vorschau UP

Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
Phone: (+49-331) 977-1658, Fax : (+49-331) 977-1045

Email: Udo.Schwarz AT uni-potsdam.de

DFG SFB 1294

DFG Sonderforschungsbereich 1294 Data assimilation

DFG SPP 1488

DFG Schwerpunktprogramm 1488 Planetmag


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