Interdisciplinary Centre for Bioinformatics (IZBI)

Research Activities at the Centre

(1) In the field of Genetic Evolution, IZBI pursues projects in the area of genetic diversity and the underlying evolutionary relationships among species.

(2) In the field of Tissue Formation and Signal Transduction, IZBI researches the genotype-phenotype dependency in tissue formation and function, with a special focus on the mechanisms of spatial formation of tissue (e.g. epithelia, tumours, and engineered tissue), the architecture of signal transduction and genetic regulatory networks, and the analysis of high-dimensional genomic and molecular data from normal and diseased tissues.
The Centre maintains close ties to the Chair for Bioinformatics (Prof. Stadler) at the Faculty of Mathematics and Computer Science. IZBI and the Chair for Bioinformatics together form the Bioinformatics-Initiative, funded until 2006 by the National Research Foundation DFG.

Working Group 1: Databases and Data Integration (coordinator: Prof. E. Rahm). The Group focuses on the management and integration of molecular-biological data and annotations. It has developed, among others, a data warehouse for gene expression analysis (integration and annotation of large amounts of diverse genomic information), which is available for research projects in the areas of cell biology and medicine.

Working Group 2/Junior Researcher Group: Tissue Organisation (coordinator: Dr. D. Drasko). The Group's research concentrates on single-cell based simulation models of tissue organisation (e.g. tumours and epithelia) on different time and length scales and related data analyses, like e.g. 3D reconstruction of microscopic data.

Working Group 3: Cellular Signal Transduction and Gene Expression (coordinator: Prof. F. Horn). The Group concentrates its research on questions of functional genomics in the context of pathogen processes with the particular application of gene expression analysis through microarrays. The Group coordinates its activities with the Working Group 1 and with the Core Unit "Microchip Technologies" at the Interdisciplinary Centre for Clinical Research IZKF.

Working Group 4: Genetic Evolution (coordinator: Prof. P. Stadler). The Group develops gene and protein sequences with a special focus on population genetics and phylogenetics, e.g. for the purpose of phylogenic tree reconstruction or for the purpose of the identification of uncoded RNA.

(1) The scientific standing of the Working Groups formed in 2002 was verified by 25 publications in international refereed journals in 2004 (compared to 16 publications in 2003).

(2) In 2004, externally funded projects with a total budget of EUR 410,000 could be brought to IZBI. Two projects lead by Prof. M.Löffler and Prof. E. Rahm and supported by the Deutsche Krebshilfe (German Cancer Aid Society) studied molecular causes of cancer (malign lymphoma and glioma). IZBI also provides bioinformatic analysis of gene expression data for interdisciplinary projects. It designs and maintains a database where cooperation partners can store, analyse, and exchange histological and molecular results. In a further project, supported by the 6th EU-Framework Programme, the Centre studies the organisational principles of complex biological systems (project coordinators are Prof. P. Stadler and Prof. M. Middendorf).

(3) The following collaborations with Institutes of the Faculty of Medicine were initiated or continued:

• Dr. Ahnert (Centre for Biotechnology and Biomedicine BBZ): genetic variability of autoimmune diseases
• Prof. Paschke (Department of Internal Medicine III): gene expression in thyroid cancer
• Prof. Höckel (Department of Obstetrics and Gynaecology): 3D characterisation of uterine cervix carcinoma
• Prof. Horn (Institute of Clinical Immunology and Transfusion Medicine IKIT): gene expression analysis, reconstruction of transcriptional networks
• PD Dr. Krohn (Interdisciplinary Centre for Clinical Research Leipzig IZKF): microarray technologies and analyses
• Prof. Löffler (Institute of Medical Informatics, Statistics and Epidemiology IMISE, Coordination Centre for Clinical Trials KKSL): biometry and statistical analysis of gene expression data, development of an infrastructure for comparative analysis of molecular and clinical data, tissue modelling
• Prof. Aust (Institute of Anatomy): mechanisms of tumour invasion and metastasis (esp. cell migration)
• Prof. Hengstler (Institute of Clinical Pharmacology): analysis and modelling of xenograft experiments

(4) IZBI continues to cooperate with the following scientists within the Universität Leipzig:

• Prof. Rahm (Institute for Computer Science): databases and data integration
• Prof. Middendorf (Institute for Computer Science): complex models of evolution
• Prof. Robitzki (Biosciences, Centre for Biotechnology and Biomedicine BBZ): cell and tissue modelling
• Prof. Schlegel (Biosciences): molecular evolution of animals/phylogenetic tree reconstruction
• Prof. Käs (Physics): cell elasticity
• Prof. Müller and Prof. Truyen (Veterinary Medicine): evolution of viruses

IZBI also works together with the Max-Planck-Institutes of Evolutionary Anthropology (Prof. S. Pääbo) and Mathematics in the Natural Sciences (Prof. J. Jost, Dr. A. Stevens).

(5) Work progressed on the evaluation platform for gene expression analysis. IZBI offers its partners a specially developed database (GeWare, Genexpressions-Warehouse) in which microarray data can be stored and documented (among others, in the MIAME-standard), and be made available for comparative analyses within a security concept. For statistical analysis of chip data, a team of advisers from the IZBI staff are available with the requisite evaluation tools (e.g. BioConductor, S+-Statserver). The evaluation platform is part of the East German Microarray Technology Centre ORMA and complements the microarray service unit at the Interdisciplinary Centre for Clinical Research IZKF. In June 2004, a one-day workshop "Gene Expression Analysis in Clinical and Cell-Biological Research" with over 80 participants took place.

(6) A junior researcher group "Tissue Modelling - Computational Tissue" was installed at IZBI under the direction of Dr. Dirk Drasdo.

(7) Under the direction of Prof. E. Rahm and together with the Institute of Computer Science (Database Group), IZBI organised "DILS 2004 - International Workshop on Data Integration in the Life Sciences." Together with Max-Planck-Institute for Mathematics in the Sciences, it also organised a workshop about "Phylogenetic Combinatorics."