Interdisciplinary Centre for Bioinformatics (IZBI)

General

The Interdisciplinary Centre for Bioinformatics (IZBI) is an institutional centre of the Universität Leipzig, for which the infrastructure is funded proportionately by third-party grants and internal budget means. The Centre works in its own separate rooms and has at its disposal a scientific staff and administration.

The IZBI is managed by a five-man management board of representatives from the Faculties of Mathematics and Computer Science, the Faculty of Bio-Sciences, the Faculty of Medicine and the Leipzig Max-Planck-Institute. Prof. Markus Löffler is the Scientific Director of the IZBI.

Research content of the Centre is orientated around the strategic research profile of the Universität Leipzig and helps to shape it. The IZBI is involved in the Top-Level Research Area 3 (PbF 3) “Molecular and Cellular Communication: Bio-Technology, Bio-Computer Science and Bio-Medicine in Therapy and Diagnostics”, as well as PbF 2 (“Mathematics in the Natural Sciences”) and PbF 6 (“Changed Environment and Disease”).

The IZBI concentrates on the following research areas:

• Modelling of Biological Processes, Regenerative Medicine: The modelling of life-processes under system-biological aspects has become a strategy that is increasing in significance, in order to understand their manner of functioning, to plan experiments and also to guide bio-technological processes. This latter application has special significance in Regenerative Medicine, for example with the conditioning of bio-reactors for the generation of tissue. Mechanisms and processes of gene regulation are modelled as well as the intra-cellular signal processing, cell differentiation and self-organization of tissues.
• Computational Microscopy: High-definition in-vitro microscopy (ultra-sound-, infra-red-, in-vivo electron-microscopy, fluorescent microscopy with special labelling and staining techniques), allows examinations with cellular and molecular definition. It will be possible thereby to obtain, for a tissue sample, various image modalities with complementary informational content. The comparative analysis of data places huge demands on image processing and on further informational methods of comparison with findings from molecular diagnostics (see next point).
• Molecular Medicine: Analysis of high-dimensional genomic, proteomic, genetic-impression chemical data (e.g. transcriptome) has evolved to become a highly significant approach to molecular characterisation and demarcation of disease-identities. The data obtained by several partners, as a rule, in the context of large research cooperations require management and a concerted effort in assessment, for which the IZBI develops suitable technological platforms (data bases with integrated analysis-programmes and analysis-algorithms) and makes them available. The high-dimensional structure of the data requires application of qualified statistical data-mining procedures, which can adequately form an image of the biological problem (e.g. for genomic regulation - see next point).
• Interactomics and non-encoded RNA: In regulation of gene activity in the cell, a multitude of processes interplays in a net-like (reticulated) fashion. Interactions between various molecular components (proteins, RNA, DNA, etc) play a decisive role in this context. In addition to the (protein)-encoded genes, a considerable part of the genome’s higher organisms is attributed to so-called non-coded RNA (ncRNA). The probable and (in part) previously proved function of disease processes makes extreme effort in the disclosure of the role of non-coded RNA necessary, although particularly micro-array and sequence technologies are being developed further and implemented. This focus is targeted at, among other things, the development of adequate analysis methods for micro-arrays of the most-current generation.

Under methodological reference points, the following points of emphasis have been established at the IZBI:

• Comparative sequence analyses for the identification of specific functional sections of the genome.
• Computer-science-analysis methods for microscopic imaging procedures.
• In-silico simulation and mathematical modelling of cell-differentiation formation and tissue formation in time and space.
• Multivariate statistics and deterministic models for the analysis of high-dimensional molecular-biological data.
• Warehousing, integration and documentation of biological and medical data.
  The IZBI cooperates with the Chair, led by Prof. Stadler, for Bioinformatics (Department of Mathematics and Computer Science). IZBI and the Chair for Bioinformatics together form the Bioinformatics-Initiative funded by the German Research Community (DFG).

Results 2007

1. In cooperation with the IMISE, the IZBI, with its module “Ontological Tools” (leader Prof. Rahm), is participating in the BMBF-sponsored inter-operational project MEDIGRID. It is the goal of the interoperation to develop and apply GRID services in bio-medical research. Among other things, highly complex data are evaluated and interpreted with use of the resources of networked computational technology. Furthermore, the project develops methods which are made available through the data-processing cooperation.
2. In two of the projects sponsored by the German Cancer Relief (Deutsche Krebshilfe), molecular causes for cancerous diseases (malignant lymphoma and neuroglioma) are examined (project leaders: Prof. M. Löffler, Prof. Rahm). In this interdisciplinary effort, the IZBI assumes bio-informatics analyses of gene expression data and matrix-CGH data, as well as the construction and ministration of a data-base, in which the cooperation-partners deposit, analyse and exchange histological and molecular findings. Both projects continue to be accomplished in this second phase of funding.
3. It is the goal of the BMBF-project (project leaders: Prof. Löffler, Dr. Galle) to develop a bio-reactor which could enable reasonably-priced and automatic production of articular-cartilage-replacement tissue from stem-cells. Research groups cooperate here from the Center for Biotechnology and Biomedicine (BBZ, Prof. Bader, reactors for the growth of tissues), physics (Prof. Käs, cell-elasticity measurements; Prof. Grill, ultra-sound microscopy) and bio-physics (Dr. Schiller, MALDI-TOF analytics). Single-cell based computer models are being developed at IZBI, which are meant to systematically examine the factors relevant for tissue formation and provide thereby the prerequisites for targeted supervision of cartilage regeneration.
4. In the BMBF project HepatoSys (Dr. Drasdo), issues concerning liver regeneration are being handled with several collaboration partners with regard to system-biological key points. Tissue models of liver are developed at IZBI.
5. The topic of “Gene expression analysis“ combines several research groups from the Leipzig University with the IZBI. Statistical procedures and evaluation strategies are developed together with the INISE (Prof. Löffler and staff) und the IKIT (Prof. Horn). The IZBI oversees together with the Core-Unit the DNA technologies of the IZKF (PD Dr. Krohn) GeneChip studies under the auspices of the East German Reference Centre for Micro-Array Technology.
6. In collaboration with the IKIT (Prof. Horn), a project was initiated for the target-gene orientated analysis of regulatory gene-sets on gene expression arrays in oncology, which is being funded for two years at IZKF.
7. The topic “Computational Microscopy“ has, to date, developed quite successfully. Dr. Braumann has assumed the position of project leader for the Core Unit “Computational Microscopy“ at the Translation Centre for Regenerative Medicine, which continues to be located at the IZBI.
8. With the combination of the Institute of Zoology (Prof. Schlegel) and the Institute of Computer Science (Prof. Middendorf), there exists a close collaboration on the topic of pedigree reconstruction and population genetics in complex biological systems. Nine associate partners are taking part in the cooperative project, funded by the EU, “Emergent organisation in complex bio-molecular systems (EMBIO)“. The organizational principles of complex biological systems are being researched in this undertaking (project leaders: Prof. Dr. P. Stadler, Prof. Dr. M. Middendorf, Prof. M. Schlegel).
9. In 2007 24 publications and 6 book contributions from the IZBI appeared in internationally recognized journals.