It is the goal of the project to gain detailed understanding of two key processes: the p53-MDM2 regulatory network and its role in cell proliferation, differentiation and tumor development, and spindle formation process whereby chromatin controls microtubule nucleation and organization. A major objective is development of modeling and simulation methods to generate useful hypotheses for experimentalists. The project combines experimental, bioinformatics and simulation approaches. The contribution of the Dept. of Bioinformatics is to add data about and influences of pathologically relevant mutations to the p53-MDM2 network model.
It was the aim of this project, that run from 2000 to June 2004, to develop bioinformatics tools for investigating genetic mutations which exhibit clinically relevant phenotypes. That included developing, adapting and integrating data sources about transcriptional regulation, signal transduction pathways, metabolic pathways, cellular systems, and metabolic diseases with programs for the prediction of regulatory genome regions and simulation of regulatory pathways. It also aimed at creating an integrative system that provides a unifying view of molecular mechanisms in gene regulation, signal transduction, metabolic pathways, and clinical consequences of their aberrations.
The project aims at developing approaches and tools for the computer-assisted representation and modeling of various cellular states associated with diseases. The capacity of such approaches and tools will be verified by applying to some selected disease examples and available experimental data.
The complete name of the project: Molecular representation of disease states in biological regulatory networks
It is funded by the Land Niedersachsen and the European Regional Development Fund (ERDF, German: EFRE)
Time: 01.01.2009 - 31.12.2010
BIOBASE GmbH (Wolfenbüttel, Germany) [link: www.biobase-international.com]
The project aims at analyzing and ultimately predicting the behaviour of human cells in a complex environment, using a combination of cell biology, bioinformatics, mathematical modeling and systems biology approaches and tools. The term ?complex environment? applies to any combination of two or more stimuli, which could be well-defined biological factors or therapeutic compounds, but also biological fluids or cell supernatants of physiopathological relevance (for example, a tumour cell supernatant to mimic a tumor microenvironment). Such environment should best reflect the complexity of physiological or pathological conditions that elicit a specific response of a given cell type.
The complete name of the project: Global scale analysis and prediction of human cellular behavior in a complex environment
Funded by ETB / BMBF
Time: 01.07.2008 - 30.06.2010
BIOBASE GmbH (Wolfenbüttel, Germany; coordinator: A. Kel) [link: www.biobase-international.com]
Helios Biosciences (Créteil, France) [link: www.helios-bioscience.com]
Institut Curie (Paris, France) [link: www.curie.fr/recherche/themes/detail_equipe.cfm/lang/_gb/id_equipe/334.htm]
The Helmholtz Network for Bioinformatics provides a framework for integrating complex bioinformatics tasks. It was a joint venture of 12 German bioinformatics research groups that was finished in December 2003. It has offered convenient access to numerous bioinformatics resources through a single, user-friendly web portal. The portal will be maintained for at least two more years. The follow-up project HOBIT will extend the range of resources offered and provide an interface for programmatic access to databases and software tools based on open standards and protocols.
The HNB-Webservice has been terminated in june 2007. more
HOBIT is a follow-up project to HNB. The goal of HOBIT is to develop an open network of bioinformatic resources. Where HNB provides a user-friendly web interface aiming primarily at bioscientists not particularly educated in bioinformatics, HOBIT is set up as open network where third party bioscientists are invited to both utilize the offered tools and offer there one ones to the community. It is based on open standards and protocols. The BioSchemas project as part of the HOBIT project develops XML schemas for the exchange of biological data. HOBIT offers webservices for use, see our webservices here.
The goal of the research and development of ?Intergenomics? is to provide a range of bioinformatics tools that are suitable to model the interaction of genome-driven processes during the infection of mammalian and plant organisms.
For that purpose, an integrated infrastructure shall be generated which comprises the knowledge bases, tools and services that already exist in this region as well as those which will be specifically developed in the course of this project. It is designed as a sustained and long-term concept with promising exploitation perspectives for the tools to be developed. Therefore, its consortium also comprises a commercial partner who could act as exploitation partner, but also will articulate the professional needs for bioinformatic achievements. Finally, the project also has a strong educational component which accomodates the interdisciplinary requirements of bioinformatics and which is supported by all partners of the competence center. more
The project aims to exploit the recent developments in lipidomics technology to establish high-throughput methods, to define druggable targets and novel biomarkers related to lipid droplet (LD) composition. It focuses on lipid protein interactions and investigates the dynamics of fat deposition and release in relevant cells as a hallmark of energy overload diseases with major health care impact in Europe.
The complete name of the project: Lipid droplets as dynamic organelles of fat deposition and release: Translational research towards human disease
Funded by the European Commission within FP7, under the thematic area "High throughput analysis of lipid and lipid-protein interactions", contract number HEALTH 2007-2.1.1-6
University Regensburg (Prof. G. Schmitz, coordinator)
24 further partners
Project page: www.lipidomicnet.org
The project aims at developing a set of tools that combines different experimental high-throughput methods together with bio- and chemoinformatical approaches, to exploit the full potential of the included methods as well as the generated data. This toolbox shall provide a cost- and time-effective, knowledge-based approach that allows identification of signal transduction mediators and/or transcriptional regulators responsible for certain changes or responses of the cell, in particular those which lead to diseases. Thereby it shall facilitate the discovery of new targets and consequently the rational design of target-specific drugs.
The complete name of the project: From gene regulatory networks to drug prediction.
Funded by the European Commission within FP6, contract number LSH-2005-1.2.5-4
BIOBASE GmbH (Wolfenbüttel, Germany) [link: link: www.biobase-international.com]
Progenika Biopharma S.L., (Spain )
National Public Health Institute, (Finland )
Fraunhofer Gesellschaft zur Forderung der angewandten Forschung e.V., (Hanover, Germany)
Institute of Systems Biology, Ltd, (Russia )
Institute of Biomedical Chemistry of Russian Academy of Medical Sciences, (Russia )
Karolinska Institutet, (Sweden)
Institute for Biomedical Technology - National Research Council, (Italy)
funded by the European Commission within its FP6 Programme, under the thematic area "Life, sciences, genomics and biotechnology for health", contract number LSHG-CT-2004-503568
The European Molecular Biology Linked Original Resources (TEMBLOR) was founded by the European Commission in 2002 to take place in the "Quality of Life and Management of Living Resources " programme.
The aim of TEMBLOR is to connect databases of major bioinformatics centres in Europe through an integration layer (Integr8).
Our department is involved in the Integr8 projekt, where we provide access to our databases S/MARtDB, ReAlSplice and PathoDB. The following people are involved: Dr. Petra Hummel, Knut Schwarzer, Dr. Ines Liebich, Juergen Doenitz. Please contact them via email.
funded by the European Commission as the TEMBLOR, contract-no. QLRI-CT-2001-00015 under the RTD programme "Quality of Life and Management of Living Resources"