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With the support
of the European Commission
Systems Biology and Bioinformatics S1: ENFIN Synergy of Experimental and Computational Research in Systems Biology S4: BIOSAPIENS From Genome to Proteome and Biological Function S8: SYBILLA Systems Biology of T cell Activation in Health and Disease Disease Mechanisms S5: LYMPHANGIOGENOMICS The Vascular Transcriptome, Cell Differentiation and Disease S6: PATHOGENOMICS Functional Genomics of Human Pathogenic Microorganisms S12: EXGENESIS Trends of Functional Genomics in the Metabolic Syndrome S14: LIPIDOMICSNET Lipid Translational Research towards Human Disease Ageing S11: PROTEOMAGE Genome Expression and Regulation S13: HEROIC Epigenetic Profiling during ES Cell Differentiation S15: EUREXPRESS II Large Scale Gene Expression Studies: implications for human disease Resources and Technologies S2: PROTEOMEBINDERS S3: EMERALD Microarray Quality and Clinical Applications S10: RIGHT RNA Interference Technology as Human Therapeutic Tool Infrastructures S7: EUCOMM The European Conditional Mouse Mutagenesis Program S9: BBMRI European Biobanking and Biomolecular Resources
S1: Synergy of Experimental and Computational Research in Systems Biology (ENFIN)
Organisers: Pascal Kahlem & Ewan Birney, EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Although bioinformatics tools are often developed in conjunction with high-throughput large-scale experimental projects in biology, there is still the need for both software development and the necessary social changes (by both computational and experimental researchers) to make the computer as useful as the PCR machine in the standard wet laboratory. This is particularly true in the era of mid- to high-throughput experimental techniques, often requiring systems-biology modelling techniques to understanding how the interacting components work. With the aim of bridging the gap existing between standard wet laboratories and bioinformatics, the European Network of Excellence ENFIN develops integrative technologies to bring the latest computational techniques to bear directly on questions dedicated to Systems Biology in the wet laboratory. At this Session, we will make these computational approaches accessible to a broader range of experimentalists and bioinformaticians without a modelling background, therefore progressively growing the area of computational systems biology beyond its traditionally theoretical level on one hand, and on the other hand introducing more “wet” experimentalists to power of these “dry” computational tools. Selected biologists will expose their areas of research and their use and needs in terms of computational analysis tools. Some areas of the activity of the ENFIN Network will also be illustrated by examples driven by both specific method development and an extensive integration across computational tools. A discussion will be constructed upon the different experiences that will be presented. Reference: Kahlem P. and Birney E. (2007) ENFIN - A Network to enhance Integrative Systems Biology. Annals of the New York Academy of Sciences. in press.
S2: Affinity Proteomics (ProteomeBinders)
Organisers: Mike Taussig & Oda Stoevesandt, Babraham Bioscience Technologies, Babraham, Cambridge , CB22 3AT ProteomeBinders (www.proteomebinders.org) is a European consortium proposing to establish a comprehensive infrastructure resource of affinity binding reagents for detection of the human proteome, together with tools for their use and applications in studying proteome function and organisation. This 4-year FP6 Research Infrastructures Coordination Action, started in 2006, is funded with 1.8 M€ and links 25 EU and 2 USA partners, leaders in the area of binders (including antibodies and also novel binder types based on alternative protein scaffolds or nucleic acids) and their applications. We advocate the organisation of an infrastructure of binders, available at cost and with no restrictions for research use. Currently there is no pan-European platform for the systematic development and quality control for these essential reagents. We aim to provide a set of consistently characterised binders, required to detect all the relevant human proteins in tissues and fluids in health and disease. Reference: Taussig et al, (2007) ProteomeBinders: planning a European resource of affinity reagents for analysis of the human proteome, Nature Methods 4, 13-17.
S3: Microarray Quality and Clinical Applications (EMERALD)
Organisers: Martin Kuiper, Computational Biology, VIB Department of Plant Systems Biology, UGent-VIB Research Building FSVM, Technologiepark 927, 9052 Gent, Belgium; Vidar Beisvåg & Arne Sandvik, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway The “Microarray quality and clinical application symposium” is organised and supported by the EMERALD project. EMERALD is a EU FP6 coordination action that aims to establish and disseminate quality metrics, microarray standards and best laboratory practices throughout the European microarray community. At the 3rd Functional Genomics & Disease Conference, we will illustrate and discuss the importance of (microarray) data quality when microarray technology is used as a clinical tool. More information about EMERALD can be found on the project web page: http://www.microarray-quality.org/index.html
S4: From Genome to Proteome and Biological Function (BIOSAPIENS)
Organiser: Janet Thornton, EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
S5: The Vascular Transcriptome, Cell Differentiation and Disease (LYMPHANGIOGENOMICS)
S6: Functional Genomics of Human Pathogenic Microorganisms (PathoGenoMics)
Organiser: Marion Karresch,
S7: The European Conditional Mouse Mutagenesis Program (EUCOMM)
The
European Conditional Mouse Mutagenesis Program (EUCOMM) is an Integrated
Project funded by the EU in FP6. Its main goal is the establishment of a
large resource of conditionally mutated mouse embryonic stem (ES) cells
which will be freely accessible to the scientific community for the
generation of a wide variety of mouse models for disease research. EUCOMM
is a cornerstone of the International Knockout Mouse Consortium (IKMC),
together with the US KOMP and Canadian NorCOMM projects as well as the
Texas Institute for Genomic Medicine (TIGM). This international consortium
plans to mutate virtually all mouse genes in the next 4-5 years. The scientific community is invited to prioritize genes for conditional gene targeting. The prioritization procedure as well as more EUCOMM information is found at: www.eucomm.org
S8: Systems Biology of T cell Activation in Health and Disease (SYBILLA)
Organiser: Wolfgang Schamel, Max-Planck-Institute for Immunobiology, Freiburg, Germany The immune system has to fulfill the difficult task of discriminating pathogens (e.g. bacteria or viruses and cancerous cells) from cells of the own body. Foreign cells should be attacked and eliminated, whereas self-tissues should not be harmed. The main cell type involved in this decision is the T-cell. T-cell activation is a complex process relying on multiple layers of tightly controlled signaling molecules, which form an intricate intracellular network. Defects in this network can cause inadequate immune responses and severe disorders such as type-1 diabetes or multiple sclerosis. In order to understand the behaviour of this network it is crucial to study it as a complete system and not only its isolated parts. Therefore, the European Union is funding the SYBILLA “Systems Biology of T-cell activation in health and disease” project for 5 years. SYBILLA (www.sybilla-t-cell.de) is a consortium of 17 scientific and industrial partners (14 are from Europe and 3 from the US and India). Through a multidisciplinary effort it aims to understand at systems level, how T-cells discriminate foreign- from self-peptides by activating quantitatively distinct signaling pathways. Data obtained in mouse models are extended to human T cells and to a mouse model of multiple sclerosis. SYBILLA develops new technological and mathematical tools to generate and integrate high-density quantitative data describing T-cell activation. Proteomics, transcriptomics, imaging and biochemical techniques will be applied to obtain holistic maps of the T-cell signaling network and to achieve a quantitative and dynamic understanding of signaling networks and their regulation in response to different signal inputs. Building upon already existing schemes of the network connectivity, constant iteration between experiment and mathematical modelling will be used to develop robust and predictive models that describe the functioning of the T-cell signaling network. SYBILLA will allow the identification of new drug targets and the discovery of new biomarkers to refine prognosis of autoimmune diseases.
S9: European Biobanking and Biomolecular Resources (BBMRI)
S10: RNA Interference Technology as Human Therapeutic Tool (RIGHT)
Organisers: Thomas Meyer & Simone Hess, Max Planck Institute for Infection Biology, Charitéplatz 1, D-10117 Berlin, Germany The RIGHT (RNA Interference
Technology as Human Therapeutic Tool) project aims to exploit the vast
potential of RNA interference (RNAi) for human therapy. RIGHT involves 25
research institutes and enterprises throughout Europe and in RIGHT combines the strengths of several synergistic competence domains to overcome key technological barriers such as undesired interferon response and insufficient delivery, stability and targeting of RNAi to the appropriate cells. Efficient RNAi reagents are generated through both chemical synthesis of modified siRNAs and vector based gene therapy approaches using shRNAs. Strategies are developed for efficient delivery to cells and tissues of diseased organisms. Relevant disease models are used to evaluate the function and effectiveness of the inhibitors. At this symposium, partners of the RIGHT consortium will talk about their outstanding achievements aimed towards the therapeutic application of RNAi.
S11: Molecular Ageing (ProteomAge)
S12: Trends of Functional Genomics in the Metabolic Syndrome (EXGENESIS)
Organiser: Allan Vaag,
Steno Diabetes Centre, Forårsvej 17 , DK-2920
S13: Epigenetic Profiling during ES cell Differentiation (HEROIC)
Organiser: Henk Stunnenberg, Department of Molecular Biology, NCMLS #274, Radboud, University Nijmegen, PO Box 9101, 6500 HB Nijmegen
S14: Lipid Translational Research Towards Human Disease (LipidomicsNet)
S15: Large Scale Gene Expression Studies: implications for human disease
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