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Customers & Collaborators
SystemsX.ch
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SystemsX.ch is determined to become a world-leading initiative in quantitative Systems Biology. This goal shall be achieved by combining Switzerland’s strengths in genomics and biomedical research with its flourishing core sciences as chemistry, mathematics, physics and engineering. In a paradigm shift biology is moving from a descriptive, qualitative science to a predictive, quantitative one. SystemsX.ch aims to accelerate this shift on three avenues: developing innovative technology to obtain and analyze quantitative biomedical data, via building mathematical models that accurately simulate and predict the behaviour of biological systems, and most importantly: asking the right biological questions. |
SyBIT
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SyBIT, the SystemsX.ch Biology IT project has been initiated by SystemsX.ch to assure that the data produced by all projects is well-documented and made gradually available to the research community for further use. SyBIT will supply tools and infrastructure for data management, data analysis and archiving for all SystemsX.ch projects; develop and promote standard interfaces for data access and establish processes and policies for quality and knowledge management. SyBIT cooperates with all SystemsX.ch partner institutions and their infrastructure providers. |
Swiss Institute of Bioinformatics
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The SIB (Swiss Institute of Bioinformatics) is an academic, non-profit foundation recognised of public utility and established in 1998. SIB coordinates research and education in bioinformatics throughout Switzerland and provides high quality bioinformatics services to the national and international research community. |
Novartis
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Novartis has a diverse healthcare portfolio, including innovative pharmaceuticals, eye care products, generics, consumer health products, and vaccines and diagnostic tools. |
Genedata
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Genedata transforms data into intelligence with innovative software solutions that support large-scale, experimental processes in life science research. Founded in 1997, Genedata delivers enterprise solutions for data analytics that streamline R&D workflows and improve research productivity. Today, most of the leading pharmaceutical, agrochemical, and biotechnology companies, as well as some of the most innovative life science research institutions rely on Genedata. |
BaSynthec
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BaSynthec (Bacterial Synthetic minimal genomes for biotechnology) is a collaborative research project funded by the European Commission, with a financial support of 3 M€ (total cost of 5 M€) from the 7th Framework program under the Knowledge Based Bio-Economy (KBBE) priority. BaSynthec involves 8 partners from academia and industry, and gathers scientific teams from 5 European countries and the USA. The project will run over a period of 3 years, starting June 1st, 2010. BaSynthec is coordinated by Dr. Philippe Noirot of the Institut National de la Recherche Agronomique (INRA). |
IMSB - ETH Zurich / Aebersold & Sauer
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Prof. Ruedi Aebersold is one of the pioneers in the field of proteomics. He is known for developing a series of methods that have found wide application in analytical protein chemistry and proteomics like a new class of reagents termed Isotope Coded Affinity Tag (ICAT) reagents used in quantitative mass spectrometry. Prof. Dr. Aebersold and his team of researchers use the protein profiles determined by this method to differentiate cells in different states, such as noncancerous versus cancerous cells, and to systematically study how cells respond to external stimuli. These "snapshot" profiles indicate which cells contain abnormal levels of certain proteins. This is expected to lead to new diagnostic markers for disease and to a more complete understanding of the biochemical processes that control and constitute cell physiology. The mission of the systems biology research in the Zamboni and Sauer labs is to identify and quantify the key regulation mechanisms that control cellular metabolism in microbes and mammalian cells. The speciality of our interdisciplinary team of biologists, engineers, and computer scientists are high-throughput experimental technologies for quantitative metabolomics, 13C-based intracellular flux analysis, and dynamic GFP analysis in mini-scale cultivations. Different types of mathematical models are then used to quantitatively relate metabolomics, expression and proteomics data to the functional network output in terms of fluxes. |
Universität Basel, Biozentrum, Center for Cellular Imaging and NanoAnalytics (C-CINA)
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The Center for Cellular Imaging and NanoAnalytics (C-CINA) is a research laboratory of the Biozentrum of the University Basel. It is integrated into the Department for Biosystems Science and Engineering (D-BSSE) of the ETH Zürich, which is located in the northern part of Basel, Switzerland. |
ETH Zürich, D-BSSE, Computational Systems Biology (csb) Group
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The group develops computational methods for studying complex networks that establish cellular functions to elucidate their operating and design principles. It focuses on concepts and tools for network inference, for system modeling and analysis, and for experimental design at larger scales in different biological systems. More specifically, it aims at elucidating design principles of the integration of cellular regulation across metabolism, signal transduction and gene regulation. All projects involve close collaborations with experimental biologists and computer / systems scientists. |
Sanofi
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Sanofi, a global and diversified healthcare leader, discovers, develops and distributes therapeutic solutions focused on patients’ needs. Sanofi has core strengths in healthcare, with 6 growth platforms: emerging markets, vaccines, consumer healthcare, diabetes treatments, innovative products and animal health. Through the acquisition of Genzyme, Sanofi has strongly reinforced its footprint in rare diseases. |
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Agios is focused on cancer metabolism, a new approach to the treatment of cancer patients.
Cancer metabolism is the study of the altered metabolism of cancer cells – what nutrients they consume and how they use them – that allows them to grow rapidly and form tumors. Agios is pioneering research and creating a portfolio of first-in-class anticancer drugs that will allow us to “starve” cancer cells by interrupting the metabolic processes that fuel their growth. |
Universität Basel, Departement Biomedizin, Developmental Genetics, Zeller Group
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The Zeller group uses a systems biology approach that combines mouse molecular genetics, transcriptome analysis, biochemistry with mathematical simulations of the relevant interactions (in collaboration with D. Iber from D-BSSE) to gain insight into signalling interactions that control vertebrate limb bud organogenesis. |
Universität Basel, Departement Biomedizin, Cell Migration and Neuritogenesis, Pertz group
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The research focus of the Pertz group is spatio-temporal Rho GTPase signaling programs in directed cell migration and neuritogenesis. |
Universität Basel, Biozentrum, Dehio Group
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The research in Christoph Dehio’s group is focused on molecular mechanisms of bacterial pathogenesis. In particular it is studying the role of type IV secretion systems (T4SS) in the evolution and pathogenesis of the related bacterial pathogens Bartonella and Brucella.
Specific Contribution to Research in InfectX: |
University of Massachusetts Medical School, Strambio Lab
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Attempts to block virus infections, including those caused by Retroviridae, require a fundamental understanding of the molecular events governing individual steps of the viral life cycle. Despite progress, the sub-cellular localization, timing and kinetics of individual molecular events remain elusive. Using dynamic imaging followed by rigorous computational analysis of viral particle trajectories, the complex interplay between viral and cellular components can be solved. |
Universität Tübingen
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The group of Oliver Kohlbacher was established in 2003 and is primarily working on computer-aided drug design, immunoinformatics, structural bioinformatics as well as bioinformatics applications in proteomics, metabolomics and systems biology. The group collaborates closely with a large number of experimental groups to gain access to up-to-date and relevant datasets. |
Freie Universität Berlin
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The Algorithmic Bioinformatics group of Prof. Dr. Ing. Knut Reinert focuses on the development of novel algorithms and data structures for problems in the analysis of biomedical mass data. In particular, we are interested in developing mathematical models for analyzing large genomic sequences, especially in the context of next generation sequencing (NGS), and data derived from mass spectrometry experiments, for example for detecting differential expression of proteins between normal and diseased samples. |
bio.logis
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bio.logis GmbH was established as an independent startup in 2008 and is located at the "Frankfurt Biotechnology Information Center (FIZ)". bio.logis provides genetic diagnostics and information for medical decision making and is specialized in the development of IT systems for biological and medical data. The company’s focus is information that has been determined medically relevant by scientific tests and provides direct benefits for the health of customers, for example, through personalized pharmacotherapy. |
ETH Zürich, D-BSSE, Quantitative Genomics Facility (QGF)
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The Quantitative Genomics Facility (QGF) at the D-BSSE provides Next Generation Sequencing technologies to research institutions and companies in the whole Basel area. Currently there is one Illumina HiSeq2000 and one Genome Analyzer IIx which produce high quality sequencing data. |
ETH Zürich, D-BSSE, Single Cell Analysis Unit (SCU)
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The Single Cell Unit (SCU) is a newly established central scientific facility within the ETH Department of Biosystems Science and Engineering (D-BSSE), located in Basel. The SCU supports users in flow cytometry, microscopy and laboratory automation. |
Light Microscopy and Screening Centre of ETH Zürich
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The Light Microscopy and Screening Centre LMSC of the ETH Zurich is a facility created through the effort of a group of ETH professors in order to offer its users a collection of state-of-the-art light microscopy equipment and accessory services. While the LMSC serves primarily the need of its members and their groups, it is basically open to any researcher at the ETH Zurich, and under certain circumstances to external, UniZh/academic/industrial users. The LMSC has three main parts: high-end microscopy, histology and the RNAi image-based screening center. |
HDF Group
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The HDF Group provides a unique suite of technologies and supporting services that make possible the management of large and complex data collections. Its mission is to advance and support HDF (Hierarchical Data Format) technologies and ensure long-term access to HDF data. |
ISB, Seattle, USA
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The Institute for Systems Biology in Seattle, USA is a nonprofit research institute, and was founded in 2000 with the mission of transforming biological and medical research by creating and using systems approaches to unravel the workings of complex biological systems. The Institute’s ultimate goal is to enhance people’s lives by using the science of systems biology to predict, prevent, and cure disease. |
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