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The meaning of systems biology
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Kirschner M.W. The meaning of systems biology. Cell 121 (2005) 503-504
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Systems biology: a brief overview
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Kitano H. Systems biology: a brief overview. Science 295 (2002) 1662-1664
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Kitano, H.1
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33750795440
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Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways
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By standardization of protocols and materials the authors present how quantitative data generation is reproducibly achieved studying primary hepatocytes.
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Klingmüller U., Bauer A., Bohl S., Nickel P.J., Breitkopf K., Dooley S., Zellmer S., Kern C., Merfort I., Sparna T., et al. Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways. IEE Proc Syst Biol 153 (2006) 433-447. By standardization of protocols and materials the authors present how quantitative data generation is reproducibly achieved studying primary hepatocytes.
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IEE Proc Syst Biol
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Klingmüller, U.1
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Sparna, T.10
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29144434998
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Computational processing and error reduction strategies for standardized quantitative data in biological networks
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The authors identify steps in quantitative immunoblotting most prone to errors. They present a combination of experimental and software-based approaches to significantly improve the quality of quantitative data based on a criteria-based normalization method.
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Schilling M., Maiwald T., Bohl S., Kollmann M., Kreutz C., Timmer J., and Klingmüller U. Computational processing and error reduction strategies for standardized quantitative data in biological networks. FEBS J 272 (2005) 6400-6411. The authors identify steps in quantitative immunoblotting most prone to errors. They present a combination of experimental and software-based approaches to significantly improve the quality of quantitative data based on a criteria-based normalization method.
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FEBS J
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Schilling, M.1
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Klingmüller, U.7
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Beyond standardization: dynamic software infrastructures for systems biology
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Swertz M.A., and Jansen R.C. Beyond standardization: dynamic software infrastructures for systems biology. Nat Rev Genet 8 (2007) 235-243
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Swertz, M.A.1
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Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
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Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25 (2000) 25-29
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Using process diagrams for the graphical representation of biological networks
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Kitano H., Funahashi A., Matsuoka Y., and Oda K. Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 23 (2005) 961-966
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Kitano, H.1
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Tools for quantitative and validated measurements of cells
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Plant A.L., Elliott J.T., Tona A., McDaniel D., and Langenbach K.J. Tools for quantitative and validated measurements of cells. Methods Mol Biol 356 (2007) 95-107
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Yeast systems biology to unravel the network of life
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Mustacchi R., Hohmann S., and Nielsen J. Yeast systems biology to unravel the network of life. Yeast 23 (2006) 227-238
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Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisers
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Schilling M., Maiwald T., Bohl S., Kollmann M., Kreutz C., Timmer J., and Klingmüller U. Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisers. IEE Proc Syst Biol 152 (2005) 193-200
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Schilling, M.1
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Klingmüller, U.7
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Data reproducibility in fluorescence image analysis
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Souchier C., Brisson C., Batteux B., Robert-Nicoud M., and Bryon P.A. Data reproducibility in fluorescence image analysis. Methods Cell Sci 25 (2003) 195-200
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Evaluation of confocal microscopy system performance
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Zucker R.M. Evaluation of confocal microscopy system performance. Methods Mol Biol 319 (2006) 77-135
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Methods Mol Biol
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Standards for reporting bioscience data: a forward look
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Taylor C.F. Standards for reporting bioscience data: a forward look. Drug Discov Today 12 (2007) 527-533
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Minimum information about a microarray experiment (MIAME)-toward standards for microarray data
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Brazma A., Hingamp P., Quackenbush J., Sherlock G., Spellman P., Stoeckert C., Aach J., Ansorge W., Ball C.A., Causton H.C., et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29 (2001) 365-371
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Making a new technology work: the standardization and regulation of microarrays
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Rogers S., and Cambrosio A. Making a new technology work: the standardization and regulation of microarrays. Yale J Biol Med 80 (2007) 165-178
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Rogers, S.1
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Standardizing the standards
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Quackenbush J. Standardizing the standards. Mol Syst Biol 2 (2006) 2006-2010
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Mol Syst Biol
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The minimum information about a proteomics experiment (MIAPE)
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Taylor C.F., Paton N.W., Lilley K.S., Binz P.A., Julian Jr. R.K., Jones A.R., Zhu W., Apweiler R., Aebersold R., Deutsch E.W., et al. The minimum information about a proteomics experiment (MIAPE). Nat Biotechnol 25 (2007) 887-893
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Taylor, C.F.1
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28544447780
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The open microscopy environment (OME) data model and XML file: open tools for informatics and quantitative analysis in biological imaging
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Goldberg I.G., Allan C., Burel J.M., Creager D., Falconi A., Hochheiser H., Johnston J., Mellen J., Sorger P.K., and Swedlow J.R. The open microscopy environment (OME) data model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol 6 (2005) R47
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Goldberg, I.G.1
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Sorger, P.K.9
Swedlow, J.R.10
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22
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33750314698
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Collecting and organizing systematic sets of protein data
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The authors review affinity-based, physical and enzymatic assays available to study how signals within protein networks change in space and time. They discuss methods for the transformation of raw data from different techniques into systematic sets of data.
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Albeck J.G., MacBeath G., White F.M., Sorger P.K., Lauffenburger D.A., and Gaudet S. Collecting and organizing systematic sets of protein data. Nat Rev Mol Cell Biol 7 (2006) 803-812. The authors review affinity-based, physical and enzymatic assays available to study how signals within protein networks change in space and time. They discuss methods for the transformation of raw data from different techniques into systematic sets of data.
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Nat Rev Mol Cell Biol
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Albeck, J.G.1
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Flexible informatics for linking experimental data to mathematical models via DataRail
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The paper presents a toolbox to store experimental data into flexible, multidimensional arrays to link and preserve connections of experimental data and mathematical models to facilitate data-based model calibrations.
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Saez-Rodriguez J., Goldsipe A., Muhlich J., Alexopoulos L.G., Millard B., Lauffenburger D.A., and Sorger P.K. Flexible informatics for linking experimental data to mathematical models via DataRail. Bioinformatics 24 (2008) 840-847. The paper presents a toolbox to store experimental data into flexible, multidimensional arrays to link and preserve connections of experimental data and mathematical models to facilitate data-based model calibrations.
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Bioinformatics
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Saez-Rodriguez, J.1
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Tools for kinetic modeling of biochemical networks
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Alves R., Antunes F., and Salvador A. Tools for kinetic modeling of biochemical networks. Nat Biotechnol 24 (2006) 667-672
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Nat Biotechnol
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Alves, R.1
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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
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Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19 (2003) 524-531
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Hucka, M.1
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Systems biology standards - the community speaks
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Klipp E., Liebermeister W., Helbig A., Kowald A., and Schaber J. Systems biology standards - the community speaks. Nat Biotechnol 25 (2007) 390-391
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Minimum information requested in the annotation of biochemical models (MIRIAM)
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Le Novère N., Finney A., Hucka M., Bhalla U.S., Campagne F., Collado-Vides J., Crampin E.J., Halstead M., Klipp E., Mendes P., et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nat Biotechnol 23 (2005) 1509-1515
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BioModels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
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Dynamic pathway modeling: feasibility analysis and optimal experimental design
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Maiwald T., Kreutz C., Pfeifer A.C., Bohl S., Klingmüller U., and Timmer J. Dynamic pathway modeling: feasibility analysis and optimal experimental design. Ann N Y Acad Sci 1115 (2007) 212-220
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