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Issues in Computational Methods for Functional Genomics and Systems Biology

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Computational Methods in Systems Biology (CMSB 2003)

Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 2602))

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Abstract

Systems Biology starts by defining the components of a biological system and collecting the relevant previous biochemical and genetic data on a global scale, using high throughput platforms, formulating an initial model of the system, systematically perturbing the components of the system, and analysing the results. By comparing the observed responses to those predicted by the model,it is then possible to iteratively refine the model so that its prediction fit best to the experimental observations. Finally, new experimental perturbations are conceived and tested in order to distinguish between the multiple competing hypotheses.

We discuss the computational methods used for high throughput data collection in functional genomics, emphasizing the strong need for standardization and quality assurance. We then review the computational needs required for biological system modeling and semantic integration in the systemic framework, arguing that the Unified Modeling Language (UML) seems appropriate to support the iterative process of Systems Biology.

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References

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Author information

Authors and Affiliations

  1. Biosystemics, Modeling, Engineering, Institut Pasteur, Paris, France

    Magali Roux-Rouquié

  2. Institute for Systems Biology, Seattle, USA

    Leroy Hood

  3. Genexpress - Functional Genomics and Systemic Biology for Health CNRS FRE 2571, 7 , rue Guy Moquet, BP8, 94801, Villejuif cedex, France

    Sandrine Imbeaud & Charles Auffray

Authors
  1. Magali Roux-Rouquié
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  2. Leroy Hood
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  3. Sandrine Imbeaud
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  4. Charles Auffray
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Editor information

Editors and Affiliations

  1. Dipartimento di Informatica e Telecomunicazioni, Università di Trento, Via Sommarive, 14, 38050, Povo (TN), Italy

    Corrado Priami

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© 2003 Springer-Verlag Berlin Heidelberg

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Roux-Rouquié, M., Hood, L., Imbeaud, S., Auffray, C. (2003). Issues in Computational Methods for Functional Genomics and Systems Biology. In: Priami, C. (eds) Computational Methods in Systems Biology. CMSB 2003. Lecture Notes in Computer Science, vol 2602. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36481-1_26

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  • DOI: https://doi.org/10.1007/3-540-36481-1_26

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-00605-3

  • Online ISBN: 978-3-540-36481-8

  • eBook Packages: Springer Book Archive

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