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A Methodology Based on MP Theory for Gene Expression Analysis

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Membrane Computing (CMC 2011)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7184))

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Abstract

In this paper we develop an application of the MP theory to gene expression analysis. After introducing some general concepts about transcriptome analysis and about gene networks, we delineate a methodology for modelling such kind of networks by means of Metabolic P systems. MP systems were initially introduced as models of metabolic processes, but they can be successfully used in each context where we want to infer models of a system from a given set of time series. In the case of gene expression analysis, we found a standard way for translating MP grammars involving gene expressions into corresponding quantitative gene networks. Pre-processing methods of raw time series have been also elaborated in order to achieve a successful MP modelling of the underlying gene network.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy

    Luca Marchetti & Vincenzo Manca

Authors
  1. Luca Marchetti
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  2. Vincenzo Manca
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Editor information

Editors and Affiliations

  1. Dept. of Computer Science, University of Sheffield, Regent Court, Portobello Street, S1 4DP, Sheffield, UK

    Marian Gheorghe

  2. Institute of Mathematics of the Romanian Academy, P.O. Box 1-764, 014700, Bucharest, Romania

    Gheorghe Păun

  3. Leiden Center of Advanced Computer Science (LIACS), Leiden University, Niels Bohrweg 1, 2333, Leiden, CA, The Netherlands

    Grzegorz Rozenberg

  4. Turku Centre for Computer Science (TUCS), Leminkaisenkatu 14, 20520, Turku, Finland

    Arto Salomaa

  5. Faculté des Sciences et Technologie, Laboratoire d’Algorithmique, Complexité et Logique (LACL), Université Paris Est – Créteil Val de Marne, 61, av. Général de Gaulle, 94010, Créteil, France

    Sergey Verlan

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Marchetti, L., Manca, V. (2012). A Methodology Based on MP Theory for Gene Expression Analysis. In: Gheorghe, M., Păun, G., Rozenberg, G., Salomaa, A., Verlan, S. (eds) Membrane Computing. CMC 2011. Lecture Notes in Computer Science, vol 7184. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28024-5_20

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  • DOI: https://doi.org/10.1007/978-3-642-28024-5_20

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-28023-8

  • Online ISBN: 978-3-642-28024-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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