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Issue 2, 2013
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From time series to biological network regulations: an evolutionary approach

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Abstract

In this paper we present a new methodology, based on genetic algorithms and multiple linear regression, for discovering regulation mechanisms responsible for observed time series in biological networks. The modeling framework employed is called Metabolic P systems; they are deterministic and time-discrete dynamical systems proposed as an effective alternative to ordinary differential equations for modeling biochemical systems. Our methodology is here successfully applied to the mitotic oscillator in early amphibian embryos. Starting from the time series of substances involved in this system, we are able to reconstruct an MP system reproducing the observed dynamics, where the regulatory components were discovered by our evolutionary methodology. In particular, genetic algorithms are used as a variable selection technique to identify the best representation of any regulation function in terms of some given primitive functions.

Graphical abstract: From time series to biological network regulations: an evolutionary approach

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Publication details

The article was received on 16 May 2012, accepted on 22 Oct 2012 and first published on 25 Oct 2012


Article type: Paper
DOI: 10.1039/C2MB25191D
Citation: Mol. BioSyst., 2013,9, 225-233
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    From time series to biological network regulations: an evolutionary approach

    A. Castellini, M. Zucchelli, M. Busato and V. Manca, Mol. BioSyst., 2013, 9, 225
    DOI: 10.1039/C2MB25191D

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