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EURASIP Journal on Bioinformatics and Systems Biology
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Algorithms for Finding Small Attractors in Boolean Networks

EURASIP Journal on Bioinformatics and Systems Biology volume 2007, Article number: 20180 (2007) Cite this article

Abstract

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.

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Authors and Affiliations

  1. Advanced Modeling and Applied Computing Laboratory, Department of Mathematics, The University of Hong Kong, Pokfulam Road, Hong Kong

    Shu-Qin Zhang & Wai-Ki Ching

  2. Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan

    Morihiro Hayashida & Tatsuya Akutsu

  3. Department of Mathematics, Hong Kong Baptist University, Kowloon Tong, Hong Kong

    Michael K Ng

Authors
  1. Shu-Qin Zhang
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  2. Morihiro Hayashida
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  3. Tatsuya Akutsu
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  4. Wai-Ki Ching
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  5. Michael K Ng
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Correspondence to Shu-Qin Zhang.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Zhang, SQ., Hayashida, M., Akutsu, T. et al. Algorithms for Finding Small Attractors in Boolean Networks. J Bioinform Sys Biology 2007, 20180 (2007). https://doi.org/10.1155/2007/20180

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