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Modeling gene regulatory systems by random Boolean networks
KTH, School of Information and Communication Technology (ICT), Microelectronics and Information Technology, IMIT.ORCID iD: 0000-0001-7382-9408
2005 (English)In: Bioengineered and Bioinspired Systems II / [ed] Carmona, RA; LinanCembrano, G, SPIE - International Society for Optical Engineering, 2005, Vol. 5839, 56-65 p.Conference paper (Refereed)
Abstract [en]

A random Boolean network is a synchronous Boolean automaton with n vertices. The parameters of an RBN can be tuned so that its statistical features match the characteristics of the gene regulatory system. The number of vertices of the RBN represents the number of genes in tile cell. The number of cycles in the RBN's state space, called attractors, corresponds the number of different cell types. Attractor's length corresponds to the cell cycle time. Sensitivity of the attractors to different kind of perturbations, modeled by changing the state of a particular vertex, associated Boolean function, or network edge, reflects the stability of the cell to damage, mutations and virus attacks. In order to evaluate the attractors, their number and length have to be re-computed repeatedly. For large RBN's, searching for attractors in the O(2(n)) state space is an infeasible task. Fortunately, only a subset of vertices of an RBN, called relevant vertices, determines its dynamics. The remaining vertices are redundant. In this paper, we present an algorithm for identifying redundant vertices in RBNs which allows us to reduce the search space for computing at.tractors from O(2(n)) to Theta(2 root n). We also show how RBNs can be used for studying evolution.

Place, publisher, year, edition, pages
SPIE - International Society for Optical Engineering, 2005. Vol. 5839, 56-65 p.
, Proceedings of SPIE - International Society for Optical Engineering, ISSN 0277-786X ; 5839
Keyword [en]
Random Boolean Network, gene regulatory network, relevant vertex, attractor
National Category
Atom and Molecular Physics and Optics
URN: urn:nbn:se:kth:diva-43005DOI: 10.1117/12.607825ISI: 000231788300005ScopusID: 2-s2.0-28344449596ISBN: 0-8194-5834-1OAI: diva2:447733
Conference on Bioengineered and Bioinspired Systems II. Seville, SPAIN. May 09-11, 2005

QC 20111013

Available from: 2011-10-13 Created: 2011-10-13 Last updated: 2012-09-26Bibliographically approved

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