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Boolean Networks and Their Applications in Science and Engineering

Jose C. Valverde, Henning S. Mortveit, Carlos Gershenson, Yongtang Shi
2020 Complexity  
For these kinds of models, which are usually known as sequential dynamical systems (SDS) on maxterm and minterm Boolean functions, the authors solve the predecessor-existence problems algebraically.  ...  In the paper "Predecessors Existence Problems and Gardens of Eden in Sequential Dynamical Systems", Aledo et al. deal with network models which are deterministic, asynchronously updated, homogeneous and  ...  Acknowledgments The editors thank all the authors of the papers submitted to this special issue and all the reviewers for their time and effort in conducting the corresponding review processes.  ... 
doi:10.1155/2020/6183798 fatcat:a2kdkdc4dndmdfzy4qnhiximhy

An efficient algorithm for finding attractors in synchronous Boolean networks with biochemical applications

D. Zheng, G. Yang, X. Li, Z. Wang, W.N.N. Hung
2013 Genetics and Molecular Research  
Self-organized systems, genetic regulatory systems and other living systems can be modeled as synchronous Boolean networks with stable states, which are also called state-cycle attractors (SCAs).  ...  This paper summarizes three classes of SCAs and presents a new efficient binary decision diagram based algorithm to find all SCAs of synchronous Boolean networks.  ...  ACKNOWLEDGMENTS Research supported by the National Natural Science Foundation of China (Grant #60973016) and "973" Foundation (#2010CB328004).  ... 
doi:10.4238/2013.october.18.4 pmid:24222242 fatcat:x756fuv5ofdetnl2pbqbebejzm

Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length

John Dougherty, Ioan Tabus, Jaakko Astola
2008 EURASIP Journal on Bioinformatics and Systems Biology  
in Boolean networks.  ...  The Boolean network paradigm is a simple and effective way to interpret genomic systems, but discovering the structure of these networks remains a difficult task.  ...  Acknowledgments This work was supported by the Academy of Finland (Application no. 213462, Finnish Programme for Centres of Excellence in Research 2006-2011), and the Tampere Graduate School in Information  ... 
doi:10.1155/2008/482090 pmid:18437238 pmcid:PMC3171396 fatcat:oiwswxvasfhbfl74opdfsqpgpa

An efficient algorithm for computing fixed length attractors based on bounded model checking in synchronous Boolean networks with biochemical applications

X.Y. Li, G.W. Yang, D.S. Zheng, W.S. Guo, W.N.N. Hung
2015 Genetics and Molecular Research  
One condition of the genetic regulatory network under different living environments can be modeled as a synchronous Boolean network.  ...  The attractors of these Boolean networks will help biologists to identify determinant and stable factors.  ...  ties (Grant #ZYGX2011YB022), the National Natural Science Foundation of China (Grant #61272175, and #973 Foundation #2010CB328004).  ... 
doi:10.4238/2015.april.28.5 pmid:25966195 fatcat:trpym7xjtrho7cuaeldbmwf5ou

Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions

Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano
1997 Genome Informatics Series  
Acknowledgments This work was supported in part by a Grant-in-Aid "Genome Science" for Scientific Research on Priority Areas from The Ministry of Education, Science, Sports and Culture in Japan.  ...  As mentioned above, we consider a gene regulatory network model such that the expression of a gene is determined by a boolean function of the expressions of the genes directly affecting it.  ...  We define the indegree of a gene by the number of genes directly affecting it in a gene regulatory network. The indegree of most genes may be only one or two except some special genes.  ... 
doi:10.11234/gi1990.8.254 fatcat:jsumcm63znd6hlqs4nl63qsoxy

Improving BDD-based attractor detection for synchronous Boolean networks

Qixia Yuan, Hongyang Qu, Jun Pang, Andrzej Mizera
2016 Science China Information Sciences  
We demonstrate the performance of our approach on a number of examples and on a realistic model of apoptosis in hepatocytes. We compare it with one existing technique in the literature.  ...  Boolean networks are an important formalism for modelling biological systems and have attracted much attention in recent years.  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1007/s11432-016-5594-9 fatcat:3lu7kltxtvatjpwi4koybpyx2a

Improving BDD-based Attractor Detection for Synchronous Boolean Networks

Hongyang Qu, Qixia Yuan, Jun Pang, Andrzej Mizera
2015 Proceedings of the 7th Asia-Pacific Symposium on Internetware - Internetware '15  
We demonstrate the performance of our approach on a number of examples and on a realistic model of apoptosis in hepatocytes. We compare it with one existing technique in the literature.  ...  Boolean networks are an important formalism for modelling biological systems and have attracted much attention in recent years.  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1145/2875913.2875925 dblp:conf/internetware/QuYPM15 fatcat:qcc3w5qeejgbtisupsjxrhff2e

FINDING AND ANALYZING THE MINIMUM SET OF DRIVER NODES IN CONTROL OF BOOLEAN NETWORKS

WENPIN HOU, TAKEYUKI TAMURA, WAI-KI CHING, TATSUYA AKUTSU
2016 Advances in Complex Systems  
On the other hand, structural controllability has recently attracted considerable attentions in the field of complex networks.  ...  In many of these works, necessary and sufficient conditions of the controllability of Boolean control networks are derived.  ...  Gene regulatory networks are models of sets of interactions among genes, the analysis of which is one of the key topics in systems biology and theoretical biology.  ... 
doi:10.1142/s0219525916500065 fatcat:cuf4uggor5gr3bzeiigavy5gxm

Inferring gene regulatory networks from time series data using the minimum description length principle

W. Zhao, E. Serpedin, E. R. Dougherty
2006 Bioinformatics  
This paper addresses the problem of inferring genetic regulatory networks from time-series gene-expression profiles.  ...  By adopting a probabilistic modeling framework compatible with the family of models represented by dynamic Bayesian networks and probabilistic Boolean networks, this paper proposes a network inference  ...  ACKNOWLEDGEMENTS The authors would like to appreciate the reviewers' comments for improving the quality of this paper.  ... 
doi:10.1093/bioinformatics/btl364 pmid:16845143 fatcat:plkzt652vjbrhg63jgvt4gyjqm

Overcoming the complexity barrier of the dynamic message-passing method in networks with fat-tailed degree distributions [article]

Giuseppe Torrisi, Alessia Annibale, Reimer Kühn
2021 arXiv   pre-print
As a case study, we analyse the dynamics of a random Boolean network with a fat-tailed degree distribution and fully asymmetric binary ± J couplings, and we use the power of the algorithm to unlock the  ...  However, the complexity of the cavity approach grows exponentially with the in-degrees of the interacting units, which creates a de-facto barrier for the successful analysis of systems with fat-tailed  ...  THE MODEL We consider a Boolean network model defined on a finitely connected directed graph of N nodes labelled i = 1, . . . , N .  ... 
arXiv:2105.04197v2 fatcat:3zdpzcvzszdf7cjvogdig2lixa

Spatial Information and Boolean Genetic Regulatory Networks [chapter]

Matthieu Manceny, Marc Aiguier, Pascale Le Gall, Joan Hérisson, Ivan Junier, François Képès
2009 Lecture Notes in Computer Science  
One of the main problems with such modelling frameworks is to determine the dynamics of gene regulatory networks (GRN).  ...  Modelling frameworks for biological networks are used to reason on the models and their properties.  ...  Introduction To understand Genetic Regulatory Networks (GRN), modelling frameworks and simulation techniques are often useful since the complexity of the interactions between constituents of the network  ... 
doi:10.1007/978-3-642-00727-9_26 fatcat:f5ppp5apxzcbznkqgge5u2r2jq

Analysis of Gene Interactions Using Restricted Boolean Networks and Time-Series Data [chapter]

Carlos H. A. Higa, Vitor H. P. Louzada, Ronaldo F. Hashimoto
2010 Lecture Notes in Computer Science  
A popular model for gene regulatory networks is the Boolean network model.  ...  In this paper, we propose an algorithm to perform an analysis of gene regulatory interactions using the Boolean network model and time-series data.  ...  In fact, the inference of gene regulatory networks is a one-to-many inverse problem in the sense that there may exist several networks consistent with the dataset.  ... 
doi:10.1007/978-3-642-13078-6_9 fatcat:bweyoyo2zrfi5dglj6c3dsx4ui

Analyses and Algorithms for Predecessor and Control Problems for Boolean Networks of Bounded Indegree

Tatsuya Akutsu, Morihiro Hayashida, Shu-Qin Zhang, Wai-Ki Ching, Michael K. Ng
2008 IPSJ Transactions on Bioinformatics  
We study the predecessor and control problems for Boolean networks (BNs).  ...  In this paper, we focus on BNs of bounded indegree and show some hardness results on the computational complexity of the predecessor and control problems.  ...  Acknowledgments TA was partially supported by a Grant-in-Aid "Systems Genomics" from MEXT and by the Cell Array Project from NEDO, Japan.  ... 
doi:10.2197/ipsjtbio.1.23 fatcat:ouyb7bzm6jawhihlbuexuif3aq

Modeling of gene regulatory networks: A review

Nedumparambathmarath Vijesh, Swarup Kumar Chakrabarti, Janardanan Sreekumar
2013 Journal of Biomedical Science and Engineering  
Gene regulatory networks play an important role the molecular mechanism underlying biological processes. Modeling of these networks is an important challenge to be addressed in the post genomic era.  ...  In this paper we tried to review the different methods for reconstructing gene regulatory networks.  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge the financial support provided by Department of Information Technology (DIT) Government of India for carrying out this work.  ... 
doi:10.4236/jbise.2013.62a027 fatcat:dxpzycz4cbd47oz6oa32prmpiy

Synchronous versus asynchronous modeling of gene regulatory networks

A. Garg, A. Di Cara, I. Xenarios, L. Mendoza, G. De Micheli
2008 Bioinformatics  
Results: In this manuscript, we provide algorithms based on reduced ordered binary decision diagrams (ROBDDs) for Boolean modeling of gene regulatory networks.  ...  Motivation: In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems.  ...  ACKNOWLEDGEMENTS Funding: This work was supported in part by ENFIN, a Network of Excellence funded by the European Commission within its FP6 Program, under the thematic area 'Life Sciences, genomics and  ... 
doi:10.1093/bioinformatics/btn336 pmid:18614585 pmcid:PMC2519162 fatcat:cqhzrugswvfr3aewmv4laazygm
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