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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

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

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

Improving BDD-based attractor detection for synchronous Boolean networks

Qixia Yuan, Hongyang Qu, Jun Pang, Andrzej Mizera
2016 Science China Information Sciences  
Boolean networks are an important formalism for modelling biological systems and have attracted much attention in recent years.  ...  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.  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1007/s11432-016-5594-9 fatcat:3lu7kltxtvatjpwi4koybpyx2a

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  
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.  ...  in Boolean networks.  ...  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

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  
Boolean networks are an important formalism for modelling biological systems and have attracted much attention in recent years.  ...  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.  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
doi:10.1145/2875913.2875925 dblp:conf/internetware/QuYPM15 fatcat:qcc3w5qeejgbtisupsjxrhff2e

Computing preimages of Boolean Networks [article]

Johannes Georg Klotz, Martin Bossert, Steffen Schober
2013 arXiv   pre-print
In this paper we present an algorithm to address the predecessor problem of feed-forward Boolean networks.  ...  Finally, we evaluate our algorithm for random Boolean networks and the regulatory network of Escherichia coli.  ...  INTRODUCTION In systems and computational biology Boolean networks (BN) are widely used to model regulative dependencies of organisms [1, 2] .  ... 
arXiv:1302.3723v1 fatcat:zmeuirmoufdq7alvm4hpo3kdua

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.  ...  By this reason, we define a gene regulatory network as a boolean network where it deals with the cases "gene expresses (1)" and "gene does not express (0)" as in Table 1 .  ... 
doi:10.11234/gi1990.8.254 fatcat:jsumcm63znd6hlqs4nl63qsoxy

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

Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction

Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang, Niko Beerenwinkel, Achim Tresch
2013 Computer applications in the biosciences : CABIOS  
Results: In this work, we present a novel model-based approach involving Boolean networks to reconstruct small to medium-sized regulatory networks.  ...  In particular, we solve the problem of exact likelihood computation in Boolean networks with probabilistic exponential time delays. Simulations demonstrate the high accuracy of our approach.  ...  ACKNOWLEDGEMENT The authors thank Holger Fro¨hlich for useful suggestions during the preparation of the manuscript. Funding: Deutsche Forschungsgemeinschaft (SFB646 to A.T.). Conflict of interest  ... 
doi:10.1093/bioinformatics/btt696 pmid:24292937 fatcat:w5nfnoryafgwfnakmm7xl3dbh4

Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks

I. Shmulevich, E. R. Dougherty, S. Kim, W. Zhang
2002 Bioinformatics  
Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i) incorporates rule-based dependencies between genes; (ii) allows the systematic study of global  ...  Results: We introduce Probabilistic Boolean Networks (PBN) that share the appealing rule-based properties of Boolean networks, but are robust in the face of uncertainty.  ...  ACKNOWLEDGEMENTS The authors are grateful to the Referees for their careful reading of the manuscript and many helpful suggestions.  ... 
doi:10.1093/bioinformatics/18.2.261 pmid:11847074 fatcat:5fh6dt6mlnabjfrblt7kqir6iu

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

Computing preimages of Boolean networks

Johannes Klotz, Martin Bossert, Steffen Schober
2013 BMC Bioinformatics  
In this paper we present an algorithm based on the sum-product algorithm that finds elements in the preimage of a feed-forward Boolean networks given an output of the network.  ...  We evaluate our algorithm for randomly constructed Boolean networks and a regulatory network of Escherichia coli and found that it gives a valid solution in most cases.  ...  Acknowledgements The authors would like to thank Shrief Rizkalla for implementing parts of the simulation. Declarations  ... 
doi:10.1186/1471-2105-14-s10-s4 pmid:24267277 pmcid:PMC3750533 fatcat:k3y3qgjmwfhypicpplfvverhue

Percolation on the gene regulatory network [article]

Giuseppe Torrisi, Reimer Kühn, Alessia Annibale
2020 arXiv   pre-print
expression of the gene.  ...  Results reveal the strong dependence of the gene knockout cascade on the logic implemented in the underlying network dynamics, highlighting in particular that avalanche sizes cannot be easily related to  ...  Acknowledgments GT supported by the EPSRC Centre for Doctoral Training in Cross-Disciplinary Approaches to Non-Equilibrium Systems (CANES EP/L015854/1).  ... 
arXiv:2005.03144v2 fatcat:5aqozgyekffcrev2tcmznatwi4

Parallel One-Step Control of Parametrised Boolean Networks [article]

Lubos Brim, Samuel Pastva, David Safranek, Eva Smijakova
2020 arXiv   pre-print
Boolean network (BN) is a simple model widely used to study complex dynamic behaviour of biological systems.  ...  We evaluate the performance of our approach on real biological models.  ...  Solutions of the Boolean network control problem for a model of a cell in silico provide the basis for experimental designs allowing to reprogram the cell in vitro.  ... 
arXiv:2009.00359v1 fatcat:i7dh7l5375hynlxfeoi4memmiu
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