NDLI: A Parallel Attractor Finding Algorithm Based on Boolean Satisfiability for Genetic Regulatory Networks

Content Provider	PubMed Central
Author	Guo, Wensheng Yang, Guowu Wei, Wu Lei, He Sun, Mingyu
Editor	Helmer-citterich, Manuela
Copyright Year	2014
Abstract	In biological systems, the dynamic analysis method has gained increasing attention in the past decade. The Boolean network is the most common model of a genetic regulatory network. The interactions of activation and inhibition in the genetic regulatory network are modeled as a set of functions of the Boolean network, while the state transitions in the Boolean network reflect the dynamic property of a genetic regulatory network. A difficult problem for state transition analysis is the finding of attractors. In this paper, we modeled the genetic regulatory network as a Boolean network and proposed a solving algorithm to tackle the attractor finding problem. In the proposed algorithm, we partitioned the Boolean network into several blocks consisting of the strongly connected components according to their gradients, and defined the connection between blocks as decision node. Based on the solutions calculated on the decision nodes and using a satisfiability solving algorithm, we identified the attractors in the state transition graph of each block. The proposed algorithm is benchmarked on a variety of genetic regulatory networks. Compared with existing algorithms, it achieved similar performance on small test cases, and outperformed it on larger and more complex ones, which happens to be the trend of the modern genetic regulatory network. Furthermore, while the existing satisfiability-based algorithms cannot be parallelized due to their inherent algorithm design, the proposed algorithm exhibits a good scalability on parallel computing architectures.
Related Links	http://dx.doi.org/10.1371/journal.pone.0094258
Starting Page	94258
File Format	PDF
ISSN	19326203
e-ISSN	19326203
Journal	PLoS ONE
Issue Number	4
Volume Number	9
Language	English
Publisher	Public Library of Science
Publisher Date	2014-04-01
Access Restriction	Open
Rights Holder	Public Library of Science
Subject Keyword	Biochemistry, Genetics and Molecular Biology(all) Agricultural and Biological Sciences(all) Medicine(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Multidisciplinary

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

An Attractor-Based Complexity Measurement for Boolean Recurrent Neural Networks

Scalable Steady State Analysis of Boolean Biological Regulatory Networks

An Efficient Algorithm for Computing Attractors of Synchronous And Asynchronous Boolean Networks

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks

Majority Rules with Random Tie-Breaking in Boolean Gene Regulatory Networks

A Mismatch-Based Model for Memory Reconsolidation and Extinction in Attractor Networks

An Algorithm for Finding Biologically Significant Features in Microarray Data Based on A Priori Manifold Learning

Evolving Sensitivity Balances Boolean Networks

optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks

A Parallel Attractor Finding Algorithm Based on Boolean Satisfiability for Genetic Regulatory Networks

Similar Documents

An Attractor-Based Complexity Measurement for Boolean Recurrent Neural Networks

Scalable Steady State Analysis of Boolean Biological Regulatory Networks

An Efficient Algorithm for Computing Attractors of Synchronous And Asynchronous Boolean Networks

A Semiquantitative Framework for Gene Regulatory Networks: Increasing the Time and Quantitative Resolution of Boolean Networks

Majority Rules with Random Tie-Breaking in Boolean Gene Regulatory Networks

A Mismatch-Based Model for Memory Reconsolidation and Extinction in Attractor Networks

An Algorithm for Finding Biologically Significant Features in Microarray Data Based on A Priori Manifold Learning

Evolving Sensitivity Balances Boolean Networks

optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks

A Parallel Attractor Finding Algorithm Based on Boolean Satisfiability for Genetic Regulatory Networks