Parameter estimation of qualitative biological regulatory networks on high performance computing hardware
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Jamil Ahmad | Aamir Shafi | Amjad Ali | Rehan Zafar Paracha | Jan Baumbach | Josch Pauling | Muhammad Tariq Saeed | Asad Hayat | A. Shafi | J. Baumbach | R. Z. Paracha | Amjad Ali | J. Ahmad | J. Pauling | M. T. Saeed | Asad Hayat | Asad Hayat | Jamil Ahmad
[1] Marco Pistore,et al. NuSMV 2: An OpenSource Tool for Symbolic Model Checking , 2002, CAV.
[2] Dragan Bosnacki,et al. The Design of a Multicore Extension of the SPIN Model Checker , 2007, IEEE Transactions on Software Engineering.
[3] Edmund M. Clarke,et al. Design and Synthesis of Synchronization Skeletons Using Branching-Time Temporal Logic , 1981, Logic of Programs.
[4] Gerald C. Chu,et al. Oncogenic Kras Maintains Pancreatic Tumors through Regulation of Anabolic Glucose Metabolism , 2012, Cell.
[5] R. Thomas,et al. Dynamical behaviour of biological regulatory networks--II. Immunity control in bacteriophage lambda. , 1995, Bulletin of mathematical biology.
[6] Lubos Brim,et al. On Parameter Synthesis by Parallel Model Checking , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[7] David A. Rosenblueth,et al. An overview of existing modeling tools making use of model checking in the analysis of biochemical networks , 2012, Front. Plant Sci..
[8] J. Comet,et al. The SMBioNet Method for Discovering Models of Gene Regulatory Networks , 2009 .
[9] Qianqian Zhu,et al. O-GlcNAcylation plays a role in tumor recurrence of hepatocellular carcinoma following liver transplantation , 2012, Medical Oncology.
[10] R. Thomas,et al. Logical analysis of systems comprising feedback loops. , 1978, Journal of theoretical biology.
[11] D. E. Atkinson,et al. Biological feedback control at the molecular level. , 1965, Science.
[12] T. Henzinger,et al. Executable cell biology , 2007, Nature Biotechnology.
[13] L. Glass,et al. The logical analysis of continuous, non-linear biochemical control networks. , 1973, Journal of theoretical biology.
[14] Giovanni De Micheli,et al. Synchronous versus asynchronous modeling of gene regulatory networks , 2008, Bioinform..
[15] El Houssine Snoussi,et al. Logical identification of all steady states: The concept of feedback loop characteristic states , 1993 .
[16] David S Wishart,et al. Computational systems biology in drug discovery and development: methods and applications. , 2007, Drug discovery today.
[17] P. Shannon,et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.
[18] H. Müller,et al. Functions and Mechanisms of Fibroblast Growth Factor (FGF) Signalling in Drosophila melanogaster , 2013, International journal of molecular sciences.
[19] D Thieffry,et al. GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. , 2006, Bio Systems.
[20] Rosita Guido,et al. Taming the complexity of biological pathways through parallel computing , 2008, Briefings Bioinform..
[21] Franck Delaplace,et al. Semantics of Biological Regulatory Networks , 2007, Electron. Notes Theor. Comput. Sci..
[22] Lubos Brim,et al. DiVinE: Parallel Distributed Model Checker , 2010, 2010 Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology.
[23] Arne Meier,et al. Model Checking CTL is Almost Always Inherently Sequential , 2009, TIME.
[24] U. Niazi,et al. Formal Modeling and Analysis of the MAL-Associated Biological Regulatory Network: Insight into Cerebral Malaria , 2012, PloS one.
[25] M. Reginato,et al. Critical Role of O-Linked β-N-Acetylglucosamine Transferase in Prostate Cancer Invasion, Angiogenesis, and Metastasis* , 2012, The Journal of Biological Chemistry.
[26] Jamil Ahmad,et al. A parallel approach for accelerated parameter identification of Gene Regulatory Networks , 2014, IWBBIO.
[27] François Fages,et al. Symbolic Model Checking of Biochemical Networks , 2003, CMSB.
[28] Jaco van de Pol,et al. Sylvan: multi-core framework for decision diagrams , 2017, International Journal on Software Tools for Technology Transfer.
[29] Dragan Bosnacki,et al. Multi-Core Model Checking with SPIN , 2007, 2007 IEEE International Parallel and Distributed Processing Symposium.
[30] Lubos Brim,et al. Designing fast LTL model checking algorithms for many-core GPUs , 2012, J. Parallel Distributed Comput..
[31] Amir Pnueli,et al. Jtlv: A Framework for Developing Verification Algorithms , 2010, CAV.
[32] Muhammad Tariq Saeed,et al. Formal Modelling and Analysis of the role of Hexosamine Biosynthetic Pathway in Cancer: Exploiting Parallelism in Qualitative Biological Regulatory Networks , 2018 .
[33] M. Bryś,et al. Expression of genes encoding for enzymes associated with O-GlcNAcylation in endometrial carcinomas: clinicopathologic correlations. , 2012, Ginekologia polska.
[34] Mark Baker,et al. Multicore-enabling the MPJ express messaging library , 2010, PPPJ.
[35] M. Bryś,et al. Prediction of bladder cancer based on urinary content of MGEA5 and OGT mRNA level. , 2012, Clinical laboratory.
[36] Adrien Richard,et al. Formal Methods for Modeling Biological Regulatory Networks , 2006 .
[37] T. Lefebvre,et al. O-GlcNAcylation: A New Cancer Hallmark? , 2013, Front. Endocrinol..
[38] René Thomas. On the Relation Between the Logical Structure of Systems and Their Ability to Generate Multiple Steady States or Sustained Oscillations , 1981 .
[39] Didier Lime,et al. Hybrid Modelling and Dynamical Analysis of Gene Regulatory Networks with Delays , 2007, Complexus.
[40] Alfons Laarman,et al. Multi-Core BDD Operations for Symbolic Reachability , 2013, Electron. Notes Theor. Comput. Sci..
[41] Marco Pistore,et al. Nusmv version 2: an opensource tool for symbolic model checking , 2002, CAV 2002.
[42] Alfons Laarman,et al. Scalable multi-core model checking , 2014 .
[43] Aurélien Naldi,et al. Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle , 2006, ISMB.
[44] T. Mestl,et al. A mathematical framework for describing and analysing gene regulatory networks. , 1995, Journal of theoretical biology.
[45] Alexander Bockmayr,et al. Time Series Dependent Analysis of Unparametrized Thomas Networks , 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.
[46] R. Albert,et al. Boolean Modelingof Genetic Regulatory Networks , 2004 .
[47] René Thomas,et al. Logical identification of all steady states: The concept of feedback loop characteristic states , 1993 .
[48] Wengong Yu,et al. O-GlcNAcylation is a novel regulator of lung and colon cancer malignancy. , 2011, Biochimica et biophysica acta.
[49] Lubos Brim,et al. Scalable Multi-core LTL Model-Checking , 2007, SPIN.
[50] Alexander E. Kel,et al. Bifurcation analysis of the regulatory modules of the mammalian G1/S transition , 2004, Bioinform..
[51] Adrien Richard,et al. Boolean Models of Biosurfactants Production in Pseudomonas fluorescens , 2012, PloS one.
[52] R. Albert. Boolean modeling of genetic regulatory networks , 2004 .
[53] David Safránek,et al. Parameter Identification and Model Ranking of Thomas Networks , 2012, CMSB.
[54] Igor Goryanin,et al. Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration. , 2009, Journal of biotechnology.
[55] Adrien Richard,et al. Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. , 2004, Journal of theoretical biology.
[56] Radu Mateescu,et al. Temporal logic patterns for querying dynamic models of cellular interaction networks , 2008, ECCB.
[57] Feng Han,et al. Tumor and Stem Cell Biology Cancer Research GlcNAcylation Plays an Essential Role in Breast Cancer Metastasis , 2010 .
[58] E. Furlong,et al. Logical modelling of Drosophila signalling pathways. , 2013, Molecular bioSystems.
[59] Aamir Shafi,et al. Formal modeling and analysis of the hexosamine biosynthetic pathway: role of O-linked N-acetylglucosamine transferase in oncogenesis and cancer progression , 2016, PeerJ.
[60] Hidde de Jong,et al. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review , 2002, J. Comput. Biol..
[61] Joseph Sifakis,et al. Model checking , 1996, Handbook of Automated Reasoning.
[62] B. Shilo,et al. The Drosophila FGF-R homolog is expressed in the embryonic tracheal system and appears to be required for directed tracheal cell extension. , 1991, Genes & development.
[63] Amir Pnueli,et al. The temporal logic of programs , 1977, 18th Annual Symposium on Foundations of Computer Science (sfcs 1977).
[64] Lubos Brim,et al. Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE , 2007, FBTC@CONCUR.