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Showing results 21 to 38 of 38
   Model-checking based approaches to parameter estimation of gene regulatory networksMizera, Andrzej  ; Pang, Jun ; Yuan, Qixia in Proceedings of 19th IEEE Conference on Engineering of Complex Computer Systems (2014) Detailed reference viewed: 140 (11 UL)Recent development and biomedical applications of probabilistic Boolean networksTrairatphisan, Panuwat ; Mizera, Andrzej ; Pang, Jun et alin Cell Communication and Signaling (2013), 11(46), Probabilistic Boolean network (PBN) modelling is a semi-quantitative approach widely used for the study of the topology and dynamic aspects of biological systems. The combined use of rule-based ... [more ▼] Probabilistic Boolean network (PBN) modelling is a semi-quantitative approach widely used for the study of the topology and dynamic aspects of biological systems. The combined use of rule-based representation and probability makes PBN appealing for large-scale modelling of biological networks where degrees of uncertainty need to be considered. A considerable expansion of our knowledge in the field of theoretical research on PBN can be observed over the past few years, with a focus on network inference, network intervention and control. With respect to areas of applications, PBN is mainly used for the study of gene regulatory networks though with an increasing emergence in signal transduction, metabolic, and also physiological networks. At the same time, a number of computational tools, facilitating the modelling and analysis of PBNs, are continuously developed. A concise yet comprehensive review of the state-of-the-art on PBN modelling is offered in this article, including a comparative discussion on PBN versus similar models with respect to concepts and biomedical applications. Due to their many advantages, we consider PBN to stand as a suitable modelling framework for the description and analysis of complex biological systems, ranging from molecular to physiological levels. [less ▲] Detailed reference viewed: 305 (32 UL) A balancing act: Parameter estimation for biological models with steady-state measurementsMizera, Andrzej ; Pang, Jun ; Sauter, Thomas et alin Proceedings of 11th Conference on Computational Methods in Systems Biology (CMSB'13) (2013) Detailed reference viewed: 113 (8 UL)Mathematical modelling of the Platelet-Derived Growth Factor (PDGF) signalling pathwayMizera, Andrzej ; Pang, Jun ; Sauter, Thomas et alin Proceedings of 4th Workshop on Computational Models for Cell Processes (CompMod'13) (2013) Detailed reference viewed: 113 (10 UL)Computational methods for quantitative submodel comparisonMizera, Andrzej ; ; in Katz, Evgeny (Ed.) Biomolecular Information Processing. From Logic Systems to Smart Sensors and Actuators (2012) Detailed reference viewed: 90 (1 UL)Self-assembly models of variable resolutionMizera, Andrzej ; ; in Lecture Notes in Computer Science (2012), 7625 Detailed reference viewed: 80 (0 UL)A Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel; Mizera, Andrzej ; in Fundamenta Informaticae (2012), 116(1-4), 51-63 Detailed reference viewed: 69 (1 UL)Quantitative analysis of the self-assembly strategies of intermediate filaments from tetrameric vimentin; Mizera, Andrzej ; et alin IEEE/ACM Transactions on Computational Biology and Bioinformatics (2012), 9(3), 885-898 Detailed reference viewed: 93 (2 UL)Methods for construction and analysis of computational models in systems biology: applications to the modelling of the heat shock response and the self-assembly of intermediate filamentsMizera, Andrzej Doctoral thesis (2011) Detailed reference viewed: 36 (4 UL)Methods for Biochemical Model Decomposition and Quantitative Submodel ComparisonMizera, Andrzej ; ; in Israel Journal of Chemistry (2011), 51(1), 151164 Detailed reference viewed: 97 (0 UL)A simple mass-action model for the eukaryotic heat shock response and its mathematical validation; Mizera, Andrzej ; et alin Natural Computing (2011), 10(1), 595-612 Detailed reference viewed: 117 (0 UL)Modelling of ultrasound therapeutic heating and numerical study of the dynamics of the induced heat shock responseMizera, Andrzej ; in Communications in Nonlinear Science and Numerical Simulation (2011), 16(5), 23422349 Detailed reference viewed: 109 (3 UL)Stochastic modelling of the eukaryotic heat shock responseMizera, Andrzej ; in Journal of Theoretical Biology (2010), 265(3), 455466 Detailed reference viewed: 98 (2 UL)The Dynamics of Heat Shock Response Induced by Ultr asound Therapeutic TreatmentMizera, Andrzej ; in Awrejcewicz, J.; Kaźmierczak, M.; Mrozowski, J. (Eds.) et al 10th Conference on Dynamical Systems – Theory and Applications, DSTA-2009 (2009) Detailed reference viewed: 41 (1 UL)A New Mathematical Model for the Heat Shock Response; Mizera, Andrzej ; et alin Condon, Anne; Harel, David; Kok, Joost N. (Eds.) et al Algorithmic Bioprocesses (2009) Detailed reference viewed: 120 (0 UL)Computational heuristics for simplifying a biological model; Mizera, Andrzej ; in Lecture Notes in Computer Science (2009), 5635 Detailed reference viewed: 170 (0 UL)Temperature Fields Induced by Low Power Focused Ultrasound in Soft Tissues During Gene Therapy. Numerical Predictions and Experimental Results; ; et al in Archives of Acoustics (2009), 34(4), 445459 Detailed reference viewed: 60 (2 UL)Applying dynamic Bayesian networks to perturbed gene expression data; ; Mizera, Andrzej et alin BMC Bioinformatics (2006), 7 Detailed reference viewed: 82 (6 UL)
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