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Department: Any ÅAU / Department of Information Technologies UTU / Department of Information Technology UTU / Department of Mathematics and Statistics UTU / Turku School of Economics, Institute of Information Systems Sciences

Research Unit: Any Algorithmics and Computational Intelligence Group (ACI) Biomathematics Research Unit (BIOMATH) Communication Systems (ComSys) Computational Biomodeling Laboratory (Combio Lab) Data Mining and Knowledge Management Laboratory Distributed Systems Laboratory (DS Lab) Embedded Computer and Electronic Systems (ECES) Embedded Systems Laboratory (ESLAB) FUNDIM, Fundamentals of Computing and Discrete Mathematics Institute for Advanced Management Systems Research (IAMSR) Learning and Reasoning Lab Software Construction Laboratorium Software Development Laboratory (SwDev) Software Engineering Laboratory (SE Lab) Turku BioNLP Group Turku Optimization Group (TOpGroup) UTU Information Systems Science (ISS)

Publication type: Any Monographs Edited books Edited special issues of journals Edited proceedings Articles in journals Articles in proceedings Chapters in edited books Ph.D. thesis Lic. thesis Technical reports

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Articles in journals (12):

• Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, Ion Petre, Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems. International Journal of Foundations of Computer Science 28(8), 1007–1020, 2017.
• Elena Czeizler, Andrzej Mizera, Ion Petre, A Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel. Fundamenta Informaticae 116(1-4), 51–63, 2012.
• Eugen Czeizler, Andrzej Mizera, Elena Czeizler, Ralph-Johan Back, John E. Eriksson, Ion Petre, Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentins. IEEE-ACM Transactions on Computational Biology and Bioinformatics 9(3), 885–898, 2012.
• Andrzej Mizera, Eugen Czeizler, Ion Petre, Self-Assembly Models of Variable Resolution. Transactions on Computational Systems Biology XIV(7625), 181–203, 2012.
• Andrzej Mizera, Elena Czeizler, Ion Petre, Methods for Biochemical Decomposition and Quantitative Submodel Comparison. Israel Journal of Chemistry 51, 151–164, 2011.
• Andrzej Mizera, Barbara Gambin, Modelling of Ultrasound Therapeutic Heating and Numerical Study of the Dynamics of the Induced Heat Shock Response. Communications in Nonlinear Science and Numerical Simulation 16(5), 2342–2349, 2011.
• Ion Petre, Andrzej Mizera, Claire Hyder, Annika Meinander, Andrey Mikhailov, Richard Morimoto, Lea Sistonen, John Eriksson, Ralph-Johan Back, A Simple Mass-Action Model for the Eukaryotic Heat Shock Response and its Mathematical Validation. Natural Computing 10(1), 595–612, 2011.
• Andrzej Mizera, Barbara Gambin, Stochastic Modelling of the Eukaryotic Heat Shock Response. Journal of Theoretical Biology 265(3), 455–466, 2010.
• Ion Petre, Andrzej Mizera, Claire Hyder, Annika Meinander, Andrey Mikhailov, Richard Morimoto, Lea Sistonen, John Eriksson, Ralph-Johan Back, A Simple Mass-Action Model for the Eukaryotic Heat Shock Response and Its Mathematical Validation. Natural Computing , 2010.
• Barbara Gambin, Tamara Kujawska, Eleonora Kruglenko, Andrzej Mizera, Andrzej Nowicki, Temperature Fields Induced by Low Power Focused Ultrasound in Soft Tissues During Gene Therapy. Numerical Predictions and Experimental Results. Archives of Acoustics 34(4), 445-459, 2009.
• Norbert Dojer, Anna Gambin, Andrzej Mizera, Bartek Wilczyński, Jerzy Tiuryn, Applying Dynamic Bayesian Networks to Perturbed Gene Expression Data. BMC Bioinformatics 7, 249–259, 2006.
• Eugen Czeizler, Andrzej Mizera, Elena Czeizler, Ralph-Johan Back, John E. Eriksson, Ion Petre, Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin. 9, 885–98, 2000.

Articles in proceedings (3):

• Andrzej Mizera, Barbara Gambin, The Dynamics of Heat Shock Response Induced by Ultrasound Therapeutic Treatment. In: 10th Conference on Dynamical Systems - Theory and Applications, 2, 847-852, 2009.
• Ion Petre, Andrzej Mizera, Ralph-Johan Back, Computational Heuristics for Simplifying a Biological Model. In: Klaus Löwe Benedikt Merkle Wolfgang Ambos-Spies (Ed.), Mathematical Theory and Computational Practice: 5th Conference on Computability in Europe, CiE 2009, Proceedings, Lecture Notes in Computer Science 5635, 399–408, Springer, 2009.
• Ion Petre, Andrzej Mizera, Claire Hyder, Andrey Mikhailov, John Eriksson, Lea Sistonen, Ralph-Johan Back, A New Mathematical Model for the Heat Shock Response. In: Ion Petre, Ralph-Johan Back (Eds.), Proceedings of COMPMOD 2008: Workshop on Computational Models for Cell Processes, 39-52, Turku Centre for Computer Science (TUCS), 2008.

Chapters in edited books (2):

• Andrzej Mizera, Elena Czeizler, Ion Petre, Computational methods for quantitative submodel comparison. In: Evgeny Katz (Ed.), Biomolecular Information Processing. From Logic Systems to Smart Sensors and Actuators, 323–346, Wiley-VCH Verlagsgesellschaft, 2012.
• Ion Petre, Andrzej Mizera, Claire L. Hyder, Andrey Mikhailov, John E. Eriksson, Lea Sistonen, Ralph-Johan Back, A New Mathematical Model for the Heat Shock Response. In: Anne Condon, David Harel, Joost N. Kok, Arto Salomaa, Erik Winfree (Eds.), Algorithmic Bioprocesses, 411–425, Springer, 2009.

Ph.D. thesis (1):

• Andrzej Mizera, 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 Filaments.. TUCS Dissertations 138. Turku Centre for Computer Science, 2011.

Technical reports (7):

• Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, Ion Petre, Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems. TUCS Technical Reports 1167, TUCS, 2016.
• Elena Czeizler, Andrzej Mizera, Ion Petre, A Boolean Approach for Disentangling the Numerical Contribution of Modules to the System-Level Behavior of a Biomodel. TUCS Technical Reports 997, Turku Centre for Computer Science, 2011.
• Andrzej Mizera, Elena Czeizler, Ion Petre, Methods for Biochemical Model Decomposition and Quantitative Submodel Comparison. TUCS Technical Reports 1005, Turku Centre for Computer Science, 2011.
• Andrzej Mizera, Eugen Czeizler, Ion Petre, Self-Assembly Models of Variable Resolution. TUCS Technical Reports 1014, Turku Centre for Computer Science, 2011.
• Eugen Czeizler, Andrzej Mizera, Elena Czeizler, Ralph-johan Back, John Eriksson, Ion Petre, Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments From Tetrameric Vimentin. TUCS Technical Reports 963, Turku Centre for Computer Science, 2009.
• Ion Petre, Andrzej Mizera, Ralph-Johan Back, Computational heuristics for simplifying a biological model. TUCS Technical Reports 933, Turku Centre for Computer Science, 2009.
• Ion Petre, Andrzej Mizera, Claire Hyder, Andrey Mikhailov, John Eriksson, Lea Sistonen, Ralph-Johan Back, A New Mathematical Model for the Heat Shock Response. TUCS Technical Reports 883, Turku Centre for Computer Science, 2008.