Publications

Andrzej Mizera

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• Publications

• 2020


• An efficient approach towards the source-target control of Boolean networks.
  Soumya Paul, Cui Su, Jun Pang, and Andrzej Mizera.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 17(6):1932--1945, 2020.
• 2019


• A new decomposition-based method for detecting attractors in synchronous Boolean networks.
  Qixia Yuan, Andrzej Mizera, Jun Pang, and Hongyang Qu. Science of Computer Programming, 180:18--35, 2019.


• GPU-accelerated steady-state computation of large probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  Formal Aspects of Computing, 31(1):27--46, 2019.


• Taming asynchrony for attractor detection in large Boolean networks.
  Andrzej Mizera, Jun Pang, Hongyang Qu, and Qixia Yuan.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(1):31--42, 2019.
• 2018


• ASSA-PBN: A toolbox for probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, Cui Su, and Qixia Yuan.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(4):1203--1216, 2018.


• A decomposition-based approach towards the control of Boolean networks.
  Soumya Paul, Cui Su, Jun Pang, and Andrzej Mizera.
  In Proc. 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB'18, pp. 11--20. ©ACM Press, 2018.


• ASSA-PBN 3.0: Analysing context-sensitive probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, Hongyang Qu, and Qixia Yuan.
  In Proc. 16th International Conference on Computational Methods in Systems Biology - CMSB'18, Lecture Notes in Computer Science 11095, pp. 277--284. ©Springer, 2018.


• Reviving the two-state Markov chain approach.
  Andrzej Mizera, Jun Pang, and Qixia Yuan. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15(5):1525--1537, 2018.
• 2017


• A new decomposition method for attractor detection in large synchronous Boolean networks.
  Andrzej Mizera, Jun Pang, Hongyang Qu, and Qixia Yuan.
  In Proc. 3rd International Symposium on Dependable Software Engineering: Theories, Tools, and Applications - SETTA'17, Lecture Notes in Computer Science 10606, pp. 232--249. ©Springer, 2017. (Best Paper Award Honorable Mention)


• Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems.
  Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, and Ion Petre. International Journal of Foundations of Computer Science, 28(8):1007--1020, 2018.
• 2016


• Fast simulation of probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  In Proc. 14th International Conference on Computational Methods in Systems Biology - CMSB'16, Lecture Notes in Computer Science 9859, pp. 216-231. ©Springer-Verlag, 2016.


• ASSA-PBN 2.0: A software tool for probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  In Proc. 14th International Conference on Computational Methods in Systems Biology - CMSB'16, Lecture Notes in Computer Science 9859, pp. 309-315. ©Springer-Verlag, 2016.


• GPU-accelerated steady-state analysis of probabilistic Boolean networks. (poster)
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  In Proc. 14th International Conference on Computational Methods in Systems Biology - CMSB'16, Lecture Notes in Computer Science 9859, ©Springer-Verlag, 2016.


• GPU-accelerated steady-state computation of large probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  In Proc. 2nd International Symposium on Dependable Software Engineering: Theories, Tools, and Applications - SETTA'16, Lecture Notes in Computer Science xxxx, pp. xx-xx. ©Springer-Verlag, 2016. (To appear)


• Improving BDD-based attractor detection for synchronous Boolean networks.
  Qixia Yuan, Hongyang Qu, Jun Pang, and Andrzej Mizera. SCIENCE CHINA Information Sciences, 59(8): 080101:1-080101:16, 2016.


• Chemometric analysis of attenuated total reflectance infrared spectra of Proteus mirabilis strains with defined structures of LPS.
  Zarnowiec P, Mizera A, Chrapek M, Urbaniak M, and Kaca W. Innate Immunity, 22(5):325-335, 2016.


• Parallel approximate steady-state analysis of large probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  In Proc. 31st ACM Symposium on Applied Computing (SAC'16), pages 1-8, ©ACM Press, 2016.
• 2015


• Improving BDD-based attractor detection for synchronous Boolean networks.
  Hongyang Qu, Qixia Yuan, Jun Pang, and Andrzej Mizera.
  In Proc. 7th Asia-Pacific Symposium on Internetware (Internetware'15), pages xx-xx, ©ACM Press, 2015. (To appear)


• Activity tracking: A new attack on location privacy.
  Xihui Chen, Andrzej Mizera, and Jun Pang.
  In Proc. 3rd IEEE Conference on Communications and Network Security (CNS'15), pages 22-30, IEEE Computer Society, 2015.


• ASSA-PBN: An approximate steady-state analyser for probabilistic Boolean networks.
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  In Proc. 13th International Symposium on Automated Technology for Verification and Analysis (ATVA'15), pages 214-220, Lecture Notes in Computer Science 9364, Springer, 2015.
• 2014


• Model-checking based approaches to parameter estimation of gene regulatory networks.
  Andrzej Mizera, Jun Pang, and Qixia Yuan.
  In Proc. 19th International Conference on Engineering of Complex Computer Systems - ICECCS'14, pages 206-209, IEEE Computer Society, Conference Publishing Services, 2014.


• optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks.
  Panuwat Trairatphisan, Andrzej Mizera, Jun Pang, Alexandru-Adrian Tantar, and Thomas Sauter. PLoS ONE, 9(7):980011-15, 2014.
• 2013


• Recent development and biomedical applications of probabilistic boolean networks.
  Panuwat Trairatphisan, Andrzej Mizera, Jun Pang, Alexandru-Adrian Tantar, Jochen Schneider, and Thomas Sauter.
  Cell Communication and Signaling, 11:46, 2013.


• A balancing act: Parameter estimation for biological models with steady-state measurements.
  Andrzej Mizera, Jun Pang, Thomas Sauter, and Panuwat Trairatphisan.
  In A. Gupta and T. A. Henzinger, editors, Computational Methods in Systems Biology. 11th International Conference, CMSB 2013, Klosterneuburg, Austria, Lecture Notes in Bioinformatics 8130, pages 253-254, Berlin Heidelberg, Springer-Verlag, 2013.


• Mathematical modelling of the Platelet-Derived Growth Factor (PDGF) signalling pathway.
  Andrzej Mizera, Jun Pang, Thomas Sauter, and P. Trairatphisan.
  In I. Petre, editor, Proceedings 4th International Workshop on Computational Models for Cell Processes (CompMod’13), volume 116 of Electronic Proceedings in Theoretical Computer Science, page 35, 2013.
• 2012


• A boolean approach for disentangling the numerical contribution of modules to the system-level behavior of a biomodel.
  Elena Czeizler, Andrzej Mizera, and Ion Petre.
  Fundamenta Informaticae, 116(1-4):51-63, 2012.


• Quantitative analysis of the self-assembly strategies of intermediate filaments from tetrameric vimentin.
  Eugen Czeizler, Andrzej Mizera, Elena Czeizler, Ralph-Johan Back, John E. Eriksson, and Ion Petre.
  IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(3):885-898, 2012.


• Computational methods for quantitative submodel comparison.
  Andrzej Mizera, Elena Czeizler, and Ion Petre.
  In E. Katz, editor, Biomolecular Information Processing. From Logic Systems to Smart Sensors and Actuators, pages 323-346. Wiley-VCH Verlag GmbH, Weinheim, DE, 2012.


• Self-assembly models of variable resolution.
  Andrzej Mizera, Eugen Czeizler, and Ion Petre.
  Transactions on Computational Systems Biology, 7625:181-203, 2012.
• 2011


• Methods for biochemical model decomposition and quantitative submodel comparison.
  Andrzej Mizera, Elena Czeizler, and Ion Petre.
  Israel Journal of Chemistry, 51(1):151-164, 2011.


• A simple mass-action model for the eukaryotic heat shock response and its mathematical validation.
  Ion Petre, Andrzej Mizera, Claire L. Hyder, Annika Meinander, Andrey Mikhailov, Richard I. Morimoto, Lea Sistonen, John E. Eriksson, and Ralph-Johan Back.
  Natural Computing, 10(1):595-612, 2011.


• Modelling of ultrasound therapeutic heating and numerical study of the dynamics of the induced heat shock response.
  Andrzej Mizera and Barbara Gambin.
  Communications in Nonlinear Science and Numerical Simulation, 16(5):2342-2349, 2011.
• 2010


• Stochastic modelling of the eukaryotic heat shock response.
  Andrzej Mizera and Barbara Gambin.
  Journal of Theoretical Biology, 265(3):455-466, 2010.
• 2009


• The dynamics of heat shock response induced by ultrasound therapeutic treatment.
  Andrzej Mizera and Barbara Gambin.
  In J. Awrejcewicz, M. Kaźmierczak, J. Mrozowski, and P. Olejnik, editors, 10th Conference on Dynamical Systems - Theory and Applications, DSTA-2009, Łódź, Poland, volume 2, pages 847-852, Łódź, 2009. Left Grupa.


• Temperature fields induced by low power focused ultrasound in soft tissues during gene therapy. Numerical predictions and experimental results.
  Barbara Gambin, Tamara Kujawska, Eleonora Kruglenko, Andrzej Mizera, and Andrzej Nowicki.
  Archives of Acoustics, 34(4):445-459, 2009.


• A new mathematical model for the heat shock response.
  Ion Petre, Andrzej Mizera, Claire L. Hyder, Andrey Mikhailov, John E. Eriksson, Lea Sistonen, and Ralph-Johan Back.
  In A. Condon, D. Harel, J. N. Kok, A. Salomaa, and E. Winfree, editors, Algorithmic Bioprocesses, pages 411-425. Springer, Dordrecht Heidelberg London New York, 2009.


• Computational heuristics for simplifying a biological model.
  Ion Petre, Andrzej Mizera, and Ralph-Johan Back.
  In K. Ambos-Spies, B. Löwe, and W. Merkle, editors, Mathematical Theory and Computational Practice: 5th Conference on Computability in Europe, CiE 2009, pages 399-408, Berlin Heidelberg NewYork, 2009. Springer.
• 2006


• Applying dynamic bayesian networks to perturbed gene expression data.
  Norbert Dojer, Anna Gambin, Andrzej Mizera, Bartek Wilczyński, and Jerzy Tiuryn.
  BMC Bioinformatics, 7:249, 2006.

Theses

• 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.
  Andrzej Mizera.
  PhD thesis, Turku Centre for Computer Science, 2011.