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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 (24):

• Alexandru Amarioarei, Gefry Barad, Elena Czeizler, Eugen Czeizler, Ana-Maria Dobre, Corina Itcus, Andrei Paun, Mihaela Paun, Trandafir Romica, Iris Tusa, One Dimensional DNA Tiles Self Assembly Model Simulation. International Journal of Unconventional Computing 13(4-5), 399 – 415, 2018.
• Eugen Czeizler, Kai-Chiu Wu, Cristian Gratie, Krishna Kanhaiya, Ion Petre, Structural Target Controllability of Linear Networks. IEEE-ACM Transactions on Computational Biology and Bioinformatics 15(4), 1217–1228, 2018.
• Corina Itcus, Alecsandru Amarioarei, Eugen Czeizler, Ana-Maria Dobre, Victor Mitrana, Florentina Negre, Andrei Paun, Mihaela Paun, Manuela Sidoroff, Romica Trandafir, Iris Tusa, 3D DNA Origami Map Structure Simulation. Romanian Journal of Information Science and Technology (ROMJIST) 21(3), 249 – 255, 2018.
• Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre, NetContrl4BioMed: A pipeline for biomedical data acquisition and analysis of network controllability. BMC Bioinformatics 19(7), 3–12, 2018.
• Krishna Kanhaiya, Eugen Czeizler, Cristian Gratie, Ion Petre, Controlling Directed Protein Interaction Networks in Cancer. Scientific Reports 7(1), 10327, 2017.
• Abdulmelik Mohammed, Elena Czeizler, Eugen Czeizler, Computational Modelling of the Kinetic Tile Assembly Model Using a Rule-Based Approach. Theoretical Computer Science 701, 203 – 215, 2017.
• Sepinoud Azimi, Charmi Panchal, Eugen Czeizler, Ion Petre, Reaction Systems Models for the Self-Assembly of Intermediate Filaments. Annals of University of Bucharest LXII(2), 9–24, 2015.
• Erik Benson, Abdulmelik Mohammed, Johan Gardell, Sergej Masich, Eugen Czeizler, Pekka Orponen, Bjorn Hogberg, DNA Rendering of Polyhedral Meshes At the Nanoscale. Nature 523(7561), 4, 2015.
• Eugen Czeizler, Pekka Orponen, Fault Tolerant Design and Analysis of Carbon Nanotube Circuits Affixed on DNA Origami Tiles. IEEE Transactions on Nanotechnology 14(5), 7, 2015.
• Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre, Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels. Electronic Notes in Theoretical Computer Science 284, 35–53, 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.
• Eugen Czeizler, Vladimir Rogojin, Ion Petre, The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 9(5), 1326–1337, 2012.
• Bogdan Iancu, Elena Czeizler, Eugen Czeizler, Ion Petre, Quantitative Refinement of Reaction Models. International Journal of Unconventional Computing 8(5-6), 529–550, 2012.
• Andrzej Mizera, Eugen Czeizler, Ion Petre, Self-Assembly Models of Variable Resolution. Transactions on Computational Systems Biology XIV(7625), 181–203, 2012.
• Eugen Czeizler, Lila Kari, Towards a Neighborhood Simplification of Tile Systems: From Moore to Quasi-Linear Dependencies. Natural Computing , 2010.
• Elena Czeizler, Eugen Czeizler, Lila Kari, Kai Salomaa, On the Descriptional Complexity of Watson-Crick Automata. Theoretical Computer Science 410(35), 3250–3260, 2009.
• Eugen Czeizler, Lila Kari, Geometrical Tile Design for Complex Neighborhoods . Frontiers in Computational Neuroscience , 2009.
• Marie-Pierre Beal, Eugen Czeizler, Jarkko Kari, Dominique Perrin, Unambiguous Automata. Mathematics in Computer Science 1(4), 625–638, 2008.
• Eugen Czeizler, Jarkko Kari, A Tight Linear Bound on the Synchronization Delay of Bijective Automata. Theoretical Computer Science 380(1-2), 23–36, 2007.
• Elena Czeizler, Eugen Czeizler, A Short Survey on Watson-Crick Automata. Bulletin of the EATCS (88), 104-119, 2006.
• Elena Czeizler, Eugen Czeizler, On the Power of Parallel Communicating Watson-Crick Automata Systems. Theoretical Computer Science 358(1), 142–147, 2006.
• Elena Czeizler, Eugen Czeizler, Parallel Communicating Watson-Crick Automata Systems. Acta Cybernetica 17(4), 685–700, 2006.
• Eugen Czeizler, On the Size of the Inverse Neighborhoods for One-Dimensional Reversible Cellular Automata. Theoretical Computer Science 325(2), 273–284, 2004.
• 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 (14):

• Alexandru Amărioarei, Gefry Barad, Eugen Czeizler, Ana-Maria Dobre, Corina Iţcuş, Victor Mitrana, Andrei Păun, Mihaela Păun, Frankie Spencer, Romică Trandafir, Iris Tuşa, DNA-Guided Assembly of Nanocellulose Meshes. In: David Fagan, Carlos Martin-Vide, Michael O'Neill, Miguel A. Vega-Rodriguez (Eds.), Theory and Practice of Natural Computing, Lecture Notes in Computer Science 11324, 253 – 265, Springer International Publishing, 2018.
• Eugen Czeizler, Alexandru Popa, Victor Popescu, Fixed Parameter Algorithms and Hardness of Approximation Results for the Structural Target Controllability Problem. In: Jesper Jansson, Carlos Martin-Vide, Miguel Vega-Rodriguez (Eds.), Algorithms for Computational Biology, Lecture Notes in Computer Science 10849, 103 – 114, Springer International Publishing, 2018.
• Eugen Czeizler, Cristian Gratie, Wu Kai Chiu, Krishna Kanhaiya, Ion Petre, Target Controllability of Linear Networks. In: Ezio Bartocci, Pietro Lio, Nicola Paoletti (Eds.), Computational Methods in Systems Biology, Lecture Notes in Bioinformatics 9859, 67–81, Springer, 2016.
• Vladimir Rogojin, Keivan Kazemi, Krishna Kanhaiya, Eugen Czeizler, Ion Petre, Automatic Discovery of Combined Drug Therapy. In: Andrea Bracciali, David Gilbert, Gilbert MacKenzie (Eds.), Thirteenth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, University of Stirling, UK, 2016.
• Eugen Czeizler, Vladimir Rogojin, Ion Petre, The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. In: F. Fages (Ed.), Proceedings of the 9th International Conference on Computational Methods in Systems Biology, 9-24, ACM, 2011.
• Elena Czeizler, Eugen Czeizler, Ralph-Johan Back, Ion Petre, Control Strategies for the Regulation of the Eukaryotic Heat Shock Response. In: Pierpaolo Gorrieri Roberto Degano (Ed.), Proceedings of Computational Mehods in Systems Biology, 111-125, Springer, 2009.
• Elena Czeizler, Eugen Czeizler, Lila Kari, Shinnosuke Seki, An Extension of Lyndon and Schutzenberger's Result to DNA-Like Strings. In: Proceedings of the 13th International Conference on Developments in Language Theory, 183-194, Springer, 2009.
• Marie-Pierre Beal, Eugen Czeizler, Dominique Perrin, Jarkko Kari, On the Synchronization Delay of Complete Local Automata. In: Proceedings of London Algorithmic Workshop, 2007.
• Eugen Czeizler, Bijective Automata: Linear Synchronization Delay and Decision Algorithms. In: Pre-proceedings of CANT 2006: EMS Summer School, International School and Conference on Combinatorics, Automata and Number Theory, 2006.
• Eugen Czeizler, Jarkko Kari, On Testing the Equality of Sofic Systems. In: Internal Proceedings of XIth Mons Days of Theoretical Computer Science, August 30th - September 2nd, 2006, Rennes, France, 2006.
• Elena Czeizler, Eugen Czeizler, Parallel Communicating Watson-Crick Automata Systems. In: Z. Fulop Z. Esik (Ed.), Proceedings of 11th International Conference, AFL 2005, 83-96, 2005.
• Eugen Czeizler, Jarkko Kari, A Tight Linear Bound on the Neighborhood of Inverse Cellular Automata. In: G. F. Italiano L. Monteiro C. Palamidessi M. Yung L. Caires (Ed.), Proceedings of the 32nd International Colloquium on Automata, Languages and Programming (ICALP 2005), LNCS 3580, 410-420, Springer, 2005.
• Eugen Czeizler, On The Size of the Inverse Neighborhoods for One-Dimensional Reversible Cellular Automata. In: Proceedings of DMCS´04, TUCS General Publication, 27-39, 2004.
• Eugen Czeizler, Self-Activating P Systems. In: Membrane Computing 2002 (WMC 2002), LNCS 2597, 234-246, Springer, 2003.

Chapters in edited books (1):

• Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri, An Excursion Through Quantitative Model Refinement. In: Grzegorz Rozenberg, Arto Salomaa, José M. Sempere, Claudio Zandron (Eds.), Membrane Computing, Lecture Notes in Computer Science 9504, 25–47, Springer, 2015.

TUCS General Series (1):

• Eugen Czeizler, Jarkko Kari (Eds.), Proceedings of DMCS'04 Workshop on Discrete Models for Complex Systems, TUCS General Publication, Turku Centre for Computer Science, 2004.

Ph.D. thesis (1):

• Eugen Czeizler, The Inverse Neighborhood Problem and Applications of Welch Sets in Automata Theory. TUCS Dissertations 85. Turku Centre for Computer Science, 2007.

Technical reports (14):

• Victor-Bogdan Popescu, Krishna Kanhaiya, Iulian Năstac, Eugen Czeizler, Ion Petre, Identifying Efficient Controls of Complex Interaction Networks Using Genetic Algorithms. TUCS Technical Reports 1208, 2020.
• Eugen Czeizler, Cristian Gratie, Kai Chiu Wu, Krishna Kanhaiya, Ion Petre, Target Controllability of Linear Networks. TUCS Technical Reports 1157, TUCS, 2016.
• Krishna Kanhaiya, Eugen Czeizler, Christian Gratie, Ion Petre, Controlling Directed Protein Interaction Networks in Cancer. TUCS Technical Reports 1155, TUCS, 2016.
• Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre, NetControl4BioMed: A Pipeline for Biomedical Data Acquisition and Analysis of Network Controllability. TUCS Technical Reports 1163, TUCS, 2016.
• Vladimir Rogojin, Keivan Kazemi, Krishna Kanhaiya, Eugen Czeizler, Ion Petre, NetControl4BioMed – Automatic Discovery of Combined Drug Therapy. TUCS Technical Reports 1162, TUCS, 2016.
• Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri, An Excursion Through Quantitative Model Refinement. TUCS Technical Reports 1150, Turku Centre for Computer Science (TUCS), 2015.
• Sepinoud Azimi, Charmi Panchal, Eugen Czeizler, Ion Petre, Reaction Systems Models for the Self-Assembly of Intermediate Filaments. TUCS Technical Reports 1131, TUCS, 2015.
• Eugen Czeizler, Vladimir Rogojin, Ion Petre, The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. TUCS Technical Reports 1041, Turku Centre for Computer Science, 2012.
• Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre, Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels. TUCS Technical Reports 1015, Turku Centre for Computer Science, 2011.