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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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Monographs (1):

• Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescot, Grzegorz Rozenberg, Computation in Living Cell: Gene Assembly in Ciliates. Natural Computing, Springer, 2004.

Edited books (1):

• Marian Gheorghe, Ion Petre, Mario J. Perez-Jimenez, Grzegorz Rozenberg, Arto Salomaa (Eds.), Multidisciplinary Creativity, Spandugino, 2015.

Edited special issues of journals (7):

• Gheorghe Paun, Ion Petre, Grzegorz Rozenberg, Arto Salomaa (Eds.), At the Intersection of Computer Science with Biology, Chemistry and Physics – In Memory of Solomon Marcus. Theoretical Computer Science 701, 2017.
• Emanuela Merelli, Ion Petre (Eds.), From Computer Science to Biology and Back. Theoretical Computer Science 608(1), 2015.
• Giorgio Ausiello, Hendrik Jan Hoogeboom, Juhani Karhumäki, Ion Petre, Arto Salomaa (Eds.), Magic in Science. Theoretical Computer Science 429, 2012.
• Jarkko Kari, Ion Petre (Eds.), Special Issue on Unconventional Computing. Natural Computing 11(4), 2012.
• Ion Petre, Corrado Priami, Erik de Vink (Eds.), Special Issue on Computational Models for Cell Processes. Transactions on Computational Systems Biology Lecture Notes in Computer Science 7625, 2012.
• Ralph-Johan Back, Ion Petre, Corrado Priami, Erik de Vink (Eds.), Special issue on Computational Models for Cell Processes. Transactions on Computational Systems Biology XIII, 2011.
• Ralph-Johan Back, Ion Petre, Corrado Priami (Eds.), Special Issue on Computational Models for Cell Processes. Transactions on Computational Systems Biology XI, 2009.

Edited proceedings (6):

• Jarkko Kari, Florin Manea, Ion Petre (Eds.), Unveiling Dynamics and Complexity, Lecture Notes in Computer Science 10307, Springer, 2017.
• Proceedings of the Fourth International Workshop on Computational Models for Cell Processes, EPTCS 116, EPTCS, 2013.
• Cristian Calude, Jarkko Kari, Ion Petre, Grzegorz Rozenberg (Eds.), Proceedings of the 10th International Conference on Unconventional Computation, Lecture Notes in Computer Science 6735, Springer, 2011.
• Ion Petre, Erik De vink (Eds.), Proceedings Third International Workshop on Computational Models for Cell Processes, 67, EPTCS, 2011.
• Ralph-Johan Back, Ion Petre, Erik de Vink (Eds.), Proceedings of Computational Models for Cell Processes, 6, EPTCS, 2009.
• Ion Petre, Grzegorz Rozenberg (Eds.), Proceedings of the Workshop on Natural Computing and Graph Transformations, University of Leicester, UK, 2008.

Articles in journals (93):

• Bogdan Iancu, Usman Sanwal, Cristian Gratie, Ion Petre, Refinement-Based Modeling of the ErbB Signaling Pathway. Computers in Biology and Medicine 106, 91–96, 2019.
• Luigia Petre, Usman Sanwal, Gohar Shah, Charmi Panchal, Dwitiya Tyagi, Ion Petre, A Computational Model for The Access to Medical Service in a Basic Prototype of a Healthcare System. Fundamenta Informaticae 168, 1–13, 2019.
• Zeyi Shang, Sergey Verlan, Ion Petre, Gexiang Zhang, Reaction Systems and Synchronous Digital Circuits. Molecules , 1–13, 2019.
• 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.
• Rafael Renatino Canevarolo, Praneeth Reddy Sudalagunta, Maria D. Coelho, Siqueira Silva, Mark B. Meads, Priscilla Granados, Anders Berglund, Amit Kulkarni, Hongyue Dai, William S. Dalton, Ion Petre, Kenneth H. Shain, Ariosto Siqueira Silva, A Systems Biology Approach to Identify Mechanisms of Therapy Resistance in Multiple Myeloma. Blood 132(1), 3266, 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.
• Sepinoud Azimi, Steady States of Constrained Reaction Systems. Theoretical Computer Science , 1–7, 2017.
• 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.
• Mikhail Barash, Ion Petre, A Foundational Framework for Step-by-Step Model Construction. Fundamenta Informaticae 154, 1–10, 2017.
• 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.
• Cecilia Sahlgren, Annika Meinander, Hongbo Zhang, Fang Cheng, Maren Preis, Chunlin Xu, Tiina Salminen, Diana Toivola, Daniel Abankwa, Didem Karaman, Outi Salo, Ronald Österbacka, John Eriksson, Stefan Willför, Ion Petre, Jouko Peltonen, Reko Leino, Mark Johnson, Jessica Rosenholm, Niklas Sandler, Tailored Approaches in Drug Development and Diagnostics – From Molecular Design to Biological Model Systems. Advanced Healthcare Materials , 1700258, 2017.
• Usman Sanwal, Luigia Petre, Ion Petre, Stepwise Construction of a Metabolic Network in Event-B: The Heat Shock Response. Computers in Biology and Medicine (91), 1–12, 2017.
• Artiom Alhazov, Rudolf Freund, Vladimir Rogozhin, Yurii Rogozhin, Computational Completeness of Complete, Star-Like, and Linear Hybrid Networks of Evolutionary Processors with a Small Number of Processors. Natural Computing 15(1), 51–68, 2016.
• Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca, Complexity of Model Checking for Reaction Systems. Theoretical Computer Science 623, 103–113, 2016.
• Cristian Gratie, Ion Petre, Complete Characterization for the Fit-Preserving Data Refinement of Mass-Action Reaction Networks. Theoretical Computer Science 641, 11–24, 2016.
• Diana-Elena Gratie, Cristian Gratie, Composition Colored Petri Nets for the Refinement of Reaction-based Models. Electronic Notes in Theoretical Computer Science 326, 51–72, 2016.
• Vladimir Rogojin, Ion Petre, Large-Scale Executable Biology Using Rapid Integration of Computational Models. Computer Science Journal of Moldova 24(1 (70)), 118 – 135, 2016.
• Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre, Dependency Graphs and Mass Conservation in Reaction Systems. Theoretical Computer Science 598, 23–39, 2015.
• 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.
• Heidi Marjonen, Alejandra Sierra, Anna Nyman, Vladimir Rogojin, Olli Grohn, Anni-Maija Linden, Sampsa Hautaniemi, Nina Kaminen-Ahola, Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model. Plos One 10(5), e0124931, 2015.
• Emanuela Merelli, Ion Petre, From Computer Science to Biology and Back. Theoretical Computer Science 608(1), 2–3, 2015.
• Vladimir Rogojin, Ion Petre, The Structure of Elementary Strategies for Gene Assembly in Ciliates. Fundamenta Informaticae 137, 1–14, 2015.
• Sepinoud Azimi, Bogdan Iancu, Ion Petre, Reaction System Models for the Heat Shock Response. Fundamenta Informaticae 131, 1–14 , 2014.
• Diana-Elena Gratie, Ion Petre, Hiding the combinatorial state space explosion of biomodels through colored Petri nets. Annals of University of Bucharest LXI, 23–41, 2014.
• Bogdan Iancu, Cristian Gratie, Ion Petre, Refinement-Based Modelling of the ErbB Signalling Pathway. Annals of University of Bucharest LXI, 7–14, 2014.
• Emanuela Mereli, Ion Petre, Preface. Electronic Notes in Theoretical Computer Science 306, 1–3, 2014.
• Ion Petre, Vladimir Rogojin, Dependency Relations Between Elementary Intramolecular Operations in Gene Assembly in Ciliates. Journal of Automata, Languages and Combinatorics 19(1-4), 265–277, 2014.
• Vladimir Rogojin, On Combinatorial Properties of Elementary Intramolecular Operations. Computer Science Journal of Moldova 22(3), 386–404, 2014.
• Riku Louhimo, Marko Laakso, Tuomas Heikkinen, Susanna Laitinen, Pekka Manninen, Vladimir Rogojin, Minna Miettinen, Carl Blomqvist, Jianjun Liu, Heli Nevanlinna, Sampsa Hautaniemi, Identification of Genetic Markers with Synergistic Survival Effect in Cancer. BMC Systems Biology 7(1), S2, 2013.
• Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Simple Gene Assembly as a Rewriting of Directed Overlap-Inclusion Graphs. Theoretical Computer Science 454, 30–37, 2012.