Ion Petre

Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre: Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels. Electr. Notes Theor. Comput. Sci. 284: 35-53 (2012)

Elena Czeizler, Andrzej Mizera, Ion Petre: A Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel. Fundam. Inform. 116(1-4): 51-63 (2012)

Bogdan Iancu, Elena Czeizler, Eugen Czeizler, Ion Petre: Quantitative Refinement of Reaction Models. IJUC 8(5-6): 529-550 (2012)

Jarkko Kari, Ion Petre: Preface. Natural Computing 11(4): 551-552 (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 Vimentin. IEEE/ACM Trans. Comput. Biology Bioinform. 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 Trans. Comput. Biology Bioinform. 9(5): 1326-1337 (2012)

Giorgio Ausiello, Hendrik Jan Hoogeboom, Juhani Karhumäki, Ion Petre, Arto Salomaa: Preface. Theor. Comput. Sci. 429: 1-20 (2012)

Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre: Simple gene assembly as a rewriting of directed overlap-inclusion graphs. Theor. Comput. Sci. 454: 30-37 (2012)

Ion Petre, Sergey Verlan: Matrix insertion-deletion systems. Theor. Comput. Sci. 456: 80-88 (2012)

Andrzej Mizera, Eugen Czeizler, Ion Petre: Self-assembly Models of Variable Resolution. T. Comp. Sys. Biology 14: 181-203 (2012)

Corrado Priami, Ion Petre, Erik P. de Vink (Eds.): Transactions on Computational Systems Biology XIV - Special Issue on Computational Models for Cell Processes. Lecture Notes in Computer Science 7625, Springer 2012, isbn 978-3-642-35523-3

Giancarlo Mauri, Ion Petre: New Robustness Paradigms: from Nature to Computing. ERCIM News 2011(85): 33 (2011)

Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin: Directed Overlap-inclusion Graphs as Representations of Ciliate Genes. Fundam. Inform. 110(1-4): 29-44 (2011)

Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Ion Petre, José M. Sempere: Complexity-preserving simulations among three variants of accepting networks of evolutionary processors. Natural Computing 10(1): 429-445 (2011)

Ion Petre, Andrzej Mizera, Claire L. Hyder, Annika Meinander, Andrey Mikhailov, Richard I. Morimoto, Lea Sistonen, John E. 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)

Eugen Czeizler, Vladimir Rogojin, Ion Petre: The phosphorylation of the heat shock factor as a modulator for the heat shock response. CMSB 2011: 9-23

Cristian S. Calude, Jarkko Kari, Ion Petre, Grzegorz Rozenberg (Eds.): Unconventional Computation - 10th International Conference, UC 2011, Turku, Finland, June 6-10, 2011. Proceedings. Lecture Notes in Computer Science 6714, Springer 2011, isbn 978-3-642-21340-3

Ion Petre, Erik P. de Vink (Eds.): Proceedings Third International Workshop on Computational Models for Cell Processes. EPTCS 67, 2011

Corrado Priami, Ralph-Johan Back, Ion Petre, Erik P. de Vink (Eds.): Transactions on Computational Systems Biology XIII. Lecture Notes in Computer Science 6575, Springer 2011, isbn 978-3-642-19747-5

Sergey Verlan, Artiom Alhazov, Ion Petre: A sequence-based analysis of the pointer distribution of stichotrichous ciliates. Biosystems 101(2): 109-116 (2010)

Miika Langille, Ion Petre, Vladimir Rogojin: Three models for gene assembly in ciliates: a comparison. The Computer Science Journal of Moldova 18(1): 15-40 (2010)

Ion Petre, Grzegorz Rozenberg: Gene assembly in Ciliates. Scholarpedia 5(1): 9269 (2010)

Robert Brijder, Miika Langille, Ion Petre: Extended strings and graphs for simple gene assembly. Theor. Comput. Sci. 411(4-5): 730-738 (2010)

Artiom Alhazov, Chang Li, Ion Petre: Computing the graph-based parallel complexity of gene assembly. Theor. Comput. Sci. 411(25): 2359-2367 (2010)

Victor Mitrana, Ion Petre, Vladimir Rogojin: Accepting splicing systems. Theor. Comput. Sci. 411(25): 2414-2422 (2010)

Ion Petre, Sergey Verlan: Matrix Insertion-Deletion Systems. CoRR abs/1012.5248 (2010)

Artiom Alhazov, Ion Petre, Vladimir Rogojin: The parallel complexity of signed graphs: Decidability results and an improved algorithm. Theor. Comput. Sci. 410(24-25): 2308-2315 (2009)

Ion Petre, Andrzej Mizera, Ralph-Johan Back: Computational Heuristics for Simplifying a Biological Model. CiE 2009: 399-408

Elena Czeizler, Eugen Czeizler, Ralph-Johan Back, Ion Petre: Control Strategies for the Regulation of the Eukaryotic Heat Shock Response. CMSB 2009: 111-125

Ralph-Johan Back, Ion Petre, Erik P. de Vink (Eds.): Proceedings Second International Workshop on Computational Models for Cell Processes. EPTCS 6, 2009

Corrado Priami, Ralph-Johan Back, Ion Petre (Eds.): Transactions on Computational Systems Biology XI. Lecture Notes in Computer Science 5750, Springer 2009, isbn 978-3-642-04185-3

Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg: Patterns of simple gene assembly in ciliates. Discrete Applied Mathematics 156(14): 2581-2597 (2008)

Tero Harju, Chang Li, Ion Petre: Graph theoretic approach to parallel gene assembly. Discrete Applied Mathematics 156(18): 3416-3429 (2008)

Tseren-Onolt Ishdorj, Remco Loos, Ion Petre: Computational Efficiency of Intermolecular Gene Assembly. Fundam. Inform. 84(3-4): 363-373 (2008)

Ion Petre, Vladimir Rogojin: Decision problem for shuffled genes. Inf. Comput. 206(11): 1346-1352 (2008)

Tseren-Onolt Ishdorj, Ion Petre: Gene Assembly Models and Boolean Circuits. Int. J. Found. Comput. Sci. 19(5): 1133-1145 (2008)

Artiom Alhazov, Ion Petre, Vladimir Rogojin: Solutions to computational problems through gene assembly. Natural Computing 7(3): 385-401 (2008)

Tero Harju, Chang Li, Ion Petre: Parallel complexity of signed graphs for gene assembly in ciliates. Soft Comput. 12(8): 731-737 (2008)

Adrian Atanasiu, Radu Atanasiu, Ion Petre: Parikh matrices and amiable words. Theor. Comput. Sci. 390(1): 102-109 (2008)

Miika Langille, Ion Petre: Sequential vs. parallel complexity in simple gene assembly. Theor. Comput. Sci. 395(1): 24-30 (2008)

Ion Petre: Mathematics of gene assembly in ciliates (Abstract). AFL 2008: 54-55

Ion Petre, Grzegorz Rozenberg: Summary of the Workshop on Natural Computing and Graph Transformations. ICGT 2008: 470-472

Tseren-Onolt Ishdorj, Ion Petre, Vladimir Rogojin: Computational Power of intramolecular gene Assembly. Int. J. Found. Comput. Sci. 18(5): 1123-1136 (2007)

Erzsébet Csuhaj-Varjú, Ion Petre, György Vaszil: Self-assembly of strings and languages. Theor. Comput. Sci. 374(1-3): 74-81 (2007)

Artiom Alhazov, Ion Petre, Vladimir Rogojin: Solutions to Computational Problems Through Gene Assembly. DNA 2007: 36-45

Robert Brijder, Miika Langille, Ion Petre: A String-Based Model for Simple Gene Assembly. FCT 2007: 161-172

Tseren-Onolt Ishdorj, Ion Petre: Computing Through Gene Assembly. UC 2007: 91-105

Miika Langille, Ion Petre: Simple Gene Assembly Is Deterministic. Fundam. Inform. 73(1-2): 179-190 (2006)

Lucian Ilie, Solomon Marcus, Ion Petre: Periodic and Sturmian languages. Inf. Process. Lett. 98(6): 242-246 (2006)

Ion Petre: Invariants of Gene-Assembly in Stichotrichous Ciliates (Invarianten der Gen-Assemblierung in Ciliaten der Unterklasse Stichotrichia). it - Information Technology 48(3): 161-167 (2006)

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg: Parallelism in Gene Assembly. Natural Computing 5(2): 203-223 (2006)

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg: Complexity Measures for Gene Assembly. KDECB 2006: 42-60

Tero Harju, Ion Petre, Grzegorz Rozenberg: Modelling Simple Operations for Gene Assembly. Nanotechnology: Science and Computation 2006: 361-373

Juhani Karhumäki, Michel Latteux, Ion Petre: Commutation with Ternary Sets of Words. Theory Comput. Syst. 38(2): 161-169 (2005)

Juhani Karhumäki, Michel Latteux, Ion Petre: Commutation with codes. Theor. Comput. Sci. 340(1): 322-333 (2005)

Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg: Simple Operations for Gene Assembly. DNA 2005: 96-111

Tero Harju, Ion Petre, Grzegorz Rozenberg: Gene Assembly in Celiates. Part I. Molecular Operations (Column: Natural Computing). Bulletin of the EATCS 82: 227-241 (2004)

Tero Harju, Ion Petre, Grzegorz Rozenberg: Two Models for Gene Assembly in Ciliates. Theory Is Forever 2004: 89-101

Tero Harju, Ion Petre, Grzegorz Rozenberg: Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs. Aspects of Molecular Computing 2004: 202-212

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg: Parallelism in Gene Assembly. DNA 2004: 138-148

Tero Harju, Ion Petre, Grzegorz Rozenberg: Tutorial on DNA Computing and Graph Transformation. ICGT 2004: 434-436

Tero Harju, Ion Petre, Grzegorz Rozenberg: Gene Assembly in Ciliates Part I. Molecular Operations. Bulletin of the EATCS 81: 236-249 (2003)

Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescott, Grzegorz Rozenberg: Formal systems for gene assembly in ciliates. Theor. Comput. Sci. 292(1): 199-219 (2003)

Ion Petre: On the Difference Problem for Semilinear Power Series. Grammars and Automata for String Processing 2003: 317-326

Juhani Karhumäki, Michel Latteux, Ion Petre: The Commutation with Codes and Ternary Sets of Words. STACS 2003: 74-84

Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg: String and Graph Reduction Systems for Gene Assembly in Ciliates. Mathematical Structures in Computer Science 12(2): 113-134 (2002)

Andrzej Ehrenfeucht, Tero Harju, Ion Petre, Grzegorz Rozenberg: Characterizing the Micronuclear Gene Patterns in Ciliates. Theory Comput. Syst. 35(5): 501-519 (2002)

Juhani Karhumäki, Ion Petre: Conway's problem for three-word sets. Theor. Comput. Sci. 289(1): 705-725 (2002)

Juhani Karhumäki, Ion Petre: The Branching Point Approach to Conway's Problem. Formal and Natural Computing 2002: 69-76

Tero Harju, Ion Petre, Grzegorz Rozenberg: Tutorial on DNA Computing and Graph Transformation - Computational Nature of Gene Assembly in Ciliates. ICGT 2002: 430-434

Juhani Karhumäki, Ion Petre: Conway's Problem and the Communication of Languages. Bulletin of the EATCS 74: 171-189 (2001)

Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg: Circularity and Other Invariants of Gene Assembly in Ciliates. Words, Semigroups, and Transductions 2001: 81-97

Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg: Universal and simple operations for gene assembly in ciliates. Where Mathematics, Computer Science, Linguistics and Biology Meet 2001: 329-342

Andrzej Ehrenfeucht, Tero Harju, Ion Petre, Grzegorz Rozenberg: Patterns of Micronuclear Genes in ciliates. DNA 2001: 279-289

Juhani Karhumäki, Ion Petre: On the Centralizer of a Finite Set. ICALP 2000: 536-546

Ion Petre: A Normal form for P-Systems. Bulletin of the EATCS 67: 165-172 (1999)

Ion Petre: Parikh's Theorem Does Not Hold for Multiplicities. Journal of Automata, Languages and Combinatorics 4(1): 17-30 (1999)

Ion Petre, Luigia Petre: Mobile Ambients and P-Systems. J. UCS 5(9): 588-598 (1999)

Ion Petre: On semilinearity in formal power series. Developments in Language Theory 1999: 220-231