Ion Petre

ORCID

Publication Activity (10 Years)

Years Active: 1999-2024
Publications (10 Years): 31

Top Venues

Publications

Patric Gustafsson, Ion Petre
Strong Regulatory Graphs. Fundam. Informaticae 191 (3-4) (2024)
Ion Petre, Andrei Paun
Special issue on Foundational Methods in Systems Biology. Theor. Comput. Sci. 1005 (2024)
Daniela Genova, Ion Petre
Preface. Nat. Comput. 23 (2) (2024)
Patric Gustafsson, Ion Petre
Strong regulatory graphs. CoRR (2023)
Nicoleta Siminea, Victor-Bogdan Popescu, José Ángel Sánchez Martín, Daniela Florea, Georgiana Gavril, Ana Maria Gheorghe, Corina Itcus, Krishna Kanhaiya, Octavian Pacioglu, Laura Ioana Popa, Romica Trandafir, Maria Iris Tusa, Manuela Sidoroff, Mihaela Paun, Eugen Czeizler, Andrei Paun, Ion Petre
Network analytics for drug repurposing in COVID-19. Briefings Bioinform. 23 (1) (2022)
Lukasz Mikulski, Ion Petre
Preface: Special Issue on Reaction Systems. Theor. Comput. Sci. 881 (2021)
Lila Kari, Ion Petre, Grzegorz Rozenberg, Arto Salomaa
A fascinating rainbow of computation - Honoring Gheorghe Păun on the occasion of his 70th birthday. Theor. Comput. Sci. 862 (2021)
Elio Nushi, Victor-Bogdan Popescu, José Ángel Sánchez Martín, Sergiu Ivanov, Eugen Czeizler, Ion Petre
Network modeling methods for precision medicine. CoRR (2021)
Paola Bonizzoni, Lila Kari, Ion Petre, Grzegorz Rozenberg
Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday. Theor. Comput. Sci. 894 (2021)
Usman Sanwal, Thai Son Hoang, Luigia Petre, Ion Petre
Towards Scalable Modeling of Biology in Event-B. CoRR (2021)
Victor-Bogdan Popescu, José Ángel Sánchez Martín, Daniela Schacherer, Sadra Safadoust, Negin Majidi, Andrei Andronescu, Alexandru Nedea, Diana Ion, Eduard Mititelu, Eugen Czeizler, Ion Petre
NetControl4BioMed: a web-based platform for controllability analysis of protein-protein interaction networks. Bioinform. 37 (21) (2021)
José Ángel Sánchez Martín, Ion Petre
Network Controllability Analysis of Three Multiple-myeloma Patient Genetic Mutation Datasets. Fundam. Informaticae 175 (1-4) (2020)
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. Fundam. Informaticae 171 (1-4) (2020)
Sergiu Ivanov, Ion Petre
Controllability of reaction systems. J. Membr. Comput. 2 (4) (2020)
Lukasz Mikulski, Ion Petre
Preface. J. Membr. Comput. 2 (3) (2020)
Sergiu Ivanov, Ion Petre
Controllability of reaction systems. CoRR (2020)
Victor-Bogdan Popescu, Krishna Kanhaiya, Iulian Nastac, Eugen Czeizler, Ion Petre
Identifying efficient controls of complex interaction networks using genetic algorithms. CoRR (2020)
Bogdan Iancu, Usman Sanwal, Cristian Gratie, Ion Petre
Refinement-based modeling of the ErbB signaling pathway. Comput. Biol. Medicine 106 (2019)
Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre
WEBRSIM: A Web-Based Reaction Systems Simulator. Enjoying Natural Computing (2018)
Eugen Czeizler, Wu Kai Chiu, Cristian Gratie, Krishna Kanhaiya, Ion Petre
Structural Target Controllability of Linear Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 15 (4) (2018)
Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre
NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability. BMC Bioinform. (7) (2018)
Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, Ion Petre
Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems. Int. J. Found. Comput. Sci. 28 (8) (2017)
Mikhail Barash, Ion Petre
A Foundational Framework for Step-by-step Model Construction. Fundam. Informaticae 154 (1-4) (2017)
Gheorghe Paun, Ion Petre, Grzegorz Rozenberg, Arto Salomaa
From finite state grammars to natural computing - In memory of Solomon Marcus. Theor. Comput. Sci. 701 (2017)
Andrzej Ehrenfeucht, Ion Petre, Grzegorz Rozenberg
Reaction Systems: A Model of Computation Inspired by the Functioning of the Living Cell. The Role of Theory in Computer Science (2017)
Usman Sanwal, Luigia Petre, Ion Petre
Stepwise construction of a metabolic network in Event-B: The heat shock response. Comput. Biol. Medicine 91 (2017)
Vladimir Rogojin, Ion Petre
Large-scale executable biology using rapid integration of computational models. Comput. Sci. J. Moldova 24 (1) (2016)
Eugen Czeizler, Cristian Gratie, Wu Kai Chiu, Krishna Kanhaiya, Ion Petre
Target Controllability of Linear Networks. CMSB (2016)
Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca
Complexity of model checking for reaction systems. Theor. Comput. Sci. 623 (2016)
Cristian Gratie, Ion Petre
Complete characterization for the fit-preserving data refinement of mass-action reaction networks. Theor. Comput. Sci. 641 (2016)
Charmi Panchal, Sepinoud Azimi, Ion Petre
Generating the Logicome of a Biological Network. AlCoB (2016)
Diana-Elena Gratie, Ion Petre
Full structural model refinement as type refinement of colored Petri nets. BioPPN@Petri Nets (2015)
Emanuela Merelli, Ion Petre
From Computer Science to Biology and Back. Theor. Comput. Sci. 608 (2015)
Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana-Elena Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri
An Excursion Through Quantitative Model Refinement. Int. Conf. on Membrane Computing (2015)
Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre
Dependency graphs and mass conservation in reaction systems. Theor. Comput. Sci. 598 (2015)
Vladimir Rogojin, Ion Petre
The Structure of Elementary Strategies for Gene Assembly in Ciliates. Fundam. Informaticae 138 (1-2) (2015)
Cristian Gratie, Ion Petre
Fit-Preserving Data Refinement of Mass-Action Reaction Networks. CiE (2014)
Sepinoud Azimi, Ion Petre
The Reduction Power of Simple Operations for Gene Assembly in Ciliates. Discrete Mathematics and Computer Science (2014)
Bogdan Iancu, Diana-Elena Gratie, Sepinoud Azimi, Ion Petre
On the Implementation of Quantitative Model Refinement. AlCoB (2014)
Sepinoud Azimi, Bogdan Iancu, Ion Petre
Reaction System Models for the Heat Shock Response. Fundam. Informaticae 131 (3-4) (2014)
Emanuela Merelli, Ion Petre
Preface. Electron. Notes Theor. Comput. Sci. 306 (2014)
Diana-Elena Gratie, Bogdan Iancu, Ion Petre
ODE Analysis of Biological Systems. SFM (2013)
Andrzej Mizera, Eugen Czeizler, Ion Petre
Self-assembly Models of Variable Resolution. Trans. Comp. Sys. Biology 14 (2012)
Ion Petre, Sergey Verlan
Matrix insertion-deletion systems. Theor. Comput. Sci. 456 (2012)
Bogdan Iancu, Elena Czeizler, Eugen Czeizler, Ion Petre
Quantitative Refinement of Reaction Models. Int. J. Unconv. Comput. 8 (5-6) (2012)
Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre
Simple gene assembly as a rewriting of directed overlap-inclusion graphs. Theor. Comput. Sci. 454 (2012)
Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre
Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels. Electron. Notes Theor. Comput. Sci. 284 (2012)
Jarkko Kari, Ion Petre
Preface. Nat. Comput. 11 (4) (2012)
Elena Czeizler, Andrzej Mizera, Ion Petre
A Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel. Fundam. Informaticae 116 (1-4) (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. Biol. Bioinform. 9 (5) (2012)
Giorgio Ausiello, Hendrik Jan Hoogeboom, Juhani Karhumäki, Ion Petre, Arto Salomaa
Preface. Theor. Comput. Sci. 429 (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. Biol. Bioinform. 9 (3) (2012)
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. Nat. Comput. 10 (1) (2011)
Eugen Czeizler, Vladimir Rogojin, Ion Petre
The phosphorylation of the heat shock factor as a modulator for the heat shock response. CMSB (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. Nat. Comput. 10 (1) (2011)
Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin
Directed Overlap-inclusion Graphs as Representations of Ciliate Genes. Fundam. Informaticae 110 (1-4) (2011)
Giancarlo Mauri, Ion Petre
New Robustness Paradigms: from Nature to Computing. ERCIM News 2011 (85) (2011)
Artiom Alhazov, Chang Li, Ion Petre
Computing the graph-based parallel complexity of gene assembly. Theor. Comput. Sci. 411 (25) (2010)
Ion Petre, Grzegorz Rozenberg
Gene assembly in Ciliates. Scholarpedia 5 (1) (2010)
Ion Petre, Sergey Verlan
Matrix Insertion-Deletion Systems CoRR (2010)
Sergey Verlan, Artiom Alhazov, Ion Petre
A sequence-based analysis of the pointer distribution of stichotrichous ciliates. Biosyst. 101 (2) (2010)
Victor Mitrana, Ion Petre, Vladimir Rogojin
Accepting splicing systems. Theor. Comput. Sci. 411 (25) (2010)
Miika Langille, Ion Petre, Vladimir Rogojin
Three models for gene assembly in ciliates: a comparison. Comput. Sci. J. Moldova 18 (1) (2010)
Robert Brijder, Miika Langille, Ion Petre
Extended strings and graphs for simple gene assembly. Theor. Comput. Sci. 411 (4-5) (2010)
Elena Czeizler, Eugen Czeizler, Ralph-Johan Back, Ion Petre
Control Strategies for the Regulation of the Eukaryotic Heat Shock Response. CMSB (2009)
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. Algorithmic Bioprocesses (2009)
Ion Petre, Andrzej Mizera, Ralph-Johan Back
Computational Heuristics for Simplifying a Biological Model. CiE (2009)
Artiom Alhazov, Ion Petre, Vladimir Rogojin
The parallel complexity of signed graphs: Decidability results and an improved algorithm. Theor. Comput. Sci. 410 (24-25) (2009)
Ion Petre
Mathematics of gene assembly in ciliates (Abstract). AFL (2008)
Artiom Alhazov, Ion Petre, Vladimir Rogojin
Solutions to computational problems through gene assembly. Nat. Comput. 7 (3) (2008)
Miika Langille, Ion Petre, Vladimir Rogojin
Three models for gene assembly in ciliates: a comparison. BIONETICS (2008)
Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg
Patterns of simple gene assembly in ciliates. Discret. Appl. Math. 156 (14) (2008)
Miika Langille, Ion Petre
Sequential vs. parallel complexity in simple gene assembly. Theor. Comput. Sci. 395 (1) (2008)
Adrian Atanasiu, Radu-Florian Atanasiu, Ion Petre
Parikh matrices and amiable words. Theor. Comput. Sci. 390 (1) (2008)
Tseren-Onolt Ishdorj, Remco Loos, Ion Petre
Computational Efficiency of Intermolecular Gene Assembly. Fundam. Informaticae 84 (3-4) (2008)
Tseren-Onolt Ishdorj, Ion Petre
Gene Assembly Models and Boolean Circuits. Int. J. Found. Comput. Sci. 19 (5) (2008)
Ion Petre, Grzegorz Rozenberg
Summary of the Workshop on Natural Computing and Graph Transformations. ICGT (2008)
Ion Petre, Vladimir Rogojin
Decision problem for shuffled genes. Inf. Comput. 206 (11) (2008)
Tero Harju, Chang Li, Ion Petre
Graph theoretic approach to parallel gene assembly. Discret. Appl. Math. 156 (18) (2008)
Tero Harju, Chang Li, Ion Petre
Parallel complexity of signed graphs for gene assembly in ciliates. Soft Comput. 12 (8) (2008)
Robert Brijder, Miika Langille, Ion Petre
A String-Based Model for Simple Gene Assembly. FCT (2007)
Tseren-Onolt Ishdorj, Ion Petre, Vladimir Rogojin
Computational Power of intramolecular gene Assembly. Int. J. Found. Comput. Sci. 18 (5) (2007)
Artiom Alhazov, Ion Petre, Vladimir Rogojin
Solutions to Computational Problems Through Gene Assembly. DNA (2007)
Tseren-Onolt Ishdorj, Ion Petre
Computing Through Gene Assembly. UC (2007)
Erzsébet Csuhaj-Varjú, Ion Petre, György Vaszil
Self-assembly of strings and languages. Theor. Comput. Sci. 374 (1-3) (2007)
Tero Harju, Ion Petre, Grzegorz Rozenberg
Modelling Simple Operations for Gene Assembly. Nanotechnology: Science and Computation (2006)
Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg
Complexity Measures for Gene Assembly. KDECB (2006)
Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg
Parallelism in Gene Assembly. Nat. Comput. 5 (2) (2006)
Miika Langille, Ion Petre
Simple Gene Assembly Is Deterministic. Fundam. Informaticae 73 (1-2) (2006)
Ion Petre
Invariants of Gene-Assembly in Stichotrichous Ciliates (Invarianten der Gen-Assemblierung in Ciliaten der Unterklasse Stichotrichia). it Inf. Technol. 48 (3) (2006)
Lucian Ilie, Solomon Marcus, Ion Petre
Periodic and Sturmian languages. Inf. Process. Lett. 98 (6) (2006)
Juhani Karhumäki, Michel Latteux, Ion Petre
Commutation with codes. Theor. Comput. Sci. 340 (1) (2005)
Juhani Karhumäki, Michel Latteux, Ion Petre
Commutation with Ternary Sets of Words. Theory Comput. Syst. 38 (2) (2005)
Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg
Simple Operations for Gene Assembly. DNA (2005)
Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg
Parallelism in Gene Assembly. DNA (2004)
Tero Harju, Ion Petre, Grzegorz Rozenberg
Gene Assembly in Celiates. Part I. Molecular Operations (Column: Natural Computing). Bull. EATCS 82 (2004)
Tero Harju, Ion Petre, Grzegorz Rozenberg
Two Models for Gene Assembly in Ciliates. Theory Is Forever (2004)
Tero Harju, Ion Petre, Grzegorz Rozenberg
Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs. Aspects of Molecular Computing (2004)
Tero Harju, Ion Petre, Grzegorz Rozenberg
Tutorial on DNA Computing and Graph Transformation. ICGT (2004)
Juhani Karhumäki, Michel Latteux, Ion Petre
The Commutation with Codes and Ternary Sets of Words. STACS (2003)

Ion Petre.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Ion Petre