Ion Petre

According to our database, Ion Petre authored at least 113 papers between 1999 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of two.

2024

Preface.

Daniela Genova, Ion Petre

Nat. Comput., June, 2024

Special issue on Foundational Methods in Systems Biology.

Ion Petre, Andrei Paun

Theor. Comput. Sci., 2024

Strong Regulatory Graphs.

Patric Gustafsson, Ion Petre

Fundam. Informaticae, 2024

2022

Network analytics for drug repurposing in COVID-19.

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

Briefings Bioinform., 2022

2021

Preface: Special Issue on Reaction Systems.

Lukasz Mikulski, Ion Petre

Theor. Comput. Sci., 2021

A fascinating rainbow of computation - Honoring Gheorghe Păun on the occasion of his 70th birthday.

Lila Kari, Ion Petre, Grzegorz Rozenberg, Arto Salomaa

Theor. Comput. Sci., 2021

Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday.

Paola Bonizzoni, Lila Kari, Ion Petre, Grzegorz Rozenberg

Theor. Comput. Sci., 2021

Towards Scalable Modeling of Biology in Event-B.

Usman Sanwal, Thai Son Hoang, Luigia Petre, Ion Petre

CoRR, 2021

Network modeling methods for precision medicine.

Elio Nushi, Victor-Bogdan Popescu, José Ángel Sánchez Martín, Sergiu Ivanov, Eugen Czeizler, Ion Petre

CoRR, 2021

NetControl4BioMed: a web-based platform for controllability analysis of protein-protein interaction networks.

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

Bioinform., 2021

2020

Preface.

Lukasz Mikulski, Ion Petre

J. Membr. Comput., 2020

Controllability of reaction systems.

Sergiu Ivanov, Ion Petre

J. Membr. Comput., 2020

A Computational Model for The Access to Medical Service in a Basic Prototype of a Healthcare System.

Luigia Petre, Usman Sanwal, Gohar Shah, Charmi Panchal, Dwitiya Tyagi, Ion Petre

Fundam. Informaticae, 2020

Network Controllability Analysis of Three Multiple-myeloma Patient Genetic Mutation Datasets.

José Ángel Sánchez Martín, Ion Petre

Fundam. Informaticae, 2020

Identifying efficient controls of complex interaction networks using genetic algorithms.

Victor-Bogdan Popescu, Krishna Kanhaiya, Iulian Nastac, Eugen Czeizler, Ion Petre

CoRR, 2020

2019

Refinement-based modeling of the ErbB signaling pathway.

Bogdan Iancu, Usman Sanwal, Cristian Gratie, Ion Petre

Comput. Biol. Medicine, 2019

2018

Structural Target Controllability of Linear Networks.

Eugen Czeizler, Wu Kai Chiu, Cristian Gratie, Krishna Kanhaiya, Ion Petre

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability.

Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre

BMC Bioinform., 2018

WEBRSIM: A Web-Based Reaction Systems Simulator.

Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre

Proceedings of the Enjoying Natural Computing, 2018

2017

From finite state grammars to natural computing - In memory of Solomon Marcus.

Gheorghe Paun, Ion Petre, Grzegorz Rozenberg, Arto Salomaa

Theor. Comput. Sci., 2017

Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems.

Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, Ion Petre

Int. J. Found. Comput. Sci., 2017

A Foundational Framework for Step-by-step Model Construction.

Mikhail Barash, Ion Petre

Fundam. Informaticae, 2017

Stepwise construction of a metabolic network in Event-B: The heat shock response.

Usman Sanwal, Luigia Petre, Ion Petre

Comput. Biol. Medicine, 2017

Reaction Systems: A Model of Computation Inspired by the Functioning of the Living Cell.

Andrzej Ehrenfeucht, Ion Petre, Grzegorz Rozenberg

Proceedings of the Role of Theory in Computer Science, 2017

2016

Complete characterization for the fit-preserving data refinement of mass-action reaction networks.

Cristian Gratie, Ion Petre

Theor. Comput. Sci., 2016

Complexity of model checking for reaction systems.

Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca

Theor. Comput. Sci., 2016

Large-scale executable biology using rapid integration of computational models.

Vladimir Rogojin, Ion Petre

Comput. Sci. J. Moldova, 2016

Target Controllability of Linear Networks.

Eugen Czeizler, Cristian Gratie, Wu Kai Chiu, Krishna Kanhaiya, Ion Petre

Proceedings of the Computational Methods in Systems Biology, 2016

Generating the Logicome of a Biological Network.

Charmi Panchal, Sepinoud Azimi, Ion Petre

Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

Quantitative Model Refinement in Four Different Frameworks, with Applications to the Heat Shock Response.

Diana-Elena Gratie, Bogdan Iancu, Sepinoud Azimi, Ion Petre

Proceedings of the From Action Systems to Distributed Systems - The Refinement Approach., 2016

2015

From Computer Science to Biology and Back.

Emanuela Merelli, Ion Petre

Theor. Comput. Sci., 2015

Dependency graphs and mass conservation in reaction systems.

Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre

Theor. Comput. Sci., 2015

The Structure of Elementary Strategies for Gene Assembly in Ciliates.

Vladimir Rogojin, Ion Petre

Fundam. Informaticae, 2015

An Excursion Through Quantitative Model Refinement.

Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana-Elena Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri

Proceedings of the Membrane Computing, 2015

Full structural model refinement as type refinement of colored Petri nets.

Diana-Elena Gratie, Ion Petre

Proceedings of the 6th International Workshop on Biological Processes & Petri Nets co-located with 36th International Conference on Application and Theory of Petri Nets and Concurreny (PETRI NETS 2015), 2015

2014

Reaction System Models for the Heat Shock Response.

Sepinoud Azimi, Bogdan Iancu, Ion Petre

Fundam. Informaticae, 2014

Preface.

Emanuela Merelli, Ion Petre

Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology, 2014

Fit-Preserving Data Refinement of Mass-Action Reaction Networks.

Cristian Gratie, Ion Petre

Proceedings of the Language, Life, Limits - 10th Conference on Computability in Europe, 2014

The Reduction Power of Simple Operations for Gene Assembly in Ciliates.

Sepinoud Azimi, Ion Petre

Proceedings of the Discrete Mathematics and Computer Science. In Memoriam Alexandru Mateescu (1952-2005)., 2014

On the Implementation of Quantitative Model Refinement.

Bogdan Iancu, Diana-Elena Gratie, Sepinoud Azimi, Ion Petre

Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

2013

ODE Analysis of Biological Systems.

Diana-Elena Gratie, Bogdan Iancu, Ion Petre

Proceedings of the Formal Methods for Dynamical Systems, 2013

2012

Computational Nature of Gene Assembly in Ciliates.

Robert Brijder, Mark Daley, Tero Harju, Natasa Jonoska, Ion Petre, Grzegorz Rozenberg

Proceedings of the Handbook of Natural Computing, 2012

Self-assembly Models of Variable Resolution.

Andrzej Mizera, Eugen Czeizler, Ion Petre

Trans. Comp. Sys. Biology, 2012

Matrix insertion-deletion systems.

Ion Petre, Sergey Verlan

Theor. Comput. Sci., 2012

Simple gene assembly as a rewriting of directed overlap-inclusion graphs.

Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre

Theor. Comput. Sci., 2012

Preface.

Giorgio Ausiello, Hendrik Jan Hoogeboom, Juhani Karhumäki, Ion Petre, Arto Salomaa

Theor. Comput. Sci., 2012

The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response.

Eugen Czeizler, Vladimir Rogojin, Ion Petre

IEEE ACM Trans. Comput. Biol. Bioinform., 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, Ion Petre

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Preface.

Jarkko Kari, Ion Petre

Nat. Comput., 2012

Quantitative Refinement of Reaction Models.

Bogdan Iancu, Elena Czeizler, Eugen Czeizler, Ion Petre

Int. J. Unconv. Comput., 2012

A Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel.

Elena Czeizler, Andrzej Mizera, Ion Petre

Fundam. Informaticae, 2012

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, Ralph-Johan Back

Nat. Comput., 2011

Complexity-preserving simulations among three variants of accepting networks of evolutionary processors.

Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Ion Petre, José M. Sempere

Nat. Comput., 2011

Directed Overlap-inclusion Graphs as Representations of Ciliate Genes.

Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin

Fundam. Informaticae, 2011

New Robustness Paradigms: from Nature to Computing.

Giancarlo Mauri, Ion Petre

ERCIM News, 2011

Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels.

Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre

Proceedings of the 2nd International Workshop on Static Analysis and Systems Biology, 2011

2010

Accepting splicing systems.

Victor Mitrana, Ion Petre, Vladimir Rogojin

Theor. Comput. Sci., 2010

Extended strings and graphs for simple gene assembly.

Robert Brijder, Miika Langille, Ion Petre

Theor. Comput. Sci., 2010

Computing the graph-based parallel complexity of gene assembly.

Artiom Alhazov, Chang Li, Ion Petre

Theor. Comput. Sci., 2010

Gene assembly in Ciliates.

Ion Petre, Grzegorz Rozenberg

Scholarpedia, 2010

Three models for gene assembly in ciliates: a comparison.

Miika Langille, Ion Petre, Vladimir Rogojin

Comput. Sci. J. Moldova, 2010

A sequence-based analysis of the pointer distribution of stichotrichous ciliates.

Sergey Verlan, Artiom Alhazov, Ion Petre

Biosyst., 2010

2009

The parallel complexity of signed graphs: Decidability results and an improved algorithm.

Artiom Alhazov, Ion Petre, Vladimir Rogojin

Theor. Comput. Sci., 2009

Control Strategies for the Regulation of the Eukaryotic Heat Shock Response.

Elena Czeizler, Eugen Czeizler, Ralph-Johan Back, Ion Petre

Proceedings of the Computational Methods in Systems Biology, 7th International Conference, 2009

Computational Heuristics for Simplifying a Biological Model.

Ion Petre, Andrzej Mizera, Ralph-Johan Back

Proceedings of the Mathematical Theory and Computational Practice, 2009

A New Mathematical Model for the Heat Shock Response.

Ion Petre, Andrzej Mizera, Claire L. Hyder, Andrey Mikhailov, John E. Eriksson, Lea Sistonen, Ralph-Johan Back

Proceedings of the Algorithmic Bioprocesses, 2009

2008

Sequential vs. parallel complexity in simple gene assembly.

Miika Langille, Ion Petre

Theor. Comput. Sci., 2008

Parikh matrices and amiable words.

Adrian Atanasiu, Radu-Florian Atanasiu, Ion Petre

Theor. Comput. Sci., 2008

Parallel complexity of signed graphs for gene assembly in ciliates.

Tero Harju, Chang Li, Ion Petre

Soft Comput., 2008

Solutions to computational problems through gene assembly.

Artiom Alhazov, Ion Petre, Vladimir Rogojin

Nat. Comput., 2008

Gene Assembly Models and Boolean Circuits.

Tseren-Onolt Ishdorj, Ion Petre

Int. J. Found. Comput. Sci., 2008

Decision problem for shuffled genes.

Ion Petre, Vladimir Rogojin

Inf. Comput., 2008

Computational Efficiency of Intermolecular Gene Assembly.

Tseren-Onolt Ishdorj, Remco Loos, Ion Petre

Fundam. Informaticae, 2008

Patterns of simple gene assembly in ciliates.

Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg

Discret. Appl. Math., 2008

Graph theoretic approach to parallel gene assembly.

Tero Harju, Chang Li, Ion Petre

Discret. Appl. Math., 2008

Summary of the Workshop on Natural Computing and Graph Transformations.

Ion Petre, Grzegorz Rozenberg

Proceedings of the Graph Transformations, 4th International Conference, 2008

Mathematics of gene assembly in ciliates (Abstract).

Ion Petre

Proceedings of the Automata and Formal Languages, 12th International Conference, 2008

2007

Self-assembly of strings and languages.

Erzsébet Csuhaj-Varjú, Ion Petre, György Vaszil

Theor. Comput. Sci., 2007

Computational Power of intramolecular gene Assembly.

Tseren-Onolt Ishdorj, Ion Petre, Vladimir Rogojin

Int. J. Found. Comput. Sci., 2007

Computing Through Gene Assembly.

Tseren-Onolt Ishdorj, Ion Petre

Proceedings of the Unconventional Computation, 6th International Conference, 2007

A String-Based Model for Simple Gene Assembly.

Robert Brijder, Miika Langille, Ion Petre

Proceedings of the Fundamentals of Computation Theory, 16th International Symposium, 2007

2006

Parallelism in Gene Assembly.

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg

Nat. Comput., 2006

Invariants of Gene-Assembly in Stichotrichous Ciliates (Invarianten der Gen-Assemblierung in Ciliaten der Unterklasse Stichotrichia).

Ion Petre

it Inf. Technol., 2006

Periodic and Sturmian languages.

Lucian Ilie, Solomon Marcus, Ion Petre

Inf. Process. Lett., 2006

Simple Gene Assembly Is Deterministic.

Miika Langille, Ion Petre

Fundam. Informaticae, 2006

Modelling Simple Operations for Gene Assembly.

Tero Harju, Ion Petre, Grzegorz Rozenberg

Proceedings of the Nanotechnology: Science and Computation, 2006

Complexity Measures for Gene Assembly.

Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg

Proceedings of the Knowledge Discovery and Emergent Complexity in Bioinformatics, 2006

2005

Commutation with codes.

Juhani Karhumäki, Michel Latteux, Ion Petre

Theor. Comput. Sci., 2005

Commutation with Ternary Sets of Words.

Juhani Karhumäki, Michel Latteux, Ion Petre

Theory Comput. Syst., 2005

Simple Operations for Gene Assembly.

Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg

Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

2004

Gene Assembly in Celiates. Part I. Molecular Operations (Column: Natural Computing).

Tero Harju, Ion Petre, Grzegorz Rozenberg

Bull. EATCS, 2004

Tutorial on DNA Computing and Graph Transformation.

Tero Harju, Ion Petre, Grzegorz Rozenberg

Proceedings of the Graph Transformations, Second International Conference, 2004

Two Models for Gene Assembly in Ciliates.

Tero Harju, Ion Petre, Grzegorz Rozenberg

Proceedings of the Theory Is Forever, 2004

Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs.

Tero Harju, Ion Petre, Grzegorz Rozenberg

Proceedings of the Aspects of Molecular Computing, 2004

2003

Formal systems for gene assembly in ciliates.

Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescott, Grzegorz Rozenberg

Theor. Comput. Sci., 2003

Gene Assembly in Ciliates Part I. Molecular Operations.

Tero Harju, Ion Petre, Grzegorz Rozenberg

Bull. EATCS, 2003

The Commutation with Codes and Ternary Sets of Words.

Juhani Karhumäki, Michel Latteux, Ion Petre

Proceedings of the STACS 2003, 20th Annual Symposium on Theoretical Aspects of Computer Science, Berlin, Germany, February 27, 2003

On the Difference Problem for Semilinear Power Series.

Ion Petre

Proceedings of the Grammars and Automata for String Processing: From Mathematics and Computer Science to Biology, 2003

2002

Conway's problem for three-word sets.

Juhani Karhumäki, Ion Petre

Theor. Comput. Sci., 2002

Characterizing the Micronuclear Gene Patterns in Ciliates.

Andrzej Ehrenfeucht, Tero Harju, Ion Petre, Grzegorz Rozenberg

Theory Comput. Syst., 2002

String and Graph Reduction Systems for Gene Assembly in Ciliates.

Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg

Math. Struct. Comput. Sci., 2002

Tutorial on DNA Computing and Graph Transformation - Computational Nature of Gene Assembly in Ciliates.

Tero Harju, Ion Petre, Grzegorz Rozenberg

Proceedings of the Graph Transformation, First International Conference, 2002

The Branching Point Approach to Conway's Problem.

Juhani Karhumäki, Ion Petre

Proceedings of the Formal and Natural Computing, 2002

2001

Conway's Problem and the Communication of Languages.

Juhani Karhumäki, Ion Petre

Bull. EATCS, 2001

Patterns of Micronuclear Genes in ciliates.

Andrzej Ehrenfeucht, Tero Harju, Ion Petre, Grzegorz Rozenberg

Proceedings of the DNA Computing, 7th International Workshop on DNA-Based Computers, 2001

Universal and simple operations for gene assembly in ciliates.

Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg

Proceedings of the Where Mathematics, 2001

Circularity and Other Invariants of Gene Assembly in Ciliates.

Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg

Proceedings of the Words, Semigroups, and Transductions, 2001

2000

On the Centralizer of a Finite Set.

Juhani Karhumäki, Ion Petre

Proceedings of the Automata, Languages and Programming, 27th International Colloquium, 2000

Uniformly Scattered Factors.

Lucian Ilie, Ion Petre, Grzegorz Rozenberg

Proceedings of the Finite Versus Infinite, 2000

1999

Mobile Ambients and P-Systems.

Ion Petre, Luigia Petre

J. Univers. Comput. Sci., 1999

Parikh's Theorem Does Not Hold for Multiplicities.

Ion Petre

J. Autom. Lang. Comb., 1999

A Normal form for P-Systems.

Ion Petre

Bull. EATCS, 1999

On semilinearity in formal power series.

Ion Petre

Proceedings of the Developments in Language Theory, 1999