Ion Petre

Affiliations:
  • Department of Mathematics and Statistics, University of Turku, Finland
  • Abo Akademi University, Turku, Finland (former)


According to our database1, Ion Petre authored at least 111 papers between 1999 and 2023.

Collaborative distances:
  • Dijkstra number2 of three.
  • Erdős number3 of two.

Timeline

Legend:

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Online presence:

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Bibliography

2023
Strong regulatory graphs.
CoRR, 2023

2022
Network analytics for drug repurposing in COVID-19.
Briefings Bioinform., 2022

2021
Preface: Special Issue on Reaction Systems.
Theor. Comput. Sci., 2021

A fascinating rainbow of computation - Honoring Gheorghe Păun on the occasion of his 70th birthday.
Theor. Comput. Sci., 2021

Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday.
Theor. Comput. Sci., 2021

Towards Scalable Modeling of Biology in Event-B.
CoRR, 2021

Network modeling methods for precision medicine.
CoRR, 2021

NetControl4BioMed: a web-based platform for controllability analysis of protein-protein interaction networks.
Bioinform., 2021

2020
Preface.
J. Membr. Comput., 2020

Controllability of reaction systems.
J. Membr. Comput., 2020

A Computational Model for The Access to Medical Service in a Basic Prototype of a Healthcare System.
Fundam. Informaticae, 2020

Network Controllability Analysis of Three Multiple-myeloma Patient Genetic Mutation Datasets.
Fundam. Informaticae, 2020

Identifying efficient controls of complex interaction networks using genetic algorithms.
CoRR, 2020

2019
Refinement-based modeling of the ErbB signaling pathway.
Comput. Biol. Medicine, 2019

2018
Structural Target Controllability of Linear Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2018

NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability.
BMC Bioinform., 2018

WEBRSIM: A Web-Based Reaction Systems Simulator.
Proceedings of the Enjoying Natural Computing, 2018

2017
From finite state grammars to natural computing - In memory of Solomon Marcus.
Theor. Comput. Sci., 2017

Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems.
Int. J. Found. Comput. Sci., 2017

A Foundational Framework for Step-by-step Model Construction.
Fundam. Informaticae, 2017

Stepwise construction of a metabolic network in Event-B: The heat shock response.
Comput. Biol. Medicine, 2017

Reaction Systems: A Model of Computation Inspired by the Functioning of the Living Cell.
Proceedings of the Role of Theory in Computer Science, 2017

2016
Complete characterization for the fit-preserving data refinement of mass-action reaction networks.
Theor. Comput. Sci., 2016

Complexity of model checking for reaction systems.
Theor. Comput. Sci., 2016

Large-scale executable biology using rapid integration of computational models.
Comput. Sci. J. Moldova, 2016

Target Controllability of Linear Networks.
Proceedings of the Computational Methods in Systems Biology, 2016

Generating the Logicome of a Biological Network.
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.
Proceedings of the From Action Systems to Distributed Systems - The Refinement Approach., 2016

2015
From Computer Science to Biology and Back.
Theor. Comput. Sci., 2015

Dependency graphs and mass conservation in reaction systems.
Theor. Comput. Sci., 2015

The Structure of Elementary Strategies for Gene Assembly in Ciliates.
Fundam. Informaticae, 2015

An Excursion Through Quantitative Model Refinement.
Proceedings of the Membrane Computing, 2015

Full structural model refinement as type refinement of colored Petri nets.
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.
Fundam. Informaticae, 2014

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

Fit-Preserving Data Refinement of Mass-Action Reaction Networks.
Proceedings of the Language, Life, Limits - 10th Conference on Computability in Europe, 2014

The Reduction Power of Simple Operations for Gene Assembly in Ciliates.
Proceedings of the Discrete Mathematics and Computer Science. In Memoriam Alexandru Mateescu (1952-2005)., 2014

On the Implementation of Quantitative Model Refinement.
Proceedings of the Algorithms for Computational Biology - First International Conference, 2014

2013
ODE Analysis of Biological Systems.
Proceedings of the Formal Methods for Dynamical Systems, 2013

2012
Computational Nature of Gene Assembly in Ciliates.
Proceedings of the Handbook of Natural Computing, 2012

Self-assembly Models of Variable Resolution.
Trans. Comp. Sys. Biology, 2012

Matrix insertion-deletion systems.
Theor. Comput. Sci., 2012

Simple gene assembly as a rewriting of directed overlap-inclusion graphs.
Theor. Comput. Sci., 2012

Preface.
Theor. Comput. Sci., 2012

The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Preface.
Nat. Comput., 2012

Quantitative Refinement of Reaction Models.
Int. J. Unconv. Comput., 2012

A Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel.
Fundam. Informaticae, 2012

2011
A simple mass-action model for the eukaryotic heat shock response and its mathematical validation.
Nat. Comput., 2011

Complexity-preserving simulations among three variants of accepting networks of evolutionary processors.
Nat. Comput., 2011

Directed Overlap-inclusion Graphs as Representations of Ciliate Genes.
Fundam. Informaticae, 2011

New Robustness Paradigms: from Nature to Computing.
ERCIM News, 2011

Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels.
Proceedings of the 2nd International Workshop on Static Analysis and Systems Biology, 2011

2010
Accepting splicing systems.
Theor. Comput. Sci., 2010

Extended strings and graphs for simple gene assembly.
Theor. Comput. Sci., 2010

Computing the graph-based parallel complexity of gene assembly.
Theor. Comput. Sci., 2010

Gene assembly in Ciliates.
Scholarpedia, 2010

Three models for gene assembly in ciliates: a comparison.
Comput. Sci. J. Moldova, 2010

A sequence-based analysis of the pointer distribution of stichotrichous ciliates.
Biosyst., 2010

2009
The parallel complexity of signed graphs: Decidability results and an improved algorithm.
Theor. Comput. Sci., 2009

Control Strategies for the Regulation of the Eukaryotic Heat Shock Response.
Proceedings of the Computational Methods in Systems Biology, 7th International Conference, 2009

Computational Heuristics for Simplifying a Biological Model.
Proceedings of the Mathematical Theory and Computational Practice, 2009

A New Mathematical Model for the Heat Shock Response.
Proceedings of the Algorithmic Bioprocesses, 2009

2008
Sequential vs. parallel complexity in simple gene assembly.
Theor. Comput. Sci., 2008

Parikh matrices and amiable words.
Theor. Comput. Sci., 2008

Parallel complexity of signed graphs for gene assembly in ciliates.
Soft Comput., 2008

Solutions to computational problems through gene assembly.
Nat. Comput., 2008

Gene Assembly Models and Boolean Circuits.
Int. J. Found. Comput. Sci., 2008

Decision problem for shuffled genes.
Inf. Comput., 2008

Computational Efficiency of Intermolecular Gene Assembly.
Fundam. Informaticae, 2008

Patterns of simple gene assembly in ciliates.
Discret. Appl. Math., 2008

Graph theoretic approach to parallel gene assembly.
Discret. Appl. Math., 2008

Summary of the Workshop on Natural Computing and Graph Transformations.
Proceedings of the Graph Transformations, 4th International Conference, 2008

Mathematics of gene assembly in ciliates (Abstract).
Proceedings of the Automata and Formal Languages, 12th International Conference, 2008

2007
Self-assembly of strings and languages.
Theor. Comput. Sci., 2007

Computational Power of intramolecular gene Assembly.
Int. J. Found. Comput. Sci., 2007

Computing Through Gene Assembly.
Proceedings of the Unconventional Computation, 6th International Conference, 2007

A String-Based Model for Simple Gene Assembly.
Proceedings of the Fundamentals of Computation Theory, 16th International Symposium, 2007

2006
Parallelism in Gene Assembly.
Nat. Comput., 2006

Invariants of Gene-Assembly in Stichotrichous Ciliates (Invarianten der Gen-Assemblierung in Ciliaten der Unterklasse Stichotrichia).
it Inf. Technol., 2006

Periodic and Sturmian languages.
Inf. Process. Lett., 2006

Simple Gene Assembly Is Deterministic.
Fundam. Informaticae, 2006

Modelling Simple Operations for Gene Assembly.
Proceedings of the Nanotechnology: Science and Computation, 2006

Complexity Measures for Gene Assembly.
Proceedings of the Knowledge Discovery and Emergent Complexity in Bioinformatics, 2006

2005
Commutation with codes.
Theor. Comput. Sci., 2005

Commutation with Ternary Sets of Words.
Theory Comput. Syst., 2005

Simple Operations for Gene Assembly.
Proceedings of the DNA Computing, 11th International Workshop on DNA Computing, 2005

2004
Gene Assembly in Celiates. Part I. Molecular Operations (Column: Natural Computing).
Bull. EATCS, 2004

Tutorial on DNA Computing and Graph Transformation.
Proceedings of the Graph Transformations, Second International Conference, 2004

Two Models for Gene Assembly in Ciliates.
Proceedings of the Theory Is Forever, 2004

Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs.
Proceedings of the Aspects of Molecular Computing, 2004

2003
Formal systems for gene assembly in ciliates.
Theor. Comput. Sci., 2003

Gene Assembly in Ciliates Part I. Molecular Operations.
Bull. EATCS, 2003

The Commutation with Codes and Ternary Sets of Words.
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.
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.
Theor. Comput. Sci., 2002

Characterizing the Micronuclear Gene Patterns in Ciliates.
Theory Comput. Syst., 2002

String and Graph Reduction Systems for Gene Assembly in Ciliates.
Math. Struct. Comput. Sci., 2002

Tutorial on DNA Computing and Graph Transformation - Computational Nature of Gene Assembly in Ciliates.
Proceedings of the Graph Transformation, First International Conference, 2002

The Branching Point Approach to Conway's Problem.
Proceedings of the Formal and Natural Computing, 2002

2001
Conway's Problem and the Communication of Languages.
Bull. EATCS, 2001

Patterns of Micronuclear Genes in ciliates.
Proceedings of the DNA Computing, 7th International Workshop on DNA-Based Computers, 2001

Universal and simple operations for gene assembly in ciliates.
Proceedings of the Where Mathematics, 2001

Circularity and Other Invariants of Gene Assembly in Ciliates.
Proceedings of the Words, Semigroups, and Transductions, 2001

2000
On the Centralizer of a Finite Set.
Proceedings of the Automata, Languages and Programming, 27th International Colloquium, 2000

Uniformly Scattered Factors.
Proceedings of the Finite Versus Infinite, 2000

1999
Mobile Ambients and P-Systems.
J. Univers. Comput. Sci., 1999

Parikh's Theorem Does Not Hold for Multiplicities.
J. Autom. Lang. Comb., 1999

A Normal form for P-Systems.
Bull. EATCS, 1999

On semilinearity in formal power series.
Proceedings of the Developments in Language Theory, 1999


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