Peer-reviewed publications

A1 Journal article (refereed)
NetControl4BioMed: A pipeline for biomedical data acquisition and analysis of network controllability (2018)
Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre
BMC Bioinformatics
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A1 Journal article (refereed)
Structural Target Controllability of Linear Networks: (2018)
Eugen Czeizler, Kai-Chiu Wu, Cristian Gratie, Krishna Kanhaiya, Ion Petre
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Advanced Healthcare Materials
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A3 Book section, Chapters in research books
WEBRSIM: A Web-Based Reaction Systems Simulator (2018)
Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre
Springer
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A1 Journal article (refereed)
A Foundational Framework for Step-by-Step Model Construction (2017)
Mikhail Barash, Ion Petre
Fundamenta Informaticae
Theoretical Computer Science
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C2 Edited book
At the Intersection of Computer Science with Biology, Chemistry and Physics: In Memory of Solomon Marcus (2017)
Gheorghe Paun, Ion Petre, Grzegorz Rozenberg, Arto Salomaa
Elsevier
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C2 Edited book
Computability in Europe 2017 (2017)
Sepinoud Azimi, Joonas Jalonen, Jarkko Kari, Ion Petre
Turku Centre for Computer Science
Springer
A1 Journal article (refereed)
Controlling Directed Protein Interaction Networks in Cancer (2017)
Krishna Kanhaiya, Eugen Czeizler, Cristian Gratie, Ion Petre
Scientific Reports
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A1 Journal article (refereed)
Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems (2017)
Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, Ion Petre
International Journal of Foundations of Computer Science
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A3 Book section, Chapters in research books
Reaction systems: a model of computation inspired by the functioning of the living cell (2017)
Andrzej Ehrenfeucht, Ion Petre, Grzegorz Rozenberg
World Scientific Publishing
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A1 Journal article (refereed)
Stepwise Construction of a Metabolic Network in Event-B: The Heat Shock Response (2017)
Usman Sanwal, Luigia Petre, Ion Petre
Computers in Biology and Medicine
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A2 Review article, Literature review, Systematic review
Tailored approaches in drug development and diagnostics: from molecular design to biological model systems (2017)
Cecilia Sahlgren, Annika Meinander, Hongbo Zhang, Fang Cheng, Maren Preis, Chunlin Xu, Tiina A. Salminen, Diana Toivola, Daniel Abankwa, Ari Rosling, Didem Şen Karaman, Outi M. H. Salo-Ahen, Ronald Österbacka, John E. Eriksson, Stefan Willför, Ion Petre, Jouko Peltonen, Reko Leino, Mark Johnson, Jessica Rosenholm, Niklas Sandler
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C2 Edited book
Unveiling Dynamics and Complexity (2017)
Jarkko Kari, Florin Manea, Ion Petre
Springer
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A4 Conference proceedings
Automatic discovery of combined drug therapy (2016)
Vladimir Rogojin, Keivan Kazemi, Krishna Kanhaiya, Eugen Czeizler, Ion Petre
A1 Journal article (refereed)
Complexity of model checking for reaction systems (2016)
Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre , Antonio E. Porreca
Theoretical Computer Science
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A4 Conference proceedings
Generating the Logicome of a Biological Network (2016)
Charmi Panchal, Sepinoud Azimi, Ion Petre
View on publisher's site
A1 Journal article (refereed)
Large-scale executable biology using rapid integration of computational models: ee (2016)
Vladimir Rogojin, Ion Petre
Computer Science Journal of Moldova
A3 Book section, Chapters in research books
Quantitative model refinement in four different frameworks, with applications to the heat shock response (2016)
Diana-Elena Gratie, Bogdan Iancu, Sepinoud Azimi, Ion Petre
CRC Press
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A4 Conference proceedings
Target Controllability of Linear Networks (2016)
Eugen Czeizler, Christian Gratie, Wu Kai Chiu, Krishna Kanhaiya, Ion Petre
Springer
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A4 Conference proceedings
An excursion through quantitative model refinement (2015)
Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri
Springer
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A1 Journal article (refereed)
Dependency Graphs and Mass Conservation in Reaction Systems (2015)
Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre
Theoretical Computer Science
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C2 Edited book
From Computer Science to Biology and Back (2015)
Emanuela Merelli, Ion Petre
Elsevier
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A4 Conference proceedings
Full Structural Model Refinement as Type Refinement of Colored Petri Nets (2015)
Diana-Elena Gratie, Ion Petre
CEUR Workshop Proceedings
CEUR-WS.org
C2 Edited book
Multidisciplinary Creativity : homage to Gheorghe Pӑun on his 65th birthday (2015)
Marian Gheorghe, Ion Petre, Mario J. Pérez-Jiménez, Grzegorz Rozenberg, Arto Salomaa
Spandugino
A3 Book section, Chapters in research books
Quantitative model refinement for guarded command models (2015)
Sepinoud Azimi, Ion Petre
Spandugino
A1 Journal article (refereed)
Reaction Systems Models for the Self-Assembly of Intermediate Filaments (2015)
Azimi S, Panchal C, Czeizler E, Petre I
Analele Universitatii Bucuresti : Matematica-Informatica
A1 Journal article (refereed)
The Structure of Elementary Strategies for Gene Assembly in Ciliates (2015)
Vladimir Rogojin, Ion Petre
Fundamenta Informaticae
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A1 Journal article (refereed)
Dependency relations between elementary intramolecular operations in gene assembly in ciliates (2014)
Petre Ion, Rogojin Vladimir
Journal of Automata, Languages and Combinatorics
A4 Conference proceedings
Fit-Preserving Data Refinement of Mass-Action Reaction Networks (2014)
Cristian Gratie and Ion Petre
Springer
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A1 Journal article (refereed)
Hiding the combinatorial state space explosion of biomodels through colored Petri nets (2014)
Diana-Elena Gratie, Ion Petre
Analele Universitatii Bucuresti
A4 Conference proceedings
On the Implementation of Quantitative Model Refinement (2014)
Iancu B, Gratie D, Azimi S, Petre I
Lecture Notes in Computer Science
Springer
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A1 Journal article (refereed)
Reaction System Models for the Heat Shock Response (2014)
Sepinoud Azimi, Bogdan Iancu, Ion Petre
Fundamenta Informaticae
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A1 Journal article (refereed)
Refinement-based modelling of the ErbB signalling pathway (2014)
Bogdan Iancu, Cristian Gratie, Ion Petre
Analele Universitatii Bucuresti
A3 Book section, Chapters in research books
The Reduction Power of Simple Operations for Gene Assembly in Ciliates (2014)
Sepinoud Azimi, Ion Petre
A3 Book section, Chapters in research books
ODE analysis of biological systems (2013)
Diana-Elena Gratie, Bogdan Iancu, Ion Petre
Springer
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A1 Journal article (refereed)
Quantitative model refinement as a solution to the combinatorial size explosion of biomodels (2012)
Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre
Electronic Notes in Theoretical Computer Science
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A1 Journal article (refereed)
Quantitative refinement of reaction models (2012)
Bogdan Iancu, Elena Czeizler, Eugen Czeizler, Ion Petre
International Journal of Unconventional Computing
A1 Journal article (refereed)
Simple Gene Assembly as a Rewriting of Directed Overlap-Inclusion Graphs (2012)
Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre
Theoretical Computer Science
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A1 Journal article (refereed)
The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response (2012)
Eugen Czeizler, Vladimir Rogojin, Ion Petre
IEEE/ACM Transactions on Computational Biology and Bioinformatics
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A1 Journal article (refereed)
A simple mass-action model for the eukaryotic heat shock response and its mathematical validation (2011)
Petre I, Mizera A, Hyder CL, Meinander A, Mikhailov A, Morimoto RI, Sistonen L, Eriksson JE, Back RJ
Natural Computing
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A1 Journal article (refereed)
Directed Overlap-Inclusion Graphs as Representations of Ciliate Genes (2011)
Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin
Fundamenta Informaticae
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A4 Conference proceedings
The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response (2011)
Eugen Czeizler, Vladimir Rogojin, Ion Petre
ACM
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A1 Journal article (refereed)
Accepting Splicing Systems (2010)
Victor Mitrana, Ion Petre, Vladimir Rogojin
Theoretical Computer Science
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A1 Journal article (refereed)
Three Models for Gene Assembly in Ciliates: A Comparison (2010)
Miika Langille, Ion Petre, Vladimir Rogojin
Computer Science Journal of Moldova
A3 Book section, Chapters in research books
A New Mathematical Model for the Heat Shock Response (2009)
Petre I, Mizera A, Hyder CL, Mikhailov A, Eriksson JE, Sistonen L, Back RJ
Springer
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A1 Journal article (refereed)
The Parallel Complexity of Signed Graphs: Decidability and an Improved Algorithm (2009)
Artiom Alhazov, Ion Petre, Vladimir Rogojin
Theoretical Computer Science
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A4 Conference proceedings
Three Models for Gene Assembly in Ciliates: A Comparison (2009)
Miika Langille, Ion Petre, Vladimir Rogojin
The Institute for Computer Sciences, Social Informatics and Telecommunications Engineering (ICST)
A1 Journal article (refereed)
Decision Problems for Shuffled Genes (2008)
Petre I, Rogojin V
Information and Computation
A1 Journal article (refereed)
Patterns of Simple Gene Assembly (2008)
Harju T, Petre I, Rogojin V, Rozenberg G
Discrete Applied Mathematics
A1 Journal article (refereed)
Solutions to Computational Problems Through Gene Assembly (2008)
Alhazov A, Petre I, Rogojin V
Natural Computing
A4 Conference proceedings
Solutions to Computational Problems Through Gene Assembly (2008)
Alhazov A, Petre I, Rogojin V
Springer
A1 Journal article (refereed)
Computational Power of Intramolecular Gene Assembly (2007)
Tseren-Onolt Ishdorj, Ion Petre, Vladimir Rogojin
International Journal of Foundations of Computer Science
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A1 Journal article (refereed)
Quantitative analysis of the self-assembly strategies of intermediate filaments from tetrameric vimentin (2000)
Czeizler E, Mizera A, Czeizler E, Back RJ, Eriksson JE, Petre I
IEEE/ACM Transactions on Computational Biology and Bioinformatics
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A1 Journal article (refereed)
Mobile Ambients and P-Systems (1999)
Petre I, Petre L
Journal of Universal Computer Science


Other publications

E3 Edited popular book
A Magician in Science: Liber Amicorum Grzegorz Rozenberg (2017)
Sepinoud Azimi, Hendrik Jan Hoogeboom, Jetty Kleijn, Marloes van der Nat, Ion Petre, Arto Salomaa
Turku Centre for Computer Science
D4 Published development or research report or study
Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems (2016)
Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, Ion Petre
D4 Published development or research report or study
NetControl4BioMed: A pipeline for biomedical data acquisition and analysis of network controllability (2016)
Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre
D4 Published development or research report or study
NetControl4BioMed – Automated discovery of combined drug therapy (2016)
Vladimir Rogojin, Keivan Kazemi, Krishna Kanhaiya, Eugen Czeizler, Ion Petre
D4 Published development or research report or study
Reaction Systems: A Model of Computation Inspired by the Functioning of the Living Cell (2016)
Andrzej Ehrenfeucht, Ion Petre, Grzegorz Rozenberg
D4 Published development or research report or study
Target Controllability of Linear Networks (2016)
Eugen Czeizler, Cristian Gratie, Kai Chiu Wu, Krishna Kanhaiya, Ion Petre
D4 Published development or research report or study
An Excursion Through Quantitative Model Refinement (2015)
Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri
D4 Published development or research report or study
Complete Characterization for the Fit-Preserving Data Refinement of Mass-Action Reaction Networks (2015)
Cristian Gratie, Ion Petre
D4 Published development or research report or study
Full Structural Model Refinement as Type Refinement of Colored Petri Nets (2015)
Diana-Elena Gratie, Ion Petre
D4 Published development or research report or study
Generating the Logicome of a Biological Network (2015)
Charmi Panchal, Sepinoud Azimi, Ion Petre
B1 Non-refereed journal articles
Preface : From Computer Science to Biology and Back (2015)
Emanuela Merelli, Ion Petre
Theoretical Computer Science
View on publisher's site
D4 Published development or research report or study
Reaction Systems Models for the Self-Assembly of Intermediate Filaments (2015)
Sepinoud Azimi, Charmi Panchal, Eugen Czeizler, Ion Petre
D4 Published development or research report or study
Complexity of Model Checking for Reaction Systems (2014)
Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca
D4 Published development or research report or study
Dependency Graphs and Mass Conservation in Reaction Systems (2014)
Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre
D4 Published development or research report or study
Fit-Preserving Data Refinement of Mass-Action Reaction Networks (2014)
Cristian Gratie, Ion Petre
D4 Published development or research report or study
Turku Centre for Computer Science, Annual Report 2013 (2014)
Irmeli Laine, Johan Lilius, Tomi Mäntylä, Ion Petre, Outi Tuohi, Ilona Tuominen
D4 Published development or research report or study
Turku Centre for Computer Science, Annual Report 2012 (2013)
Irmeli Laine, Johan Lilius, Tomi Mäntylä, Ion Petre, Outi Tuohi, Ilona Tuominen
D4 Published development or research report or study
Mobile Ambients and P-Systems (1999)
Petre I, Petre L

Last updated on 2019-01-01 at 08:10