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ORCIDBibTeX records: Ion Petre
@article{DBLP:journals/fuin/GustafssonP24,
author = {Patric Gustafsson and
Ion Petre},
title = {Strong Regulatory Graphs},
journal = {Fundam. Informaticae},
volume = {191},
number = {3-4},
pages = {299--314},
year = {2024},
url = {https://doi.org/10.3233/FI-242184},
doi = {10.3233/FI-242184},
timestamp = {Fri, 02 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fuin/GustafssonP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/GenovaP24,
author = {Daniela Genova and
Ion Petre},
title = {Preface},
journal = {Nat. Comput.},
volume = {23},
number = {2},
pages = {157--158},
year = {2024},
url = {https://doi.org/10.1007/s11047-024-09991-4},
doi = {10.1007/S11047-024-09991-4},
timestamp = {Tue, 13 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nc/GenovaP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/PetreP24,
author = {Ion Petre and
Andrei Paun},
title = {Special issue on Foundational Methods in Systems Biology},
journal = {Theor. Comput. Sci.},
volume = {1005},
pages = {114641},
year = {2024},
url = {https://doi.org/10.1016/j.tcs.2024.114641},
doi = {10.1016/J.TCS.2024.114641},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/PetreP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-08261,
author = {Patric Gustafsson and
Ion Petre},
title = {Strong regulatory graphs},
journal = {CoRR},
volume = {abs/2306.08261},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.08261},
doi = {10.48550/ARXIV.2306.08261},
eprinttype = {arXiv},
eprint = {2306.08261},
timestamp = {Sun, 18 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-08261.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/SimineaPMFGGIKP22,
author = {Nicoleta Siminea and
Victor{-}Bogdan Popescu and
Jos{\'{e}} {\'{A}}ngel S{\'{a}}nchez Mart{\'{\i}}n and
Daniela Florea and
Georgiana Gavril and
Ana Maria Gheorghe and
Corina Itcus and
Krishna Kanhaiya and
Octavian Pacioglu and
Laura Ioana Popa and
Romica Trandafir and
Maria Iris Tusa and
Manuela Sidoroff and
Mihaela Paun and
Eugen Czeizler and
Andrei Paun and
Ion Petre},
title = {Network analytics for drug repurposing in {COVID-19}},
journal = {Briefings Bioinform.},
volume = {23},
number = {1},
year = {2022},
url = {https://doi.org/10.1093/bib/bbab490},
doi = {10.1093/BIB/BBAB490},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/SimineaPMFGGIKP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/cmsb/2022,
editor = {Ion Petre and
Andrei Paun},
title = {Computational Methods in Systems Biology - 20th International Conference,
{CMSB} 2022, Bucharest, Romania, September 14-16, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13447},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-15034-0},
doi = {10.1007/978-3-031-15034-0},
isbn = {978-3-031-15033-3},
timestamp = {Mon, 22 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cmsb/2022.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PopescuMSSMANIM21,
author = {Victor{-}Bogdan Popescu and
Jos{\'{e}} {\'{A}}ngel S{\'{a}}nchez Mart{\'{\i}}n and
Daniela Schacherer and
Sadra Safadoust and
Negin Majidi and
Andrei Andronescu and
Alexandru Nedea and
Diana Ion and
Eduard Mititelu and
Eugen Czeizler and
Ion Petre},
title = {NetControl4BioMed: a web-based platform for controllability analysis
of protein-protein interaction networks},
journal = {Bioinform.},
volume = {37},
number = {21},
pages = {3976--3978},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab570},
doi = {10.1093/BIOINFORMATICS/BTAB570},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PopescuMSSMANIM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/KariPRS21,
author = {Lila Kari and
Ion Petre and
Grzegorz Rozenberg and
Arto Salomaa},
title = {A fascinating rainbow of computation - Honoring Gheorghe P{\u{a}}un
on the occasion of his 70th birthday},
journal = {Theor. Comput. Sci.},
volume = {862},
pages = {1--2},
year = {2021},
url = {https://doi.org/10.1016/j.tcs.2021.02.041},
doi = {10.1016/J.TCS.2021.02.041},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/KariPRS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/MikulskiP21,
author = {Lukasz Mikulski and
Ion Petre},
title = {Preface: Special Issue on Reaction Systems},
journal = {Theor. Comput. Sci.},
volume = {881},
pages = {1--2},
year = {2021},
url = {https://doi.org/10.1016/j.tcs.2021.07.027},
doi = {10.1016/J.TCS.2021.07.027},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/MikulskiP21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/BonizzoniKPR21,
author = {Paola Bonizzoni and
Lila Kari and
Ion Petre and
Grzegorz Rozenberg},
title = {Building bridges - Honoring Nata{\v{s}}a Jonoska on the occasion of
her 60th birthday},
journal = {Theor. Comput. Sci.},
volume = {894},
pages = {1--2},
year = {2021},
url = {https://doi.org/10.1016/j.tcs.2021.10.021},
doi = {10.1016/J.TCS.2021.10.021},
timestamp = {Sat, 21 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/BonizzoniKPR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2104-09206,
author = {Elio Nushi and
Victor{-}Bogdan Popescu and
Jos{\'{e}} {\'{A}}ngel S{\'{a}}nchez Mart{\'{\i}}n and
Sergiu Ivanov and
Eugen Czeizler and
Ion Petre},
title = {Network modeling methods for precision medicine},
journal = {CoRR},
volume = {abs/2104.09206},
year = {2021},
url = {https://arxiv.org/abs/2104.09206},
eprinttype = {arXiv},
eprint = {2104.09206},
timestamp = {Tue, 27 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2104-09206.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2105-10344,
author = {Usman Sanwal and
Thai Son Hoang and
Luigia Petre and
Ion Petre},
title = {Towards Scalable Modeling of Biology in Event-B},
journal = {CoRR},
volume = {abs/2105.10344},
year = {2021},
url = {https://arxiv.org/abs/2105.10344},
eprinttype = {arXiv},
eprint = {2105.10344},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2105-10344.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/PetreSSPTP20,
author = {Luigia Petre and
Usman Sanwal and
Gohar Shah and
Charmi Panchal and
Dwitiya Tyagi and
Ion Petre},
title = {A Computational Model for The Access to Medical Service in a Basic
Prototype of a Healthcare System},
journal = {Fundam. Informaticae},
volume = {171},
number = {1-4},
pages = {331--343},
year = {2020},
url = {https://doi.org/10.3233/FI-2020-1886},
doi = {10.3233/FI-2020-1886},
timestamp = {Fri, 18 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fuin/PetreSSPTP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/MartinP20,
author = {Jos{\'{e}} {\'{A}}ngel S{\'{a}}nchez Mart{\'{\i}}n and
Ion Petre},
title = {Network Controllability Analysis of Three Multiple-myeloma Patient
Genetic Mutation Datasets},
journal = {Fundam. Informaticae},
volume = {175},
number = {1-4},
pages = {281--299},
year = {2020},
url = {https://doi.org/10.3233/FI-2020-1957},
doi = {10.3233/FI-2020-1957},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fuin/MartinP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jmemcom/MikulskiP20,
author = {Lukasz Mikulski and
Ion Petre},
title = {Preface},
journal = {J. Membr. Comput.},
volume = {2},
number = {3},
pages = {147--148},
year = {2020},
url = {https://doi.org/10.1007/s41965-020-00047-x},
doi = {10.1007/S41965-020-00047-X},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jmemcom/MikulskiP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jmemcom/IvanovP20,
author = {Sergiu Ivanov and
Ion Petre},
title = {Controllability of reaction systems},
journal = {J. Membr. Comput.},
volume = {2},
number = {4},
pages = {290--302},
year = {2020},
url = {https://doi.org/10.1007/s41965-020-00055-x},
doi = {10.1007/S41965-020-00055-X},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jmemcom/IvanovP20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2007-04853,
author = {Victor{-}Bogdan Popescu and
Krishna Kanhaiya and
Iulian Nastac and
Eugen Czeizler and
Ion Petre},
title = {Identifying efficient controls of complex interaction networks using
genetic algorithms},
journal = {CoRR},
volume = {abs/2007.04853},
year = {2020},
url = {https://arxiv.org/abs/2007.04853},
eprinttype = {arXiv},
eprint = {2007.04853},
timestamp = {Wed, 22 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2007-04853.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2007-09461,
author = {Sergiu Ivanov and
Ion Petre},
title = {Controllability of reaction systems},
journal = {CoRR},
volume = {abs/2007.09461},
year = {2020},
url = {https://arxiv.org/abs/2007.09461},
eprinttype = {arXiv},
eprint = {2007.09461},
timestamp = {Tue, 28 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2007-09461.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/IancuSGP19,
author = {Bogdan Iancu and
Usman Sanwal and
Cristian Gratie and
Ion Petre},
title = {Refinement-based modeling of the ErbB signaling pathway},
journal = {Comput. Biol. Medicine},
volume = {106},
pages = {91--96},
year = {2019},
url = {https://doi.org/10.1016/j.compbiomed.2019.01.016},
doi = {10.1016/J.COMPBIOMED.2019.01.016},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/IancuSGP19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KanhaiyaRKCP18,
author = {Krishna Kanhaiya and
Vladimir Rogojin and
Keivan Kazemi and
Eugen Czeizler and
Ion Petre},
title = {NetControl4BioMed: a pipeline for biomedical data acquisition and
analysis of network controllability},
journal = {{BMC} Bioinform.},
volume = {19-S},
number = {7},
pages = {3--12},
year = {2018},
url = {https://doi.org/10.1186/s12859-018-2177-3},
doi = {10.1186/S12859-018-2177-3},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KanhaiyaRKCP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/CzeizlerCGKP18,
author = {Eugen Czeizler and
Wu Kai Chiu and
Cristian Gratie and
Krishna Kanhaiya and
Ion Petre},
title = {Structural Target Controllability of Linear Networks},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {15},
number = {4},
pages = {1217--1228},
year = {2018},
url = {https://doi.org/10.1109/TCBB.2018.2797271},
doi = {10.1109/TCBB.2018.2797271},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/CzeizlerCGKP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/0001RAP18,
author = {Sergiu Ivanov and
Vladimir Rogojin and
Sepinoud Azimi and
Ion Petre},
editor = {Carmen Graciani D{\'{\i}}az and
Agust{\'{\i}}n Riscos{-}N{\'{u}}{\~{n}}ez and
Gheorghe Paun and
Grzegorz Rozenberg and
Arto Salomaa},
title = {{WEBRSIM:} {A} Web-Based Reaction Systems Simulator},
booktitle = {Enjoying Natural Computing - Essays Dedicated to Mario de Jes{\'{u}}s
P{\'{e}}rez-Jim{\'{e}}nez on the Occasion of His 70th Birthday},
series = {Lecture Notes in Computer Science},
volume = {11270},
pages = {170--181},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-030-00265-7\_14},
doi = {10.1007/978-3-030-00265-7\_14},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/birthday/0001RAP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cbm/SanwalPP17,
author = {Usman Sanwal and
Luigia Petre and
Ion Petre},
title = {Stepwise construction of a metabolic network in Event-B: The heat
shock response},
journal = {Comput. Biol. Medicine},
volume = {91},
pages = {1--12},
year = {2017},
url = {https://doi.org/10.1016/j.compbiomed.2017.09.021},
doi = {10.1016/J.COMPBIOMED.2017.09.021},
timestamp = {Wed, 02 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cbm/SanwalPP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/BarashP17,
author = {Mikhail Barash and
Ion Petre},
title = {A Foundational Framework for Step-by-step Model Construction},
journal = {Fundam. Informaticae},
volume = {154},
number = {1-4},
pages = {15--24},
year = {2017},
url = {https://doi.org/10.3233/FI-2017-1549},
doi = {10.3233/FI-2017-1549},
timestamp = {Fri, 18 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fuin/BarashP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/AzimiPMP17,
author = {Sepinoud Azimi and
Charmi Panchal and
Andrzej Mizera and
Ion Petre},
title = {Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with
Reaction Systems},
journal = {Int. J. Found. Comput. Sci.},
volume = {28},
number = {8},
pages = {1007--1020},
year = {2017},
url = {https://doi.org/10.1142/S0129054117500368},
doi = {10.1142/S0129054117500368},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijfcs/AzimiPMP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/PaunPRS17,
author = {Gheorghe Paun and
Ion Petre and
Grzegorz Rozenberg and
Arto Salomaa},
title = {From finite state grammars to natural computing - In memory of Solomon
Marcus},
journal = {Theor. Comput. Sci.},
volume = {701},
pages = {2--7},
year = {2017},
url = {https://doi.org/10.1016/j.tcs.2017.10.022},
doi = {10.1016/J.TCS.2017.10.022},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcs/PaunPRS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/EhrenfeuchtPR17,
author = {Andrzej Ehrenfeucht and
Ion Petre and
Grzegorz Rozenberg},
editor = {Stavros Konstantinidis and
Nelma Moreira and
Rog{\'{e}}rio Reis and
Jeffrey O. Shallit},
title = {Reaction Systems: {A} Model of Computation Inspired by the Functioning
of the Living Cell},
booktitle = {The Role of Theory in Computer Science - Essays Dedicated to Janusz
Brzozowski},
pages = {1--32},
publisher = {World Scientific},
year = {2017},
url = {https://doi.org/10.1142/9789813148208\_0001},
doi = {10.1142/9789813148208\_0001},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/birthday/EhrenfeuchtPR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/cie/2017,
editor = {Jarkko Kari and
Florin Manea and
Ion Petre},
title = {Unveiling Dynamics and Complexity - 13th Conference on Computability
in Europe, CiE 2017, Turku, Finland, June 12-16, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10307},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-58741-7},
doi = {10.1007/978-3-319-58741-7},
isbn = {978-3-319-58740-0},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cie/2017.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/csjm/RogojinP16,
author = {Vladimir Rogojin and
Ion Petre},
title = {Large-scale executable biology using rapid integration of computational
models},
journal = {Comput. Sci. J. Moldova},
volume = {24},
number = {1},
pages = {118--135},
year = {2016},
url = {http://www.math.md/publications/csjm/issues/v24-n1/12103/},
timestamp = {Wed, 02 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/csjm/RogojinP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AzimiG0MPP16,
author = {Sepinoud Azimi and
Cristian Gratie and
Sergiu Ivanov and
Luca Manzoni and
Ion Petre and
Antonio E. Porreca},
title = {Complexity of model checking for reaction systems},
journal = {Theor. Comput. Sci.},
volume = {623},
pages = {103--113},
year = {2016},
url = {https://doi.org/10.1016/j.tcs.2015.11.040},
doi = {10.1016/J.TCS.2015.11.040},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AzimiG0MPP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/GratieP16,
author = {Cristian Gratie and
Ion Petre},
title = {Complete characterization for the fit-preserving data refinement of
mass-action reaction networks},
journal = {Theor. Comput. Sci.},
volume = {641},
pages = {11--24},
year = {2016},
url = {https://doi.org/10.1016/j.tcs.2016.03.027},
doi = {10.1016/J.TCS.2016.03.027},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/GratieP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/PanchalAP16,
author = {Charmi Panchal and
Sepinoud Azimi and
Ion Petre},
editor = {Mar{\'{\i}}a Bot{\'{o}}n{-}Fern{\'{a}}ndez and
Carlos Mart{\'{\i}}n{-}Vide and
Sergio Santander{-}Jim{\'{e}}nez and
Miguel A. Vega{-}Rodr{\'{\i}}guez},
title = {Generating the Logicome of a Biological Network},
booktitle = {Algorithms for Computational Biology - Third International Conference,
AlCoB 2016, Trujillo, Spain, June 21-22, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9702},
pages = {38--49},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-38827-4\_4},
doi = {10.1007/978-3-319-38827-4\_4},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/alcob/PanchalAP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/CzeizlerGCKP16,
author = {Eugen Czeizler and
Cristian Gratie and
Wu Kai Chiu and
Krishna Kanhaiya and
Ion Petre},
editor = {Ezio Bartocci and
Pietro Li{\`{o}} and
Nicola Paoletti},
title = {Target Controllability of Linear Networks},
booktitle = {Computational Methods in Systems Biology - 14th International Conference,
{CMSB} 2016, Cambridge, UK, September 21-23, 2016, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9859},
pages = {67--81},
publisher = {Springer},
year = {2016},
url = {https://doi.org/10.1007/978-3-319-45177-0\_5},
doi = {10.1007/978-3-319-45177-0\_5},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cmsb/CzeizlerGCKP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/crc/p/GratieIAP16,
author = {Diana{-}Elena Gratie and
Bogdan Iancu and
Sepinoud Azimi and
Ion Petre},
editor = {Luigia Petre and
Emil Sekerinski},
title = {Quantitative Model Refinement in Four Different Frameworks, with Applications
to the Heat Shock Response},
booktitle = {From Action Systems to Distributed Systems - The Refinement Approach},
pages = {201--214},
publisher = {Chapman and Hall/CRC},
year = {2016},
url = {https://doi.org/10.1201/b20053-20},
doi = {10.1201/B20053-20},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/books/crc/p/GratieIAP16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/RogojinP15,
author = {Vladimir Rogojin and
Ion Petre},
title = {The Structure of Elementary Strategies for Gene Assembly in Ciliates},
journal = {Fundam. Informaticae},
volume = {138},
number = {1-2},
pages = {145--158},
year = {2015},
url = {https://doi.org/10.3233/FI-2015-1204},
doi = {10.3233/FI-2015-1204},
timestamp = {Fri, 18 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fuin/RogojinP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AzimiGIP15,
author = {Sepinoud Azimi and
Cristian Gratie and
Sergiu Ivanov and
Ion Petre},
title = {Dependency graphs and mass conservation in reaction systems},
journal = {Theor. Comput. Sci.},
volume = {598},
pages = {23--39},
year = {2015},
url = {https://doi.org/10.1016/j.tcs.2015.02.014},
doi = {10.1016/J.TCS.2015.02.014},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AzimiGIP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/MerelliP15,
author = {Emanuela Merelli and
Ion Petre},
title = {From Computer Science to Biology and Back},
journal = {Theor. Comput. Sci.},
volume = {608},
pages = {2--3},
year = {2015},
url = {https://doi.org/10.1016/j.tcs.2015.11.009},
doi = {10.1016/J.TCS.2015.11.009},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/MerelliP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apn/GratieP15,
author = {Diana{-}Elena Gratie and
Ion Petre},
editor = {Monika Heiner and
Annegret Katrin Wagler},
title = {Full structural model refinement as type refinement of colored Petri
nets},
booktitle = {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), Brussels, Belgium, June 22, 2015},
series = {{CEUR} Workshop Proceedings},
volume = {1373},
pages = {70--84},
publisher = {CEUR-WS.org},
year = {2015},
url = {https://ceur-ws.org/Vol-1373/paper5.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:38 +0100},
biburl = {https://dblp.org/rec/conf/apn/GratieP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/membrane/AzimiCGGIIPRSS15,
author = {Sepinoud Azimi and
Eugen Czeizler and
Cristian Gratie and
Diana{-}Elena Gratie and
Bogdan Iancu and
Nebiat Ibssa and
Ion Petre and
Vladimir Rogojin and
Tolou Shadbahr and
Fatemeh Shokri},
editor = {Grzegorz Rozenberg and
Arto Salomaa and
Jos{\'{e}} M. Sempere and
Claudio Zandron},
title = {An Excursion Through Quantitative Model Refinement},
booktitle = {Membrane Computing - 16th International Conference, {CMC} 2015, Valencia,
Spain, August 17-21, 2015, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {9504},
pages = {25--47},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-28475-0\_3},
doi = {10.1007/978-3-319-28475-0\_3},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/membrane/AzimiCGGIIPRSS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/AzimiIP14,
author = {Sepinoud Azimi and
Bogdan Iancu and
Ion Petre},
title = {Reaction System Models for the Heat Shock Response},
journal = {Fundam. Informaticae},
volume = {131},
number = {3-4},
pages = {299--312},
year = {2014},
url = {https://doi.org/10.3233/FI-2014-1016},
doi = {10.3233/FI-2014-1016},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fuin/AzimiIP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/alcob/IancuGAP14,
author = {Bogdan Iancu and
Diana{-}Elena Gratie and
Sepinoud Azimi and
Ion Petre},
editor = {Adrian{-}Horia Dediu and
Carlos Mart{\'{\i}}n{-}Vide and
Bianca Truthe},
title = {On the Implementation of Quantitative Model Refinement},
booktitle = {Algorithms for Computational Biology - First International Conference,
AlCoB 2014, Tarragona, Spain, July 1-3, 2014, Proceedigns},
series = {Lecture Notes in Computer Science},
volume = {8542},
pages = {95--106},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-07953-0\_8},
doi = {10.1007/978-3-319-07953-0\_8},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/alcob/IancuGAP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/AzimiP14,
author = {Sepinoud Azimi and
Ion Petre},
editor = {Gheorghe Paun and
Grzegorz Rozenberg and
Arto Salomaa},
title = {The Reduction Power of Simple Operations for Gene Assembly in Ciliates},
booktitle = {Discrete Mathematics and Computer Science. In Memoriam Alexandru Mateescu
{(1952-2005)}},
pages = {23--36},
publisher = {The Publishing House of the Romanian Academy},
year = {2014},
timestamp = {Fri, 23 Jan 2015 14:35:08 +0100},
biburl = {https://dblp.org/rec/conf/birthday/AzimiP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cie/GratieP14,
author = {Cristian Gratie and
Ion Petre},
editor = {Arnold Beckmann and
Erzs{\'{e}}bet Csuhaj{-}Varj{\'{u}} and
Klaus Meer},
title = {Fit-Preserving Data Refinement of Mass-Action Reaction Networks},
booktitle = {Language, Life, Limits - 10th Conference on Computability in Europe,
CiE 2014, Budapest, Hungary, June 23-27, 2014. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {8493},
pages = {204--213},
publisher = {Springer},
year = {2014},
url = {https://doi.org/10.1007/978-3-319-08019-2\_21},
doi = {10.1007/978-3-319-08019-2\_21},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cie/GratieP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/entcs/MerelliP14,
author = {Emanuela Merelli and
Ion Petre},
editor = {Emanuela Merelli and
Ion Petre},
title = {Preface},
booktitle = {Proceedings of the 5th International Workshop on Interactions between
Computer Science and Biology, CS2Bio 2014, Berlin, Germany, June 6,
2014},
series = {Electronic Notes in Theoretical Computer Science},
volume = {306},
pages = {1--3},
publisher = {Elsevier},
year = {2014},
url = {https://doi.org/10.1016/j.entcs.2014.06.010},
doi = {10.1016/J.ENTCS.2014.06.010},
timestamp = {Tue, 22 Nov 2022 11:22:39 +0100},
biburl = {https://dblp.org/rec/journals/entcs/MerelliP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/cs2bio/2014,
editor = {Emanuela Merelli and
Ion Petre},
title = {Proceedings of the 5th International Workshop on Interactions between
Computer Science and Biology, CS2Bio 2014, Berlin, Germany, June 6,
2014},
series = {Electronic Notes in Theoretical Computer Science},
volume = {306},
publisher = {Elsevier},
year = {2014},
url = {https://www.sciencedirect.com/journal/electronic-notes-in-theoretical-computer-science/vol/306/suppl/C},
timestamp = {Tue, 22 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cs2bio/2014.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sfm/GratieIP13,
author = {Diana{-}Elena Gratie and
Bogdan Iancu and
Ion Petre},
editor = {Marco Bernardo and
Erik P. de Vink and
Alessandra Di Pierro and
Herbert Wiklicky},
title = {{ODE} Analysis of Biological Systems},
booktitle = {Formal Methods for Dynamical Systems - 13th International School on
Formal Methods for the Design of Computer, Communication, and Software
Systems, {SFM} 2013, Bertinoro, Italy, June 17-22, 2013. Advanced
Lectures},
series = {Lecture Notes in Computer Science},
volume = {7938},
pages = {29--62},
publisher = {Springer},
year = {2013},
url = {https://doi.org/10.1007/978-3-642-38874-3\_2},
doi = {10.1007/978-3-642-38874-3\_2},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/sfm/GratieIP13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:journals/corr/Petre13,
editor = {Ion Petre},
title = {Proceedings Fourth International Workshop on Computational Models
for Cell Processes, CompMod 2013, Turku, Finland, 11th June 2013},
series = {{EPTCS}},
volume = {116},
year = {2013},
url = {https://doi.org/10.4204/EPTCS.116},
doi = {10.4204/EPTCS.116},
timestamp = {Wed, 12 Sep 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/Petre13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/CzeizlerMP12,
author = {Elena Czeizler and
Andrzej Mizera and
Ion Petre},
title = {A Boolean Approach for Disentangling the Roles of Submodules to the
Global Properties of a Biomodel},
journal = {Fundam. Informaticae},
volume = {116},
number = {1-4},
pages = {51--63},
year = {2012},
url = {https://doi.org/10.3233/FI-2012-668},
doi = {10.3233/FI-2012-668},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fuin/CzeizlerMP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijuc/IancuCCP12,
author = {Bogdan Iancu and
Elena Czeizler and
Eugen Czeizler and
Ion Petre},
title = {Quantitative Refinement of Reaction Models},
journal = {Int. J. Unconv. Comput.},
volume = {8},
number = {5-6},
pages = {529--550},
year = {2012},
url = {http://www.oldcitypublishing.com/journals/ijuc-home/ijuc-issue-contents/ijuc-volume-8-number-5-6-2012/ijuc-8-5-6-p-529-550/},
timestamp = {Thu, 16 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijuc/IancuCCP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/KariP12,
author = {Jarkko Kari and
Ion Petre},
title = {Preface},
journal = {Nat. Comput.},
volume = {11},
number = {4},
pages = {551--552},
year = {2012},
url = {https://doi.org/10.1007/s11047-012-9345-6},
doi = {10.1007/S11047-012-9345-6},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nc/KariP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/CzeizlerMCBEP12,
author = {Eugen Czeizler and
Andrzej Mizera and
Elena Czeizler and
Ralph{-}Johan Back and
John E. Eriksson and
Ion Petre},
title = {Quantitative Analysis of the Self-Assembly Strategies of Intermediate
Filaments from Tetrameric Vimentin},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {3},
pages = {885--898},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2011.154},
doi = {10.1109/TCBB.2011.154},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/CzeizlerMCBEP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/CzeizlerRP12,
author = {Eugen Czeizler and
Vladimir Rogojin and
Ion Petre},
title = {The Phosphorylation of the Heat Shock Factor as a Modulator for the
Heat Shock Response},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {9},
number = {5},
pages = {1326--1337},
year = {2012},
url = {https://doi.org/10.1109/TCBB.2012.66},
doi = {10.1109/TCBB.2012.66},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/CzeizlerRP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AusielloHKPS12,
author = {Giorgio Ausiello and
Hendrik Jan Hoogeboom and
Juhani Karhum{\"{a}}ki and
Ion Petre and
Arto Salomaa},
title = {Preface},
journal = {Theor. Comput. Sci.},
volume = {429},
pages = {1--20},
year = {2012},
url = {https://doi.org/10.1016/j.tcs.2011.12.019},
doi = {10.1016/J.TCS.2011.12.019},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AusielloHKPS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AzimiHLP12,
author = {Sepinoud Azimi and
Tero Harju and
Miika Langille and
Ion Petre},
title = {Simple gene assembly as a rewriting of directed overlap-inclusion
graphs},
journal = {Theor. Comput. Sci.},
volume = {454},
pages = {30--37},
year = {2012},
url = {https://doi.org/10.1016/j.tcs.2012.04.018},
doi = {10.1016/J.TCS.2012.04.018},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AzimiHLP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/PetreV12,
author = {Ion Petre and
Sergey Verlan},
title = {Matrix insertion-deletion systems},
journal = {Theor. Comput. Sci.},
volume = {456},
pages = {80--88},
year = {2012},
url = {https://doi.org/10.1016/j.tcs.2012.07.002},
doi = {10.1016/J.TCS.2012.07.002},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/PetreV12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcsb/MizeraCP12,
author = {Andrzej Mizera and
Eugen Czeizler and
Ion Petre},
title = {Self-assembly Models of Variable Resolution},
journal = {Trans. Comp. Sys. Biology},
volume = {14},
pages = {181--203},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-35524-0\_8},
doi = {10.1007/978-3-642-35524-0\_8},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcsb/MizeraCP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:reference/nc/BrijderDHJPR12,
author = {Robert Brijder and
Mark Daley and
Tero Harju and
Natasa Jonoska and
Ion Petre and
Grzegorz Rozenberg},
editor = {Grzegorz Rozenberg and
Thomas B{\"{a}}ck and
Joost N. Kok},
title = {Computational Nature of Gene Assembly in Ciliates},
booktitle = {Handbook of Natural Computing},
pages = {1233--1280},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-540-92910-9\_37},
doi = {10.1007/978-3-540-92910-9\_37},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/reference/nc/BrijderDHJPR12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:journals/tcsb/2012-14,
editor = {Corrado Priami and
Ion Petre and
Erik P. de Vink},
title = {Transactions on Computational Systems Biology {XIV} - Special Issue
on Computational Models for Cell Processes},
series = {Lecture Notes in Computer Science},
volume = {7625},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-35524-0},
doi = {10.1007/978-3-642-35524-0},
isbn = {978-3-642-35523-3},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcsb/2012-14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/AzimiHLPR11,
author = {Sepinoud Azimi and
Tero Harju and
Miika Langille and
Ion Petre and
Vladimir Rogojin},
title = {Directed Overlap-inclusion Graphs as Representations of Ciliate Genes},
journal = {Fundam. Informaticae},
volume = {110},
number = {1-4},
pages = {29--44},
year = {2011},
url = {https://doi.org/10.3233/FI-2011-526},
doi = {10.3233/FI-2011-526},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/fuin/AzimiHLPR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/BottoniLMMPS11,
author = {Paolo Bottoni and
Anna Labella and
Florin Manea and
Victor Mitrana and
Ion Petre and
Jos{\'{e}} M. Sempere},
title = {Complexity-preserving simulations among three variants of accepting
networks of evolutionary processors},
journal = {Nat. Comput.},
volume = {10},
number = {1},
pages = {429--445},
year = {2011},
url = {https://doi.org/10.1007/s11047-010-9238-5},
doi = {10.1007/S11047-010-9238-5},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nc/BottoniLMMPS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/PetreMHMMMSEB11,
author = {Ion Petre and
Andrzej Mizera and
Claire L. Hyder and
Annika Meinander and
Andrey Mikhailov and
Richard I. Morimoto and
Lea Sistonen and
John E. Eriksson and
Ralph{-}Johan Back},
title = {A simple mass-action model for the eukaryotic heat shock response
and its mathematical validation},
journal = {Nat. Comput.},
volume = {10},
number = {1},
pages = {595--612},
year = {2011},
url = {https://doi.org/10.1007/s11047-010-9216-y},
doi = {10.1007/S11047-010-9216-Y},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nc/PetreMHMMMSEB11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/CzeizlerRP11,
author = {Eugen Czeizler and
Vladimir Rogojin and
Ion Petre},
editor = {Fran{\c{c}}ois Fages},
title = {The phosphorylation of the heat shock factor as a modulator for the
heat shock response},
booktitle = {Computational Methods in Systems Biology, 9th International Conference,
{CMSB} 2011, Paris, France, September 21-23, 2011. Proceedings},
pages = {9--23},
publisher = {{ACM}},
year = {2011},
url = {https://doi.org/10.1145/2037509.2037513},
doi = {10.1145/2037509.2037513},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/cmsb/CzeizlerRP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:journals/entcs/CzeizlerCIP12,
author = {Elena Czeizler and
Eugen Czeizler and
Bogdan Iancu and
Ion Petre},
editor = {J{\'{e}}r{\^{o}}me Feret and
Andre Levchenko},
title = {Quantitative Model Refinement as a Solution to the Combinatorial Size
Explosion of Biomodels},
booktitle = {Proceedings of the 2nd International Workshop on Static Analysis and
Systems Biology, {SASB} 2011, Venice, Italy, September 13, 2011},
series = {Electronic Notes in Theoretical Computer Science},
volume = {284},
pages = {35--53},
publisher = {Elsevier},
year = {2011},
url = {https://doi.org/10.1016/j.entcs.2012.05.014},
doi = {10.1016/J.ENTCS.2012.05.014},
timestamp = {Fri, 25 Nov 2022 14:17:48 +0100},
biburl = {https://dblp.org/rec/journals/entcs/CzeizlerCIP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/uc/2011,
editor = {Cristian S. Calude and
Jarkko Kari and
Ion Petre and
Grzegorz Rozenberg},
title = {Unconventional Computation - 10th International Conference, {UC} 2011,
Turku, Finland, June 6-10, 2011. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6714},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-21341-0},
doi = {10.1007/978-3-642-21341-0},
isbn = {978-3-642-21340-3},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/uc/2011.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:journals/corr/abs-1109-1044,
editor = {Ion Petre and
Erik P. de Vink},
title = {Proceedings Third International Workshop on Computational Models for
Cell Processes, CompMod 2011, Aachen, Germany, September 10, 2011},
series = {{EPTCS}},
volume = {67},
year = {2011},
url = {https://doi.org/10.4204/EPTCS.67},
doi = {10.4204/EPTCS.67},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1109-1044.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:journals/tcsb/2011-13,
editor = {Corrado Priami and
Ralph{-}Johan Back and
Ion Petre and
Erik P. de Vink},
title = {Transactions on Computational Systems Biology {XIII}},
series = {Lecture Notes in Computer Science},
volume = {6575},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-19748-2},
doi = {10.1007/978-3-642-19748-2},
isbn = {978-3-642-19747-5},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcsb/2011-13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ercim/MauriP11,
author = {Giancarlo Mauri and
Ion Petre},
title = {New Robustness Paradigms: from Nature to Computing},
journal = {{ERCIM} News},
volume = {2011},
number = {85},
pages = {33},
year = {2011},
url = {http://ercim-news.ercim.eu/en85/special/new-robustness-paradigms-from-nature-to-computing},
timestamp = {Wed, 22 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ercim/MauriP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biosystems/VerlanAP10,
author = {Sergey Verlan and
Artiom Alhazov and
Ion Petre},
title = {A sequence-based analysis of the pointer distribution of stichotrichous
ciliates},
journal = {Biosyst.},
volume = {101},
number = {2},
pages = {109--116},
year = {2010},
url = {https://doi.org/10.1016/j.biosystems.2010.05.003},
doi = {10.1016/J.BIOSYSTEMS.2010.05.003},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biosystems/VerlanAP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/csjm/LangillePR10,
author = {Miika Langille and
Ion Petre and
Vladimir Rogojin},
title = {Three models for gene assembly in ciliates: a comparison},
journal = {Comput. Sci. J. Moldova},
volume = {18},
number = {1},
pages = {15--40},
year = {2010},
url = {http://www.math.md/publications/csjm/issues/v18-n1/10224/},
timestamp = {Wed, 02 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/csjm/LangillePR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/scholarpedia/PetreR10,
author = {Ion Petre and
Grzegorz Rozenberg},
title = {Gene assembly in Ciliates},
journal = {Scholarpedia},
volume = {5},
number = {1},
pages = {9269},
year = {2010},
url = {https://doi.org/10.4249/scholarpedia.9269},
doi = {10.4249/SCHOLARPEDIA.9269},
timestamp = {Thu, 23 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/scholarpedia/PetreR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/BrijderLP10,
author = {Robert Brijder and
Miika Langille and
Ion Petre},
title = {Extended strings and graphs for simple gene assembly},
journal = {Theor. Comput. Sci.},
volume = {411},
number = {4-5},
pages = {730--738},
year = {2010},
url = {https://doi.org/10.1016/j.tcs.2009.10.011},
doi = {10.1016/J.TCS.2009.10.011},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/BrijderLP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AlhazovLP10,
author = {Artiom Alhazov and
Chang Li and
Ion Petre},
title = {Computing the graph-based parallel complexity of gene assembly},
journal = {Theor. Comput. Sci.},
volume = {411},
number = {25},
pages = {2359--2367},
year = {2010},
url = {https://doi.org/10.1016/j.tcs.2010.02.007},
doi = {10.1016/J.TCS.2010.02.007},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AlhazovLP10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/MitranaPR10,
author = {Victor Mitrana and
Ion Petre and
Vladimir Rogojin},
title = {Accepting splicing systems},
journal = {Theor. Comput. Sci.},
volume = {411},
number = {25},
pages = {2414--2422},
year = {2010},
url = {https://doi.org/10.1016/j.tcs.2010.03.025},
doi = {10.1016/J.TCS.2010.03.025},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/MitranaPR10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1012-5248,
author = {Ion Petre and
Sergey Verlan},
title = {Matrix Insertion-Deletion Systems},
journal = {CoRR},
volume = {abs/1012.5248},
year = {2010},
url = {http://arxiv.org/abs/1012.5248},
eprinttype = {arXiv},
eprint = {1012.5248},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1012-5248.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AlhazovPR09,
author = {Artiom Alhazov and
Ion Petre and
Vladimir Rogojin},
title = {The parallel complexity of signed graphs: Decidability results and
an improved algorithm},
journal = {Theor. Comput. Sci.},
volume = {410},
number = {24-25},
pages = {2308--2315},
year = {2009},
url = {https://doi.org/10.1016/j.tcs.2009.02.028},
doi = {10.1016/J.TCS.2009.02.028},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AlhazovPR09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/PetreMHMESB09,
author = {Ion Petre and
Andrzej Mizera and
Claire L. Hyder and
Andrey Mikhailov and
John E. Eriksson and
Lea Sistonen and
Ralph{-}Johan Back},
editor = {Anne Condon and
David Harel and
Joost N. Kok and
Arto Salomaa and
Erik Winfree},
title = {A New Mathematical Model for the Heat Shock Response},
booktitle = {Algorithmic Bioprocesses},
series = {Natural Computing Series},
pages = {411--425},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-540-88869-7\_21},
doi = {10.1007/978-3-540-88869-7\_21},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/birthday/PetreMHMESB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cie/PetreMB09,
author = {Ion Petre and
Andrzej Mizera and
Ralph{-}Johan Back},
editor = {Klaus Ambos{-}Spies and
Benedikt L{\"{o}}we and
Wolfgang Merkle},
title = {Computational Heuristics for Simplifying a Biological Model},
booktitle = {Mathematical Theory and Computational Practice, 5th Conference on
Computability in Europe, CiE 2009, Heidelberg, Germany, July 19-24,
2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5635},
pages = {399--408},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-03073-4\_41},
doi = {10.1007/978-3-642-03073-4\_41},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cie/PetreMB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cmsb/CzeizlerCBP09,
author = {Elena Czeizler and
Eugen Czeizler and
Ralph{-}Johan Back and
Ion Petre},
editor = {Pierpaolo Degano and
Roberto Gorrieri},
title = {Control Strategies for the Regulation of the Eukaryotic Heat Shock
Response},
booktitle = {Computational Methods in Systems Biology, 7th International Conference,
{CMSB} 2009, Bologna, Italy, August 31-September 1, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5688},
pages = {111--125},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-03845-7\_8},
doi = {10.1007/978-3-642-03845-7\_8},
timestamp = {Tue, 14 May 2019 10:00:49 +0200},
biburl = {https://dblp.org/rec/conf/cmsb/CzeizlerCBP09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:journals/corr/abs-0910-1605,
editor = {Ralph{-}Johan Back and
Ion Petre and
Erik P. de Vink},
title = {Proceedings Second International Workshop on Computational Models
for Cell Processes, {COMPMOD} 2009, Eindhoven, the Netherlands, November
3, 2009},
series = {{EPTCS}},
volume = {6},
year = {2009},
url = {https://doi.org/10.4204/EPTCS.6},
doi = {10.4204/EPTCS.6},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0910-1605.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:journals/tcsb/2009-11,
editor = {Corrado Priami and
Ralph{-}Johan Back and
Ion Petre},
title = {Transactions on Computational Systems Biology {XI}},
series = {Lecture Notes in Computer Science},
volume = {5750},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-04186-0},
doi = {10.1007/978-3-642-04186-0},
isbn = {978-3-642-04185-3},
timestamp = {Tue, 14 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcsb/2009-11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/HarjuPRR08,
author = {Tero Harju and
Ion Petre and
Vladimir Rogojin and
Grzegorz Rozenberg},
title = {Patterns of simple gene assembly in ciliates},
journal = {Discret. Appl. Math.},
volume = {156},
number = {14},
pages = {2581--2597},
year = {2008},
url = {https://doi.org/10.1016/j.dam.2007.09.026},
doi = {10.1016/J.DAM.2007.09.026},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/HarjuPRR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/dam/HarjuLP08,
author = {Tero Harju and
Chang Li and
Ion Petre},
title = {Graph theoretic approach to parallel gene assembly},
journal = {Discret. Appl. Math.},
volume = {156},
number = {18},
pages = {3416--3429},
year = {2008},
url = {https://doi.org/10.1016/j.dam.2008.01.022},
doi = {10.1016/J.DAM.2008.01.022},
timestamp = {Thu, 11 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/dam/HarjuLP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/IshdorjLP08,
author = {Tseren{-}Onolt Ishdorj and
Remco Loos and
Ion Petre},
title = {Computational Efficiency of Intermolecular Gene Assembly},
journal = {Fundam. Informaticae},
volume = {84},
number = {3-4},
pages = {363--373},
year = {2008},
url = {http://content.iospress.com/articles/fundamenta-informaticae/fi84-3-4-05},
timestamp = {Fri, 18 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fuin/IshdorjLP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/iandc/PetreR08,
author = {Ion Petre and
Vladimir Rogojin},
title = {Decision problem for shuffled genes},
journal = {Inf. Comput.},
volume = {206},
number = {11},
pages = {1346--1352},
year = {2008},
url = {https://doi.org/10.1016/j.ic.2008.07.001},
doi = {10.1016/J.IC.2008.07.001},
timestamp = {Fri, 12 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/iandc/PetreR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/IshdorjP08,
author = {Tseren{-}Onolt Ishdorj and
Ion Petre},
title = {Gene Assembly Models and Boolean Circuits},
journal = {Int. J. Found. Comput. Sci.},
volume = {19},
number = {5},
pages = {1133--1145},
year = {2008},
url = {https://doi.org/10.1142/S0129054108006182},
doi = {10.1142/S0129054108006182},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijfcs/IshdorjP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/AlhazovPR08,
author = {Artiom Alhazov and
Ion Petre and
Vladimir Rogojin},
title = {Solutions to computational problems through gene assembly},
journal = {Nat. Comput.},
volume = {7},
number = {3},
pages = {385--401},
year = {2008},
url = {https://doi.org/10.1007/s11047-008-9074-z},
doi = {10.1007/S11047-008-9074-Z},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nc/AlhazovPR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/soco/HarjuLP08,
author = {Tero Harju and
Chang Li and
Ion Petre},
title = {Parallel complexity of signed graphs for gene assembly in ciliates},
journal = {Soft Comput.},
volume = {12},
number = {8},
pages = {731--737},
year = {2008},
url = {https://doi.org/10.1007/s00500-007-0233-4},
doi = {10.1007/S00500-007-0233-4},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/soco/HarjuLP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/AtanasiuAP08,
author = {Adrian Atanasiu and
Radu{-}Florian Atanasiu and
Ion Petre},
title = {Parikh matrices and amiable words},
journal = {Theor. Comput. Sci.},
volume = {390},
number = {1},
pages = {102--109},
year = {2008},
url = {https://doi.org/10.1016/j.tcs.2007.10.022},
doi = {10.1016/J.TCS.2007.10.022},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/AtanasiuAP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/LangilleP08,
author = {Miika Langille and
Ion Petre},
title = {Sequential vs. parallel complexity in simple gene assembly},
journal = {Theor. Comput. Sci.},
volume = {395},
number = {1},
pages = {24--30},
year = {2008},
url = {https://doi.org/10.1016/j.tcs.2007.08.007},
doi = {10.1016/J.TCS.2007.08.007},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/LangilleP08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/afl/Petre08,
author = {Ion Petre},
editor = {Erzs{\'{e}}bet Csuhaj{-}Varj{\'{u}} and
Zolt{\'{a}}n {\'{E}}sik},
title = {Mathematics of gene assembly in ciliates (Abstract)},
booktitle = {Automata and Formal Languages, 12th International Conference, {AFL}
2008, Balatonf{\"{u}}red, Hungary, May 27-30, 2008, Proceedings},
pages = {54--55},
year = {2008},
timestamp = {Fri, 18 Nov 2011 12:16:10 +0100},
biburl = {https://dblp.org/rec/conf/afl/Petre08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionetics/LangillePR08,
author = {Miika Langille and
Ion Petre and
Vladimir Rogojin},
editor = {Masayuki Murata and
{\"{O}}zg{\"{u}}r B. Akan},
title = {Three models for gene assembly in ciliates: a comparison},
booktitle = {3rd International {ICST} Conference on Bio-Inspired Models of Network,
Information, and Computing Systems, {BIONETICS} 2008, Hyogo, Japan,
November 25-28, 2008},
pages = {23},
publisher = {{ICST} / {ACM}},
year = {2008},
url = {https://doi.org/10.4108/ICST.BIONETICS2008.4689},
doi = {10.4108/ICST.BIONETICS2008.4689},
timestamp = {Wed, 04 Jan 2023 13:36:13 +0100},
biburl = {https://dblp.org/rec/conf/bionetics/LangillePR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gg/PetreR08,
author = {Ion Petre and
Grzegorz Rozenberg},
editor = {Hartmut Ehrig and
Reiko Heckel and
Grzegorz Rozenberg and
Gabriele Taentzer},
title = {Summary of the Workshop on Natural Computing and Graph Transformations},
booktitle = {Graph Transformations, 4th International Conference, {ICGT} 2008,
Leicester, United Kingdom, September 7-13, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5214},
pages = {470--472},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87405-8\_35},
doi = {10.1007/978-3-540-87405-8\_35},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gg/PetreR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijfcs/IshdorjPR07,
author = {Tseren{-}Onolt Ishdorj and
Ion Petre and
Vladimir Rogojin},
title = {Computational Power of intramolecular gene Assembly},
journal = {Int. J. Found. Comput. Sci.},
volume = {18},
number = {5},
pages = {1123--1136},
year = {2007},
url = {https://doi.org/10.1142/S0129054107005169},
doi = {10.1142/S0129054107005169},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ijfcs/IshdorjPR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/Csuhaj-VarjuPV07,
author = {Erzs{\'{e}}bet Csuhaj{-}Varj{\'{u}} and
Ion Petre and
Gy{\"{o}}rgy Vaszil},
title = {Self-assembly of strings and languages},
journal = {Theor. Comput. Sci.},
volume = {374},
number = {1-3},
pages = {74--81},
year = {2007},
url = {https://doi.org/10.1016/j.tcs.2006.12.004},
doi = {10.1016/J.TCS.2006.12.004},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/Csuhaj-VarjuPV07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dna/AlhazovPR07,
author = {Artiom Alhazov and
Ion Petre and
Vladimir Rogojin},
editor = {Max H. Garzon and
Hao Yan},
title = {Solutions to Computational Problems Through Gene Assembly},
booktitle = {{DNA} Computing, 13th International Meeting on {DNA} Computing, DNA13,
Memphis, TN, USA, June 4-8, 2007, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4848},
pages = {36--45},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-77962-9\_4},
doi = {10.1007/978-3-540-77962-9\_4},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/dna/AlhazovPR07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fct/BrijderLP07,
author = {Robert Brijder and
Miika Langille and
Ion Petre},
editor = {Erzs{\'{e}}bet Csuhaj{-}Varj{\'{u}} and
Zolt{\'{a}}n {\'{E}}sik},
title = {A String-Based Model for Simple Gene Assembly},
booktitle = {Fundamentals of Computation Theory, 16th International Symposium,
{FCT} 2007, Budapest, Hungary, August 27-30, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4639},
pages = {161--172},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-74240-1\_15},
doi = {10.1007/978-3-540-74240-1\_15},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/fct/BrijderLP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/uc/IshdorjP07,
author = {Tseren{-}Onolt Ishdorj and
Ion Petre},
editor = {Selim G. Akl and
Cristian S. Calude and
Michael J. Dinneen and
Grzegorz Rozenberg and
Todd Wareham},
title = {Computing Through Gene Assembly},
booktitle = {Unconventional Computation, 6th International Conference, {UC} 2007,
Kingston, Canada, August 13-17, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4618},
pages = {91--105},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-73554-0\_10},
doi = {10.1007/978-3-540-73554-0\_10},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/uc/IshdorjP07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fuin/LangilleP06,
author = {Miika Langille and
Ion Petre},
title = {Simple Gene Assembly Is Deterministic},
journal = {Fundam. Informaticae},
volume = {73},
number = {1-2},
pages = {179--190},
year = {2006},
url = {http://content.iospress.com/articles/fundamenta-informaticae/fi73-1-2-16},
timestamp = {Fri, 18 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fuin/LangilleP06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ipl/IlieMP06,
author = {Lucian Ilie and
Solomon Marcus and
Ion Petre},
title = {Periodic and Sturmian languages},
journal = {Inf. Process. Lett.},
volume = {98},
number = {6},
pages = {242--246},
year = {2006},
url = {https://doi.org/10.1016/j.ipl.2005.05.029},
doi = {10.1016/J.IPL.2005.05.029},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ipl/IlieMP06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/it/Petre06,
author = {Ion Petre},
title = {Invariants of Gene-Assembly in Stichotrichous Ciliates (Invarianten
der Gen-Assemblierung in Ciliaten der Unterklasse Stichotrichia)},
journal = {it Inf. Technol.},
volume = {48},
number = {3},
pages = {161--167},
year = {2006},
url = {https://doi.org/10.1524/itit.2006.48.3.161},
doi = {10.1524/ITIT.2006.48.3.161},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/it/Petre06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nc/HarjuLPR06,
author = {Tero Harju and
Chang Li and
Ion Petre and
Grzegorz Rozenberg},
title = {Parallelism in Gene Assembly},
journal = {Nat. Comput.},
volume = {5},
number = {2},
pages = {203--223},
year = {2006},
url = {https://doi.org/10.1007/s11047-005-4462-0},
doi = {10.1007/S11047-005-4462-0},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nc/HarjuLPR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/kdecb/HarjuLPR06,
author = {Tero Harju and
Chang Li and
Ion Petre and
Grzegorz Rozenberg},
editor = {Karl Tuyls and
Ronald L. Westra and
Yvan Saeys and
Ann Now{\'{e}}},
title = {Complexity Measures for Gene Assembly},
booktitle = {Knowledge Discovery and Emergent Complexity in Bioinformatics, First
International Workshop, {KDECB} 2006, Ghent, Belgium, May 10, 2006.
Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4366},
pages = {42--60},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/978-3-540-71037-0\_4},
doi = {10.1007/978-3-540-71037-0\_4},
timestamp = {Mon, 15 Jun 2020 17:00:20 +0200},
biburl = {https://dblp.org/rec/conf/kdecb/HarjuLPR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ncs/HarjuPR06,
author = {Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
editor = {Junghuei Chen and
Natasa Jonoska and
Grzegorz Rozenberg},
title = {Modelling Simple Operations for Gene Assembly},
booktitle = {Nanotechnology: Science and Computation},
series = {Natural Computing Series},
pages = {361--373},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/3-540-30296-4\_23},
doi = {10.1007/3-540-30296-4\_23},
timestamp = {Thu, 25 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ncs/HarjuPR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mst/KarhumakiLP05,
author = {Juhani Karhum{\"{a}}ki and
Michel Latteux and
Ion Petre},
title = {Commutation with Ternary Sets of Words},
journal = {Theory Comput. Syst.},
volume = {38},
number = {2},
pages = {161--169},
year = {2005},
url = {https://doi.org/10.1007/s00224-004-1191-1},
doi = {10.1007/S00224-004-1191-1},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mst/KarhumakiLP05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/KarhumakiLP05,
author = {Juhani Karhum{\"{a}}ki and
Michel Latteux and
Ion Petre},
title = {Commutation with codes},
journal = {Theor. Comput. Sci.},
volume = {340},
number = {1},
pages = {322--333},
year = {2005},
url = {https://doi.org/10.1016/j.tcs.2005.03.037},
doi = {10.1016/J.TCS.2005.03.037},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/KarhumakiLP05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dna/HarjuPRR05,
author = {Tero Harju and
Ion Petre and
Vladimir Rogojin and
Grzegorz Rozenberg},
editor = {Alessandra Carbone and
Niles A. Pierce},
title = {Simple Operations for Gene Assembly},
booktitle = {{DNA} Computing, 11th International Workshop on {DNA} Computing, DNA11,
London, ON, Canada, June 6-9, 2005. Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {3892},
pages = {96--111},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11753681\_8},
doi = {10.1007/11753681\_8},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/dna/HarjuPRR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/eatcs/HarjuPR04,
author = {Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
title = {Gene Assembly in Celiates. Part I. Molecular Operations (Column: Natural
Computing)},
journal = {Bull. {EATCS}},
volume = {82},
pages = {227--241},
year = {2004},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/eatcs/HarjuPR04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/HarjuPR04a,
author = {Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
editor = {Juhani Karhum{\"{a}}ki and
Hermann A. Maurer and
Gheorghe Paun and
Grzegorz Rozenberg},
title = {Two Models for Gene Assembly in Ciliates},
booktitle = {Theory Is Forever, Essays Dedicated to Arto Salomaa on the Occasion
of His 70th Birthday},
series = {Lecture Notes in Computer Science},
volume = {3113},
pages = {89--101},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-27812-2\_9},
doi = {10.1007/978-3-540-27812-2\_9},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/birthday/HarjuPR04a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/HarjuPR04,
author = {Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
editor = {Natasa Jonoska and
Gheorghe Paun and
Grzegorz Rozenberg},
title = {Formal Properties of Gene Assembly: Equivalence Problem for Overlap
Graphs},
booktitle = {Aspects of Molecular Computing, Essays Dedicated to Tom Head on the
Occasion of His 70th Birthday},
series = {Lecture Notes in Computer Science},
volume = {2950},
pages = {202--212},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-24635-0\_14},
doi = {10.1007/978-3-540-24635-0\_14},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/birthday/HarjuPR04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dna/HarjuLPR04,
author = {Tero Harju and
Chang Li and
Ion Petre and
Grzegorz Rozenberg},
editor = {Claudio Ferretti and
Giancarlo Mauri and
Claudio Zandron},
title = {Parallelism in Gene Assembly},
booktitle = {{DNA} Computing, 10th International Workshop on {DNA} Computing, {DNA}
10, Milan, Italy, June 7-10, 2004, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {3384},
pages = {138--148},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/11493785\_12},
doi = {10.1007/11493785\_12},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/dna/HarjuLPR04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gg/HarjuPR04,
author = {Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
editor = {Hartmut Ehrig and
Gregor Engels and
Francesco Parisi{-}Presicce and
Grzegorz Rozenberg},
title = {Tutorial on {DNA} Computing and Graph Transformation},
booktitle = {Graph Transformations, Second International Conference, {ICGT} 2004,
Rome, Italy, September 28 - October 2, 2004, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3256},
pages = {434--436},
publisher = {Springer},
year = {2004},
url = {https://doi.org/10.1007/978-3-540-30203-2\_31},
doi = {10.1007/978-3-540-30203-2\_31},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gg/HarjuPR04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/eatcs/HarjuPR03,
author = {Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
title = {Gene Assembly in Ciliates Part I. Molecular Operations},
journal = {Bull. {EATCS}},
volume = {81},
pages = {236--249},
year = {2003},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/eatcs/HarjuPR03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/EhrenfeuchtHPPR03,
author = {Andrzej Ehrenfeucht and
Tero Harju and
Ion Petre and
David M. Prescott and
Grzegorz Rozenberg},
title = {Formal systems for gene assembly in ciliates},
journal = {Theor. Comput. Sci.},
volume = {292},
number = {1},
pages = {199--219},
year = {2003},
url = {https://doi.org/10.1016/S0304-3975(01)00223-7},
doi = {10.1016/S0304-3975(01)00223-7},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/EhrenfeuchtHPPR03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/Petre03,
author = {Ion Petre},
editor = {Carlos Mart{\'{\i}}n{-}Vide and
Victor Mitrana},
title = {On the Difference Problem for Semilinear Power Series},
booktitle = {Grammars and Automata for String Processing: From Mathematics and
Computer Science to Biology, and Back: Essays in Honour of Gheorghe
Paun},
series = {Topics in Computer Mathematics},
volume = {9},
pages = {317--326},
publisher = {Taylor and Francis},
year = {2003},
timestamp = {Tue, 02 Mar 2004 16:20:26 +0100},
biburl = {https://dblp.org/rec/conf/birthday/Petre03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/stacs/KarhumakiLP03,
author = {Juhani Karhum{\"{a}}ki and
Michel Latteux and
Ion Petre},
editor = {Helmut Alt and
Michel Habib},
title = {The Commutation with Codes and Ternary Sets of Words},
booktitle = {{STACS} 2003, 20th Annual Symposium on Theoretical Aspects of Computer
Science, Berlin, Germany, February 27 - March 1, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2607},
pages = {74--84},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/3-540-36494-3\_8},
doi = {10.1007/3-540-36494-3\_8},
timestamp = {Thu, 14 Oct 2021 10:38:16 +0200},
biburl = {https://dblp.org/rec/conf/stacs/KarhumakiLP03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mscs/EhrenfeuchtPPR02,
author = {Andrzej Ehrenfeucht and
Ion Petre and
David M. Prescott and
Grzegorz Rozenberg},
title = {String and Graph Reduction Systems for Gene Assembly in Ciliates},
journal = {Math. Struct. Comput. Sci.},
volume = {12},
number = {2},
pages = {113--134},
year = {2002},
url = {https://doi.org/10.1017/S0960129501003516},
doi = {10.1017/S0960129501003516},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mscs/EhrenfeuchtPPR02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mst/EhrenfeuchtHPR02,
author = {Andrzej Ehrenfeucht and
Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
title = {Characterizing the Micronuclear Gene Patterns in Ciliates},
journal = {Theory Comput. Syst.},
volume = {35},
number = {5},
pages = {501--519},
year = {2002},
url = {https://doi.org/10.1007/s00224-002-1043-9},
doi = {10.1007/S00224-002-1043-9},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mst/EhrenfeuchtHPR02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/KarhumakiP02,
author = {Juhani Karhum{\"{a}}ki and
Ion Petre},
title = {Conway's problem for three-word sets},
journal = {Theor. Comput. Sci.},
volume = {289},
number = {1},
pages = {705--725},
year = {2002},
url = {https://doi.org/10.1016/S0304-3975(01)00389-9},
doi = {10.1016/S0304-3975(01)00389-9},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/KarhumakiP02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/KarhumakiP02,
author = {Juhani Karhum{\"{a}}ki and
Ion Petre},
editor = {Wilfried Brauer and
Hartmut Ehrig and
Juhani Karhum{\"{a}}ki and
Arto Salomaa},
title = {The Branching Point Approach to Conway's Problem},
booktitle = {Formal and Natural Computing - Essays Dedicated to Grzegorz Rozenberg
[on occasion of his 60th birthday, March 14, 2002]},
series = {Lecture Notes in Computer Science},
volume = {2300},
pages = {69--76},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45711-9\_5},
doi = {10.1007/3-540-45711-9\_5},
timestamp = {Tue, 14 May 2019 10:00:52 +0200},
biburl = {https://dblp.org/rec/conf/birthday/KarhumakiP02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gg/HarjuPR02,
author = {Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
editor = {Andrea Corradini and
Hartmut Ehrig and
Hans{-}J{\"{o}}rg Kreowski and
Grzegorz Rozenberg},
title = {Tutorial on {DNA} Computing and Graph Transformation - Computational
Nature of Gene Assembly in Ciliates},
booktitle = {Graph Transformation, First International Conference, {ICGT} 2002,
Barcelona, Spain, October 7-12, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2505},
pages = {430--434},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45832-8\_31},
doi = {10.1007/3-540-45832-8\_31},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/gg/HarjuPR02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/eatcs/KarhumakiP01,
author = {Juhani Karhum{\"{a}}ki and
Ion Petre},
title = {Conway's Problem and the Communication of Languages},
journal = {Bull. {EATCS}},
volume = {74},
pages = {171--189},
year = {2001},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/eatcs/KarhumakiP01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/EhrenfeuchtPPR01,
author = {Andrzej Ehrenfeucht and
Ion Petre and
David M. Prescott and
Grzegorz Rozenberg},
editor = {Masami Ito and
Gheorghe Paun and
Sheng Yu},
title = {Circularity and Other Invariants of Gene Assembly in Ciliates},
booktitle = {Words, Semigroups, and Transductions - Festschrift in Honor of Gabriel
Thierrin},
pages = {81--97},
publisher = {World Scientific},
year = {2001},
timestamp = {Thu, 19 Mar 2020 15:28:05 +0100},
biburl = {https://dblp.org/rec/conf/birthday/EhrenfeuchtPPR01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/birthday/EhrenfeuchtPPR01a,
author = {Andrzej Ehrenfeucht and
Ion Petre and
David M. Prescott and
Grzegorz Rozenberg},
editor = {Carlos Mart{\'{\i}}n{-}Vide and
Victor Mitrana},
title = {Universal and simple operations for gene assembly in ciliates},
booktitle = {Where Mathematics, Computer Science, Linguistics and Biology Meet:
Essays in Honour of Gheorghe Paun},
pages = {329--342},
publisher = {Kluwer Academic Publishers},
year = {2001},
timestamp = {Fri, 09 Dec 2011 11:05:54 +0100},
biburl = {https://dblp.org/rec/conf/birthday/EhrenfeuchtPPR01a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dna/EhrenfeuchtHPR01,
author = {Andrzej Ehrenfeucht and
Tero Harju and
Ion Petre and
Grzegorz Rozenberg},
editor = {Natasa Jonoska and
Nadrian C. Seeman},
title = {Patterns of Micronuclear Genes in ciliates},
booktitle = {{DNA} Computing, 7th International Workshop on DNA-Based Computers,
DNA7, Tampa, Florida, USA, June 10-13, 2001, Revised Papers},
series = {Lecture Notes in Computer Science},
volume = {2340},
pages = {279--289},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-48017-X\_26},
doi = {10.1007/3-540-48017-X\_26},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/dna/EhrenfeuchtHPR01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icalp/KarhumakiP00,
author = {Juhani Karhum{\"{a}}ki and
Ion Petre},
editor = {Ugo Montanari and
Jos{\'{e}} D. P. Rolim and
Emo Welzl},
title = {On the Centralizer of a Finite Set},
booktitle = {Automata, Languages and Programming, 27th International Colloquium,
{ICALP} 2000, Geneva, Switzerland, July 9-15, 2000, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {1853},
pages = {536--546},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/3-540-45022-X\_45},
doi = {10.1007/3-540-45022-X\_45},
timestamp = {Mon, 15 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icalp/KarhumakiP00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/00/IliePR00,
author = {Lucian Ilie and
Ion Petre and
Grzegorz Rozenberg},
editor = {Cristian Calude and
Gheorghe Paun},
title = {Uniformly Scattered Factors},
booktitle = {Finite Versus Infinite},
series = {Discrete mathematics and theoretical computer science},
pages = {187--198},
publisher = {Springer},
year = {2000},
url = {https://doi.org/10.1007/978-1-4471-0751-4\_12},
doi = {10.1007/978-1-4471-0751-4\_12},
timestamp = {Mon, 16 Sep 2019 14:43:17 +0200},
biburl = {https://dblp.org/rec/books/sp/00/IliePR00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/eatcs/Petre99,
author = {Ion Petre},
title = {A Normal form for P-Systems},
journal = {Bull. {EATCS}},
volume = {67},
pages = {165--172},
year = {1999},
timestamp = {Thu, 18 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/eatcs/Petre99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jalc/Petre99,
author = {Ion Petre},
title = {Parikh's Theorem Does Not Hold for Multiplicities},
journal = {J. Autom. Lang. Comb.},
volume = {4},
number = {1},
pages = {17--30},
year = {1999},
url = {https://doi.org/10.25596/jalc-1999-017},
doi = {10.25596/JALC-1999-017},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jalc/Petre99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jucs/PetreP99,
author = {Ion Petre and
Luigia Petre},
title = {Mobile Ambients and P-Systems},
journal = {J. Univers. Comput. Sci.},
volume = {5},
number = {9},
pages = {588--598},
year = {1999},
url = {https://doi.org/10.3217/jucs-005-09-0588},
doi = {10.3217/JUCS-005-09-0588},
timestamp = {Thu, 07 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jucs/PetreP99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dlt/Petre99,
author = {Ion Petre},
editor = {Grzegorz Rozenberg and
Wolfgang Thomas},
title = {On semilinearity in formal power series},
booktitle = {Developments in Language Theory, Foundations, Applications, and Perspectives,
Aachen, Germany, 6-9 July 1999},
pages = {220--231},
publisher = {World Scientific},
year = {1999},
url = {https://doi.org/10.1142/9789812792464\_0019},
doi = {10.1142/9789812792464\_0019},
timestamp = {Thu, 27 Jun 2019 11:28:34 +0200},
biburl = {https://dblp.org/rec/conf/dlt/Petre99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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