673 lines
21 KiB
BibTeX
673 lines
21 KiB
BibTeX
% This file was created with JabRef 2.6.
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@STRING{HFL = {Handbook of Formal Languages, 3 volumes}}
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@STRING{Springer = {Springer Verlag, Berlin, Heidelberg, New York}}
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@STRING{TCS = {Theoretical Computer Science}}
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@ARTICLE{Adleman94,
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author = {Leonard M. Adleman},
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title = {Molecular Computation of Solutions to Combinatorial Problems},
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journal = {Science},
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year = {1994},
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volume = {266},
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pages = {1021-1024},
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month = nov # {~11,},
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abstract = {{\textbf{Abstract:} The tools of molecular biology were used to solve
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an instance of the directed Hamiltonian path problem. A small graph
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was encoded in molecules of {DNA}, and the "operations" of the computation
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were performed with standard protocols and enzymes. This experiment
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demonstrates the feasibility of carrying out computations at the
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molecular level. }},
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url = {\url{ftp://ftp.krl.caltech.edu/pub/users/brown/adleman.ps.gz}}
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}
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@BOOK{alberts02molecular,
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title = {Molecular Biology of the Cell, Fourth Edition},
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publisher = {Garland},
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year = {2002},
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author = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff,
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Martin and Roberts, Keith and Walter, Peter},
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abstract = {...covers every important aspect in the field, from experimental techniques
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and basic concepts to reviews... excellent university course resource.},
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howpublished = {Hardcover},
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isbn = {0815332181},
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keywords = {ref-corpus, ref-transloc},
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posted-at = {2006-06-09 22:44:14},
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priority = {2},
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url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20&path=ASIN/0815332181}
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}
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@BOOK{Benne93,
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title = {{RNA}-Editing: The Alteration of Protein Coding Sequences of {RNA}},
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publisher = {Ellis Horwood, Chichester, West Sussex},
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year = {1993},
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author = {Robert Benne},
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owner = {ver},
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timestamp = {2009.10.27}
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}
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@ARTICLE{CPPP07,
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author = {Gabriel Ciobanu and Linqiang Pan and Gheorghe P\u{a}un and Mario
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J. P\'erez-Jim\'enez},
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title = {P systems with minimal parallelism},
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journal = {Theoretical Computer Science},
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year = {2007},
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volume = {378},
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pages = {117 - 130},
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number = {1},
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doi = {DOI: 10.1016/j.tcs.2007.03.044},
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issn = {0304-3975},
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keywords = {Membrane computing},
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url = {http://www.sciencedirect.com/science/article/B6V1G-4NCJCYC-6/2/504442139c4d241b7de81f444297452f}
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}
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@ARTICLE{CockMin64,
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author = {John Cocke and Marvin Minsky},
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title = {Universality of Tag Systems with {P}=2},
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journal = {Journal of the ACM},
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year = {1964},
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volume = {11},
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pages = {15--20},
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number = {1}
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}
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@ARTICLE{CD90,
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author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and J{\"u}rgen Dassow},
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title = {On Cooperating/Distributed Grammar Systems},
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journal = {Elektronische Informationsverarbeitung und Kybernetik},
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year = {1990},
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volume = {26},
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pages = {49-63},
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number = {1/2},
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bibsource = {DBLP, http://dblp.uni-trier.de}
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}
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@INPROCEEDINGS{CVS97,
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author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and Arto Salomaa},
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title = {Networks of Parallel Language Processors},
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booktitle = {New Trends in Formal Languages},
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year = {1997},
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editor = {Gheorghe P\u{a}un and Arto Salomaa},
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volume = {1218},
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series = {Lecture Notes in Computer Science},
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pages = {299-318},
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publisher = {Springer},
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isbn = {3-540-62844-4}
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}
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@ARTICLE{CsuhajEA96A,
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author = { Erzsebet Csuhaj-Varj{\'{u}} and Lila Kari and Gheorghe P\u{a}un},
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title = {Test Tube Distributed Systems Based on Splicing},
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journal = {Computers and Artificial Intelligence},
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year = {1996},
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volume = {15},
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pages = {211-232},
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number = {2--3},
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url = {\url{http://www.csd.uwo.ca/~lila/dnapcgs.ps}}
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}
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@INPROCEEDINGS{DKGS99,
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author = {Mark Daley and Lila Kari and Greg Gloor and Rani Siromoney},
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title = {Circular Contextual Insertions/Deletions with Applications to Biomolecular
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Computation},
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booktitle = {SPIRE/CRIWG},
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year = {1999},
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pages = {47-54},
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bibsource = {DBLP, http://dblp.uni-trier.de},
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ee = {http://computer.org/proceedings/spire/0268/02680047abs.htm}
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}
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@ARTICLE{DO04,
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author = {Michael Domaratzki and Alexander Okhotin},
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title = {Representing Recursively Enumerable Languages by Iterated Deletion},
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journal = {Theoretical Computer Science},
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year = {2004},
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volume = {314},
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pages = {451-457},
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number = {3},
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bibsource = {DBLP, http://dblp.uni-trier.de},
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ee = {http://dx.doi.org/10.1016/j.tcs.2004.01.002}
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}
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@INPROCEEDINGS{FIPY05,
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author = {Rudolf Freund and Oscar H. Ibarra and Gheorghe P\u{a}un and Hsu-Chun Yen},
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title = {Matrix Languages, Register Machines, Vector Addition Systems},
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booktitle = {Proceedings of the Third Brainstorming Week on Membrane Computing},
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year = {2005},
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editor = {M.A. Guti\'errez-Naranjo and A. Riscos-N\'u\~nez and F.J. Romero Campero
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and D. Sburlan},
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pages = {155--168},
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publisher = {University of Sevilla},
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owner = {ver},
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timestamp = {2009.10.27}
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}
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@INPROCEEDINGS{FP02,
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author = {Rudolf Freund and Andrei P\u{a}un},
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title = {Membrane Systems with Symport/Antiport Rules: Universality Results},
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booktitle = {Membrane Computing, International Workshop, WMC-CdeA 2002, Curtea
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de Arges, Romania, August 19-23, 2002, Revised Papers},
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year = {2002},
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editor = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa and Claudio
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Zandron},
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volume = {2597},
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series = {Lecture Notes in Computer Science},
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pages = {270-287},
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publisher = {Springer},
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bibsource = {DBLP, http://dblp.uni-trier.de},
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ee = {http://link.springer.de/link/service/series/0558/bibs/2597/25970270.htm}
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}
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@ARTICLE{FW96,
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author = {Rudolf Freund and F. Wachtler},
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title = {Universal Systems with Operations Related to Splicing},
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journal = {Computers and Artificial Intelligence},
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year = {1996},
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volume = {15},
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pages = {273-294},
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number = {4},
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bibsource = {DBLP, http://dblp.uni-trier.de}
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}
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@INPROCEEDINGS{FH02,
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author = {Pierluigi Frisco and Hendrik Jan Hoogeboom},
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title = {Simulating Counter Automata by {P} Systems with Symport/Antiport},
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booktitle = {Membrane Computing, International Workshop, WMC-CdeA 2002, Curtea
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de Arges, Romania, August 19-23, 2002, Revised Papers},
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year = {2002},
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editor = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa and Claudio
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Zandron},
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volume = {2597},
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series = {Lecture Notes in Computer Science},
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pages = {288-301},
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publisher = {Springer},
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bibsource = {DBLP, http://dblp.uni-trier.de},
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ee = {http://link.springer.de/link/service/series/0558/bibs/2597/25970288.htm}
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}
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@ARTICLE{Galiuk81,
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author = {Boris S. Galiukschov},
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title = {Semicontextual Grammars},
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journal = {Matematicheskaya Logica i Matematicheskaya Lingvistika},
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year = {1981},
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volume = { },
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pages = {38-50},
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note = {Tallin University, (in russian)}
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}
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@BOOK{goto,
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title = {A Minimum Time Solution of the Firing Squad Problem},
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publisher = {Harvard University},
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year = {1962},
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author = {E. Goto},
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volume = {298},
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series = {Course Notes for Applied Mathematics},
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owner = {ver},
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timestamp = {2010.05.08}
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}
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@ARTICLE{GFB96,
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author = {F. Guarnieri and M. Fliss and C. Bacroft},
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title = {Making {DNA} Add},
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journal = {Science},
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year = {1996},
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volume = {273},
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pages = {220--223},
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number = {12},
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owner = {ver},
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timestamp = {2010.07.21}
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}
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@PHDTHESIS{Haussler82,
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author = {David Haussler},
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title = {Insertion and Iterated Insertion as Operations on Formal Languages},
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school = {University of Colorado at Boulder},
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year = {1982},
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owner = {ver},
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timestamp = {2009.10.27}
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}
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@ARTICLE{Haussler83,
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author = {David Haussler},
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title = {Insertion Languages},
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journal = {Information Sciences},
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year = {1983},
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volume = {31},
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pages = {77-89},
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number = {1},
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owner = {ver},
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timestamp = {2009.10.27}
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}
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@ARTICLE{head87,
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author = {T. Head},
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title = {Formal Language Theory and {DNA}: an Analysis of the Generative Capacity
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of Specific Recombinant Behaviors.},
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journal = {Bulletin of Mathematical Biology},
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year = {1987},
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volume = {49},
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pages = {737--759},
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number = {6},
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abstract = { {\textbf{Abstract:} A new manner of relating formal language theory
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to the study of informational macromolecules is initiated. A language
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is associated with each pair of sets where the first set consists
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of double-stranded {DNA} molecules and the second set consists of
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the recombinational behaviors allowed by specified classes of enzymatic
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activities. The associated language consists of strings of symbols
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that represent the primary structures of the {DNA} molecules that
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may potentially arise from the original set of {DNA} molecules under
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the given enzymatic activities.
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Attention is focused on the potential effect of sets of restriction
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enzymes and a ligase that allow {DNA} molecules to be cleaved and
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reassociated to produce further molecules. The associated languages
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are analyzed by means of a new generative formalism called a splicing
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system. A significant subclass of these languages, which we call
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the persistent splicing languages, is shown to coincide with a class
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of regular languages which have been previously studied in other
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context: the strictly locally testable languages.
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This study initiates the formal analysis of the generative power
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of recombinational behaviors in general. The splicing system formalism
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allows observations to be made concerning the generative power of
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general recombination and also of sets of enzymatic activities that
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include general recombination. } },
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owner = {ver},
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timestamp = {2010.06.12},
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www = {\url{http://math.binghamton.edu/tom/index.html}}
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}
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@INPROCEEDINGS{head97,
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author = {Tom Head},
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title = {Splicing Languages Generated with One Sided Context},
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booktitle = {Computing with Bio-Molecules. Theory and Experiments},
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year = {1998},
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pages = {158--181},
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abstract = { {\textbf{Abstract:} The splicing system concept was created in 1987
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to allow the convenient representation in formal language theoretic
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terms of recombinant actions of certain sets of enzymes on double
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stranded {DNA} molecules. Characterizations are given here for those
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regular languages that are generated by splicing systems having splicing
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rules that test context on only one side. An algorithm is given for
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deciding whether any arbitrary regular language can be generated
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by a splicing system in which all splicing rules test context on
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the same side. Schutzenberger's concept of a constant relative to
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a language provides the tool for constructing the required splicing
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rules. To provide a potential biochemical example, the formal generative
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capacity of the restriction enzyme {BpmI} in the company of a ligase
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is discussed. Experimental investigation is suggested. } },
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annotate = { Part of \cite{HeadEA97}. },
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keywords = { Splicing systems, H-Systems, {DNA}-computing, biocomputing, bioinformatics,
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regular languages, finite automata. },
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owner = {ver},
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timestamp = {2010.06.12}
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}
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@BOOK{HML,
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title = {Introduction to Automata Theory, Languages, and Computation},
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publisher = {Addison-Wesley, Reading, Mass.},
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year = {2001},
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author = {J.E. Hopcroft and R. Motwani and J.D. Ullman},
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edition = {2nd},
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owner = {ver},
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timestamp = {2010.06.12}
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}
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@PHDTHESIS{KariPhD,
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author = {Lila Kari},
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title = {On Insertion and Deletion in Formal Languages},
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school = {University of Turku},
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year = {1991},
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owner = {ver},
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timestamp = {2009.10.27}
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}
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@INPROCEEDINGS{KPTY97,
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author = {Lila Kari and Gheorghe P\u{a}un and Gabriel Thierrin and Sheng Yu},
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title = {At the Crossroads of DNA Computing and Formal Languages: Characterizing
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{RE} Using Insertion-Deletion Systems},
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booktitle = {Proc. of 3rd DIMACS Workshop on DNA Based Computing},
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year = {1997},
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pages = {318-333},
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publisher = {Philadelphia},
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owner = {ver},
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timestamp = {2009.10.27}
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}
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@ARTICLE{KT96,
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author = {Lila Kari and Gabriel Thierrin},
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title = {Contextual Insertions/Deletions and Computability},
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journal = {Information and Computation},
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year = {1996},
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volume = {131},
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pages = {47-61},
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number = {1},
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bibsource = {DBLP, http://dblp.uni-trier.de}
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}
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@INPROCEEDINGS{KKK01,
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author = {Yevgenia Khodor and Julia Khodor and Thomas F. Knight Jr.},
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title = {Experimental Conformation of the Basic Principles of Length-only
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Discrimination},
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booktitle = {DNA Computing, 7th International Workshop on DNA-Based Computers,
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DNA7, Tampa, Florida, USA, June 10-13, 2001, Revised Papers},
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year = {2001},
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editor = {Natasa Jonoska and Nadrian C. Seeman},
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volume = {2340},
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series = {Lecture Notes in Computer Science},
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pages = {223-230},
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publisher = {Springer},
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bibsource = {DBLP, http://dblp.uni-trier.de},
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ee = {http://link.springer.de/link/service/series/0558/bibs/2340/23400223.htm}
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}
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@ARTICLE{Kitano,
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author = {H. Kitano},
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title = {A Graphical Notation for Biochemical Networks},
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journal = {Biosilico},
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|
year = {2003},
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volume = {1},
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pages = {169-176},
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owner = {ver},
|
|
timestamp = {2010.07.19}
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}
|
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@INCOLLECTION{Kleene56,
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author = {Stephen Cole Kleene},
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title = {Representation of Events in Nerve Nets and Finite Automata},
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|
booktitle = {Automata Studies},
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|
publisher = {Princeton University Press},
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|
year = {1956},
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|
editor = {Claude Shannon and John McCarthy},
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pages = {3--41},
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address = {Princeton, NJ}
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}
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@ARTICLE{Kohn,
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author = {K. W. Kohn},
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|
title = {Molecular Interaction Map of the Mammalian Cell Cycle Control and
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{DNA} Repair Systems},
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|
journal = {Molecular Biology of the Cell},
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|
year = {1999},
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volume = {10},
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pages = {2703-2734},
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owner = {ver},
|
|
timestamp = {2010.07.19}
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|
}
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@ARTICLE{Korec,
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author = {Ivan Korec},
|
|
title = {Small Universal Register Machines},
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|
journal = {Theoretical Computer Science},
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|
year = {1996},
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volume = {168},
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pages = {267-301},
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number = {2},
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bibsource = {DBLP, http://dblp.uni-trier.de},
|
|
ee = {http://dx.doi.org/10.1016/S0304-3975(96)00080-1}
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}
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@ARTICLE{Marcus69,
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author = {Solomon Marcus},
|
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title = {Contextual Grammars},
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journal = {Revue Roumaine de Math\' ematiques Pures et Appliqu\' ees},
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year = {1969},
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volume = {14},
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pages = {1525-1534},
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owner = {ver},
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timestamp = {2009.10.26}
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}
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@ARTICLE{MR99,
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author = {Maurice Margenstern and Yurii Rogozhin},
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|
title = {A Universal Time-Varying Distributed {H} System of Degree 2},
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journal = {Biosystems},
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|
year = {1999},
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volume = {52},
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pages = {73--80}
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}
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|
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@ARTICLE{MVPS98,
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author = {Carlos Mart\'{\i}n-Vide and Gheorghe P\u{a}un and Arto Salomaa},
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|
title = {Characterizations of Recursively Enumerable Languages by Means of
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Insertion Grammars},
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|
journal = {Theoretical Computer Science},
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|
year = {1998},
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|
volume = {205},
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pages = {195-205},
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|
number = {1-2},
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|
bibsource = {DBLP, http://dblp.uni-trier.de},
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ee = {http://dx.doi.org/10.1016/S0304-3975(97)00079-0}
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}
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@ARTICLE{mazoyer87,
|
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author = {Jacques Mazoyer},
|
|
title = {A Six-State Minimal Time Solution to the Firing Squad Synchronization
|
|
Problem},
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|
journal = {Theoretical Computer Science},
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|
year = {1987},
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|
volume = {50},
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|
pages = {183-238},
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bibsource = {DBLP, http://dblp.uni-trier.de}
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}
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|
|
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@BOOK{minsky67,
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|
title = {Computations: Finite and Infinite Machines},
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|
publisher = {Prentice Hall, Englewood Cliffts, NJ},
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year = {1967},
|
|
author = {Marvin Minsky}
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|
}
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|
|
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@ARTICLE{Paun96,
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author = {Gheorghe P\u{a}un},
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|
title = {Regular Extended {H} Systems are Computationally Universal},
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|
journal = {Journal of Automata, Languages and Combinatorics},
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|
year = {1996},
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volume = {1},
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pages = {27-36},
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|
number = {1},
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@INPROCEEDINGS{TY02,
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author = {Akihiro Takahara and Takashi Yokomori},
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title = {On the Computational Power of Insertion-Deletion Systems},
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title = {An Efficient Mapping Scheme for Embedding Any One-Dimensional Firing
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@OTHER{Ppage,
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key = {ZZZ},
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timestamp = {2010.07.19},
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title = {The {P} systems Web Page: \texttt{http://ppage.psystems.eu/}}
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}
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