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% This file was created with JabRef 2.6.
% Encoding: Cp1252
@STRING{HFL = {Handbook of Formal Languages, 3 volumes}}
@STRING{Springer = {Springer Verlag, Berlin, Heidelberg, New York}}
@STRING{TCS = {Theoretical Computer Science}}
@ARTICLE{Adleman94,
author = {Leonard M. Adleman},
title = {Molecular Computation of Solutions to Combinatorial Problems},
journal = {Science},
year = {1994},
volume = {266},
pages = {1021-1024},
month = nov # {~11,},
abstract = {{\textbf{Abstract:} The tools of molecular biology were used to solve
an instance of the directed Hamiltonian path problem. A small graph
was encoded in molecules of {DNA}, and the "operations" of the computation
were performed with standard protocols and enzymes. This experiment
demonstrates the feasibility of carrying out computations at the
molecular level. }},
url = {\url{ftp://ftp.krl.caltech.edu/pub/users/brown/adleman.ps.gz}}
}
@BOOK{alberts02molecular,
title = {Molecular Biology of the Cell, Fourth Edition},
publisher = {Garland},
year = {2002},
author = {Alberts, Bruce and Johnson, Alexander and Lewis, Julian and Raff,
Martin and Roberts, Keith and Walter, Peter},
abstract = {...covers every important aspect in the field, from experimental techniques
and basic concepts to reviews... excellent university course resource.},
howpublished = {Hardcover},
isbn = {0815332181},
keywords = {ref-corpus, ref-transloc},
posted-at = {2006-06-09 22:44:14},
priority = {2},
url = {http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20&path=ASIN/0815332181}
}
@BOOK{Benne93,
title = {{RNA}-Editing: The Alteration of Protein Coding Sequences of {RNA}},
publisher = {Ellis Horwood, Chichester, West Sussex},
year = {1993},
author = {Robert Benne},
owner = {ver},
timestamp = {2009.10.27}
}
@ARTICLE{CPPP07,
author = {Gabriel Ciobanu and Linqiang Pan and Gheorghe P\u{a}un and Mario
J. P\'erez-Jim\'enez},
title = {P systems with minimal parallelism},
journal = {Theoretical Computer Science},
year = {2007},
volume = {378},
pages = {117 - 130},
number = {1},
doi = {DOI: 10.1016/j.tcs.2007.03.044},
issn = {0304-3975},
keywords = {Membrane computing},
url = {http://www.sciencedirect.com/science/article/B6V1G-4NCJCYC-6/2/504442139c4d241b7de81f444297452f}
}
@ARTICLE{CockMin64,
author = {John Cocke and Marvin Minsky},
title = {Universality of Tag Systems with {P}=2},
journal = {Journal of the ACM},
year = {1964},
volume = {11},
pages = {15--20},
number = {1}
}
@ARTICLE{CD90,
author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and J{\"u}rgen Dassow},
title = {On Cooperating/Distributed Grammar Systems},
journal = {Elektronische Informationsverarbeitung und Kybernetik},
year = {1990},
volume = {26},
pages = {49-63},
number = {1/2},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@INPROCEEDINGS{CVS97,
author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and Arto Salomaa},
title = {Networks of Parallel Language Processors},
booktitle = {New Trends in Formal Languages},
year = {1997},
editor = {Gheorghe P\u{a}un and Arto Salomaa},
volume = {1218},
series = {Lecture Notes in Computer Science},
pages = {299-318},
publisher = {Springer},
isbn = {3-540-62844-4}
}
@ARTICLE{CsuhajEA96A,
author = { Erzsebet Csuhaj-Varj{\'{u}} and Lila Kari and Gheorghe P\u{a}un},
title = {Test Tube Distributed Systems Based on Splicing},
journal = {Computers and Artificial Intelligence},
year = {1996},
volume = {15},
pages = {211-232},
number = {2--3},
url = {\url{http://www.csd.uwo.ca/~lila/dnapcgs.ps}}
}
@INPROCEEDINGS{DKGS99,
author = {Mark Daley and Lila Kari and Greg Gloor and Rani Siromoney},
title = {Circular Contextual Insertions/Deletions with Applications to Biomolecular
Computation},
booktitle = {SPIRE/CRIWG},
year = {1999},
pages = {47-54},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://computer.org/proceedings/spire/0268/02680047abs.htm}
}
@ARTICLE{DO04,
author = {Michael Domaratzki and Alexander Okhotin},
title = {Representing Recursively Enumerable Languages by Iterated Deletion},
journal = {Theoretical Computer Science},
year = {2004},
volume = {314},
pages = {451-457},
number = {3},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1016/j.tcs.2004.01.002}
}
@INPROCEEDINGS{FIPY05,
author = {Rudolf Freund and Oscar H. Ibarra and Gheorghe P\u{a}un and Hsu-Chun Yen},
title = {Matrix Languages, Register Machines, Vector Addition Systems},
booktitle = {Proceedings of the Third Brainstorming Week on Membrane Computing},
year = {2005},
editor = {M.A. Guti\'errez-Naranjo and A. Riscos-N\'u\~nez and F.J. Romero Campero
and D. Sburlan},
pages = {155--168},
publisher = {University of Sevilla},
owner = {ver},
timestamp = {2009.10.27}
}
@INPROCEEDINGS{FP02,
author = {Rudolf Freund and Andrei P\u{a}un},
title = {Membrane Systems with Symport/Antiport Rules: Universality Results},
booktitle = {Membrane Computing, International Workshop, WMC-CdeA 2002, Curtea
de Arges, Romania, August 19-23, 2002, Revised Papers},
year = {2002},
editor = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa and Claudio
Zandron},
volume = {2597},
series = {Lecture Notes in Computer Science},
pages = {270-287},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://link.springer.de/link/service/series/0558/bibs/2597/25970270.htm}
}
@ARTICLE{FW96,
author = {Rudolf Freund and F. Wachtler},
title = {Universal Systems with Operations Related to Splicing},
journal = {Computers and Artificial Intelligence},
year = {1996},
volume = {15},
pages = {273-294},
number = {4},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@INPROCEEDINGS{FH02,
author = {Pierluigi Frisco and Hendrik Jan Hoogeboom},
title = {Simulating Counter Automata by {P} Systems with Symport/Antiport},
booktitle = {Membrane Computing, International Workshop, WMC-CdeA 2002, Curtea
de Arges, Romania, August 19-23, 2002, Revised Papers},
year = {2002},
editor = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa and Claudio
Zandron},
volume = {2597},
series = {Lecture Notes in Computer Science},
pages = {288-301},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://link.springer.de/link/service/series/0558/bibs/2597/25970288.htm}
}
@ARTICLE{Galiuk81,
author = {Boris S. Galiukschov},
title = {Semicontextual Grammars},
journal = {Matematicheskaya Logica i Matematicheskaya Lingvistika},
year = {1981},
volume = { },
pages = {38-50},
note = {Tallin University, (in russian)}
}
@BOOK{goto,
title = {A Minimum Time Solution of the Firing Squad Problem},
publisher = {Harvard University},
year = {1962},
author = {E. Goto},
volume = {298},
series = {Course Notes for Applied Mathematics},
owner = {ver},
timestamp = {2010.05.08}
}
@ARTICLE{GFB96,
author = {F. Guarnieri and M. Fliss and C. Bacroft},
title = {Making {DNA} Add},
journal = {Science},
year = {1996},
volume = {273},
pages = {220--223},
number = {12},
owner = {ver},
timestamp = {2010.07.21}
}
@PHDTHESIS{Haussler82,
author = {David Haussler},
title = {Insertion and Iterated Insertion as Operations on Formal Languages},
school = {University of Colorado at Boulder},
year = {1982},
owner = {ver},
timestamp = {2009.10.27}
}
@ARTICLE{Haussler83,
author = {David Haussler},
title = {Insertion Languages},
journal = {Information Sciences},
year = {1983},
volume = {31},
pages = {77-89},
number = {1},
owner = {ver},
timestamp = {2009.10.27}
}
@ARTICLE{head87,
author = {T. Head},
title = {Formal Language Theory and {DNA}: an Analysis of the Generative Capacity
of Specific Recombinant Behaviors.},
journal = {Bulletin of Mathematical Biology},
year = {1987},
volume = {49},
pages = {737--759},
number = {6},
abstract = { {\textbf{Abstract:} A new manner of relating formal language theory
to the study of informational macromolecules is initiated. A language
is associated with each pair of sets where the first set consists
of double-stranded {DNA} molecules and the second set consists of
the recombinational behaviors allowed by specified classes of enzymatic
activities. The associated language consists of strings of symbols
that represent the primary structures of the {DNA} molecules that
may potentially arise from the original set of {DNA} molecules under
the given enzymatic activities.
Attention is focused on the potential effect of sets of restriction
enzymes and a ligase that allow {DNA} molecules to be cleaved and
reassociated to produce further molecules. The associated languages
are analyzed by means of a new generative formalism called a splicing
system. A significant subclass of these languages, which we call
the persistent splicing languages, is shown to coincide with a class
of regular languages which have been previously studied in other
context: the strictly locally testable languages.
This study initiates the formal analysis of the generative power
of recombinational behaviors in general. The splicing system formalism
allows observations to be made concerning the generative power of
general recombination and also of sets of enzymatic activities that
include general recombination. } },
owner = {ver},
timestamp = {2010.06.12},
www = {\url{http://math.binghamton.edu/tom/index.html}}
}
@INPROCEEDINGS{head97,
author = {Tom Head},
title = {Splicing Languages Generated with One Sided Context},
booktitle = {Computing with Bio-Molecules. Theory and Experiments},
year = {1998},
pages = {158--181},
abstract = { {\textbf{Abstract:} The splicing system concept was created in 1987
to allow the convenient representation in formal language theoretic
terms of recombinant actions of certain sets of enzymes on double
stranded {DNA} molecules. Characterizations are given here for those
regular languages that are generated by splicing systems having splicing
rules that test context on only one side. An algorithm is given for
deciding whether any arbitrary regular language can be generated
by a splicing system in which all splicing rules test context on
the same side. Schutzenberger's concept of a constant relative to
a language provides the tool for constructing the required splicing
rules. To provide a potential biochemical example, the formal generative
capacity of the restriction enzyme {BpmI} in the company of a ligase
is discussed. Experimental investigation is suggested. } },
annotate = { Part of \cite{HeadEA97}. },
keywords = { Splicing systems, H-Systems, {DNA}-computing, biocomputing, bioinformatics,
regular languages, finite automata. },
owner = {ver},
timestamp = {2010.06.12}
}
@BOOK{HML,
title = {Introduction to Automata Theory, Languages, and Computation},
publisher = {Addison-Wesley, Reading, Mass.},
year = {2001},
author = {J.E. Hopcroft and R. Motwani and J.D. Ullman},
edition = {2nd},
owner = {ver},
timestamp = {2010.06.12}
}
@PHDTHESIS{KariPhD,
author = {Lila Kari},
title = {On Insertion and Deletion in Formal Languages},
school = {University of Turku},
year = {1991},
owner = {ver},
timestamp = {2009.10.27}
}
@INPROCEEDINGS{KPTY97,
author = {Lila Kari and Gheorghe P\u{a}un and Gabriel Thierrin and Sheng Yu},
title = {At the Crossroads of DNA Computing and Formal Languages: Characterizing
{RE} Using Insertion-Deletion Systems},
booktitle = {Proc. of 3rd DIMACS Workshop on DNA Based Computing},
year = {1997},
pages = {318-333},
publisher = {Philadelphia},
owner = {ver},
timestamp = {2009.10.27}
}
@ARTICLE{KT96,
author = {Lila Kari and Gabriel Thierrin},
title = {Contextual Insertions/Deletions and Computability},
journal = {Information and Computation},
year = {1996},
volume = {131},
pages = {47-61},
number = {1},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@INPROCEEDINGS{KKK01,
author = {Yevgenia Khodor and Julia Khodor and Thomas F. Knight Jr.},
title = {Experimental Conformation of the Basic Principles of Length-only
Discrimination},
booktitle = {DNA Computing, 7th International Workshop on DNA-Based Computers,
DNA7, Tampa, Florida, USA, June 10-13, 2001, Revised Papers},
year = {2001},
editor = {Natasa Jonoska and Nadrian C. Seeman},
volume = {2340},
series = {Lecture Notes in Computer Science},
pages = {223-230},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://link.springer.de/link/service/series/0558/bibs/2340/23400223.htm}
}
@ARTICLE{Kitano,
author = {H. Kitano},
title = {A Graphical Notation for Biochemical Networks},
journal = {Biosilico},
year = {2003},
volume = {1},
pages = {169-176},
owner = {ver},
timestamp = {2010.07.19}
}
@INCOLLECTION{Kleene56,
author = {Stephen Cole Kleene},
title = {Representation of Events in Nerve Nets and Finite Automata},
booktitle = {Automata Studies},
publisher = {Princeton University Press},
year = {1956},
editor = {Claude Shannon and John McCarthy},
pages = {3--41},
address = {Princeton, NJ}
}
@ARTICLE{Kohn,
author = {K. W. Kohn},
title = {Molecular Interaction Map of the Mammalian Cell Cycle Control and
{DNA} Repair Systems},
journal = {Molecular Biology of the Cell},
year = {1999},
volume = {10},
pages = {2703-2734},
owner = {ver},
timestamp = {2010.07.19}
}
@ARTICLE{Korec,
author = {Ivan Korec},
title = {Small Universal Register Machines},
journal = {Theoretical Computer Science},
year = {1996},
volume = {168},
pages = {267-301},
number = {2},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1016/S0304-3975(96)00080-1}
}
@ARTICLE{Marcus69,
author = {Solomon Marcus},
title = {Contextual Grammars},
journal = {Revue Roumaine de Math\' ematiques Pures et Appliqu\' ees},
year = {1969},
volume = {14},
pages = {1525-1534},
owner = {ver},
timestamp = {2009.10.26}
}
@ARTICLE{MR99,
author = {Maurice Margenstern and Yurii Rogozhin},
title = {A Universal Time-Varying Distributed {H} System of Degree 2},
journal = {Biosystems},
year = {1999},
volume = {52},
pages = {73--80}
}
@ARTICLE{MVPS98,
author = {Carlos Mart\'{\i}n-Vide and Gheorghe P\u{a}un and Arto Salomaa},
title = {Characterizations of Recursively Enumerable Languages by Means of
Insertion Grammars},
journal = {Theoretical Computer Science},
year = {1998},
volume = {205},
pages = {195-205},
number = {1-2},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1016/S0304-3975(97)00079-0}
}
@ARTICLE{mazoyer87,
author = {Jacques Mazoyer},
title = {A Six-State Minimal Time Solution to the Firing Squad Synchronization
Problem},
journal = {Theoretical Computer Science},
year = {1987},
volume = {50},
pages = {183-238},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@BOOK{minsky67,
title = {Computations: Finite and Infinite Machines},
publisher = {Prentice Hall, Englewood Cliffts, NJ},
year = {1967},
author = {Marvin Minsky}
}
@ARTICLE{Paun96,
author = {Gheorghe P\u{a}un},
title = {Regular Extended {H} Systems are Computationally Universal},
journal = {Journal of Automata, Languages and Combinatorics},
year = {1996},
volume = {1},
pages = {27-36},
number = {1},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@BOOK{PaunKluwer97,
title = {Marcus Contextual Grammars},
publisher = {Kluwer Academic Publishers},
year = {1997},
author = {Gheorghe P\u{a}un},
address = {Norwell, MA, USA},
isbn = {0792347838}
}
@BOOK{Pbook,
title = {Membrane Computing. An Introduction},
publisher = {Springer--Verlag},
year = {2002},
author = {Gheorghe P\u{a}un},
owner = {ver},
timestamp = {2009.10.27}
}
@BOOK{Phandbook,
title = {The Oxford Handbook Of Membrane Computing},
publisher = {Oxford University Press},
year = {2009},
author = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto Salomaa},
owner = {ver},
timestamp = {2010.05.08}
}
@BOOK{PRSbook,
title = {{DNA} Computing: New Computing Paradigms},
publisher = {Springer},
year = {1998},
author = {Gheorghe P\u{a}un and Grzegorz Rozenberg and Aarto Salomaa},
isbn = {3-540-64196-3},
key = {PaunG}
}
@ARTICLE{Post43,
author = {Emil Post},
title = {Formal Reductions of the General Combinatorial Decision Problem},
journal = {American Journal of Mathematics},
year = {1943},
volume = {65},
pages = {197--215},
number = {2},
owner = {ver},
timestamp = {2010.07.25}
}
@ARTICLE{Rogozhin96,
author = {Yurii Rogozhin},
title = {Small Universal {T}uring Machines},
journal = {Theoretical Computer Science},
year = {1996},
volume = {168},
pages = {215-240},
number = {2},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1016/S0304-3975(96)00077-1}
}
@BOOK{HFL,
title = HFL,
publisher = Springer,
year = {1997},
editor = { },
author = {G. Rozenberg and A. Salomaa},
owner = {ver},
timestamp = {2010.06.12}
}
@INPROCEEDINGS{worsch,
author = {Hubert Schmid and Thomas Worsch},
title = {The Firing Squad Synchronization Problem with Many Generals For One-Dimensional
CA},
booktitle = {Exploring New Frontiers of Theoretical Informatics, IFIP 18th World
Computer Congress, TC1 3rd International Conference on Theoretical
Computer Science (TCS2004), 22-27 August 2004, Toulouse, France},
year = {2004},
editor = {Jean-Jacques L{\'e}vy and Ernst W. Mayr and John C. Mitchell},
pages = {111-124},
publisher = {Kluwer},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@INPROCEEDINGS{Smith96,
author = {Warren D. Smith},
title = {{DNA} Computers in Vitro and in Vivo},
booktitle = {Proceedings of DIMACS Workshop on DNA Based Computers},
year = {1996},
editor = {R.J. Lipton and E.B. Baum},
series = {DIMACS Series in Discrete Mathematicts and Theoretical Computer Science},
pages = {121-185},
publisher = {American Mathematical Society},
owner = {ver},
timestamp = {2009.10.27}
}
@ARTICLE{spellman,
author = {PT. Spellman and G. Sherlock},
title = {Reply Whole-Cell Synchronization -- Effective Tools for Cell Cycle
Studies},
journal = {Trends in Biotechnology},
year = {2004},
volume = {22},
pages = {270-273},
number = {6},
owner = {ver},
timestamp = {2010.05.08}
}
@ARTICLE{TY-NC,
author = {Akihiro Takahara and Takashi Yokomori},
title = {On the Computational Power of Insertion-Deletion Systems},
journal = {Natural Computing},
year = {2003},
volume = {2},
pages = {321-336},
number = {4},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1023/B:NACO.0000006769.27984.23}
}
@INPROCEEDINGS{TY02,
author = {Akihiro Takahara and Takashi Yokomori},
title = {On the Computational Power of Insertion-Deletion Systems},
booktitle = {DNA Computing, 8th International Workshop on DNA Based Computers,
DNA8, Sapporo, Japan, June 10-13, 2002, Revised Papers},
year = {2002},
editor = {Masami Hagiya and Azuma Ohuchi},
volume = {2568},
series = {Lecture Notes in Computer Science},
pages = {269-280},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://link.springer.de/link/service/series/0558/bibs/2568/25680269.htm}
}
@INPROCEEDINGS{umeo,
author = {Hiroshi Umeo and Masashi Maeda and Norio Fujiwara},
title = {An Efficient Mapping Scheme for Embedding Any One-Dimensional Firing
Squad Synchronization Algorithm onto Two-Dimensional Arrays},
booktitle = {Cellular Automata, 5th International Conference on Cellular Automata
for Research and Industry, ACRI 2002, Geneva, Switzerland, October
9-11, 2002, Proceedings},
year = {2002},
editor = {Stefania Bandini and Bastien Chopard and Marco Tomassini},
volume = {2493},
series = {Lecture Notes in Computer Science},
pages = {69-81},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://link.springer.de/link/service/series/0558/bibs/2493/24930069.htm}
}
@BOOK{Wolfram02,
title = {A New Kind of Science},
publisher = {Wolfram Media Inc},
year = {2002},
author = {Stephen Wolfram},
owner = {ver},
timestamp = {2010.07.20}
}
@ARTICLE{yunes,
author = {Jean-Baptiste Yun{\`e}s},
title = {Seven-State Solutions to the Firing Squad Synchronization Problem},
journal = {Theoretical Computer Science},
year = {1994},
volume = {127},
pages = {313-332},
number = {2},
bibsource = {DBLP, http://dblp.uni-trier.de}
}
@BOOK{applP,
title = {Applications of Membrane Computing},
publisher = {Springer},
year = {2006},
editor = {Gabriel Ciobanu and Mario J. P{\'e}rez-Jim{\'e}nez and Gheorghe P\u{a}un},
series = {Natural Computing Series},
bibsource = {DBLP, http://dblp.uni-trier.de},
booktitle = {Applications of Membrane Computing},
isbn = {978-3-540-25017-3}
}
@OTHER{Ppage,
key = {ZZZ},
owner = {ver},
timestamp = {2010.07.19},
title = {The {P} systems Web Page: \texttt{http://ppage.psystems.eu/}}
}
@comment{jabref-meta: selector_publisher:}
@comment{jabref-meta: selector_author:}
@comment{jabref-meta: selector_journal:}
@comment{jabref-meta: selector_keywords:}

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% This file was created with JabRef 2.6.
% Encoding: Cp1252
@STRING{TCS = {Theoretical Computer Science}}
@INCOLLECTION{FARV09,
author = {R. Freund and A. Alhazov and Y. Rogozhin and S. Verlan},
title = {Communication {P} Systems},
booktitle = {The Oxford Handbook of Membrane Computing},
publisher = {Oxford University Press},
year = {2009},
editor = {Gh. P\u{a}un and G. Rozenberg and A. Salomaa},
pages = {118--143},
crossref = {Paun:2010:OHM:1738939},
owner = {ver},
timestamp = {2010.06.14},
url = {05-Paun-C05.pdf}
}
@INCOLLECTION{VF09,
author = {S. Verlan and P. Frisco},
title = {Splicing {P} systems},
booktitle = {The Oxford Handbook of Membrane Computing},
publisher = {Oxford University Press},
year = {2009},
editor = {Gh. P\u{a}un and G. Rozenberg and A. Salomaa},
pages = {198--226},
crossref = {Phandbook},
owner = {ver},
timestamp = {2010.06.14},
url = {08-Paun-C08.pdf}
}
@INPROCEEDINGS{AFOV07,
author = {Artiom Alhazov and Rudolf Freund and Marion Oswald and Sergey Verlan},
title = {Partial Halting in {P} Systems Using Membrane Rules with Permitting
Contexts},
booktitle = {Machines, Computations, and Universality, 5th International Conference,
MCU 2007, Orl{\'e}ans, France, September 10-13, 2007, Proceedings},
year = {2007},
editor = {J{\'e}r{\^o}me Olivier Durand-Lose and Maurice Margenstern},
volume = {4664},
series = {Lecture Notes in Computer Science},
pages = {110-121},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1007/978-3-540-74593-8_10},
owner = {ver},
timestamp = {2010.06.11},
url = {phaltMCU_LNCS.pdf}
}
@INPROCEEDINGS{AKRV09,
author = {Artiom Alhazov and Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan},
title = {P Systems with Minimal Insertion and Deletion},
booktitle = {Proceedings of Seventh Brainstorming Week on Membrane Computing Sevilla,
February 2--6, 2009},
year = {2009},
editor = {Rosa Guti\'errez-Escudero and Miguel Angel Guti\'errez-Naranjo and
Gheorghe P\u{a}un and Ignacio P\'erez-Hurtado and Agust\'in Riscos-Nunez},
volume = {I},
pages = {9--21},
publisher = {F\'enix Editora, Sevilla},
note = {Also accepted to \emph{Theoretical Computer Science}.},
timestamp = {2009.07.02},
url = {mInsDel_tcs4_v1.pdf}
}
@INBOOK{AKRV10-chapter,
chapter = {1},
pages = {459--524},
title = {New Trends in Formal Language Theory
Inspired by Natural Computing:
Small Size Insertion and Deletion Systems},
publisher = {Imperial College Press},
year = {2010},
author = {Artiom Alhazov and Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan},
series = {Mathematics, Computing, Language, and Life: Frontiers in Mathematical
Linguistics and Language Theory},
owner = {ver},
timestamp = {2010.06.11},
url = {book_main.pdf}
}
@INBOOK{AKRV10-chapter-pub,
chapter = {1},
pages = {459--524},
title = {Small Size Insertion and Deletion Systems},
publisher = {World Scientific},
booktitle = {Scientific Applications of Language Methods. Mathematics, Computing, Language, and Life: Frontiers in Mathematical Linguistics and Language Theory},
year = {2010},
volume = {228},
author = {Artiom Alhazov and Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan},
series = {Mathematics, Computing, Language, and Life: Frontiers in Mathematical
Linguistics and Language Theory},
}
@INPROCEEDINGS{AMV08,
author = {Artiom Alhazov and Maurice Margenstern and Sergey Verlan},
title = {Fast Synchronization in {P} Systems},
booktitle = {Membrane Computing - 9th International Workshop, WMC 2008, Edinburgh,
UK, July 28-31, 2008, Revised Selected and Invited Papers},
year = {2008},
editor = {David W. Corne and Pierluigi Frisco and Gheorghe P\u{a}un and Grzegorz
Rozenberg and Arto Salomaa},
volume = {5391},
series = {Lecture Notes in Computer Science},
pages = {118-128},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
comment = {DBLP:conf/membrane/AlhazovMV08},
ee = {http://dx.doi.org/10.1007/978-3-540-95885-7_9},
isbn = {978-3-540-95884-0},
owner = {ver},
timestamp = {2010.05.08},
url = {fastSyncLNCS.pdf}
}
@ARTICLE{ARV07,
author = {Artiom Alhazov and Yurii Rogozhin and Sergey Verlan},
title = {Minimal Cooperation in Symport/Antiport Tissue {P} Systems},
journal = {International Journal of Foundations of Computer Science},
year = {2007},
volume = {18},
pages = {163-180},
number = {1},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1142/S0129054107004619},
owner = {ver},
timestamp = {2010.06.11},
url = {mincoIJFCS.pdf}
}
@TECHREPORT{AV08,
author = {Artiom Alhazov and Sergey Verlan},
title = {Minimization Strategies for Maximally Parallel Multiset Rewriting
Systems},
institution = {TUCS},
year = {2008},
number = {862},
note = {Also accepted to \emph{Theoretical Computer Science}},
owner = {ver},
timestamp = {2010.05.08},
url = {tiny_symanti_tcs_v2.pdf}
}
@ARTICLE{BGMV07,
author = {Francesco Bernardini and Marian Gheorghe and Maurice Margenstern
and Sergey Verlan},
title = {How to Synchronize the Activity of All Components of a {P} System?},
journal = {International Journal of Foundations of Computer Science.},
year = {2008},
volume = {19},
pages = {1183-1198},
number = {5},
bibsource = {DBLP, http://dblp.uni-trier.de},
comment = {DBLP:journals/ijfcs/BernardiniGMV08},
ee = {http://dx.doi.org/10.1142/S0129054108006224},
owner = {ver},
timestamp = {2010.07.19},
url = {syncIJFCS.pdf}
}
@ARTICLE{CMVV07,
author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and Maurice Margenstern and Gy{\"o}rgy
Vaszil and Sergey Verlan},
title = {On Small Universal Antiport {P} Systems},
journal = TCS,
year = {2007},
volume = {372},
pages = {152-164},
number = {2-3},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1016/j.tcs.2006.11.023},
owner = {ver},
timestamp = {2010.06.11},
url = {smallsantiTCS.pdf}
}
@ARTICLE{CV08,
author = {Erzs{\'e}bet Csuhaj-Varj{\'u} and Sergey Verlan},
title = {On Length-Separating Test Tube Systems},
journal = {Natural Computing},
year = {2008},
volume = {7},
pages = {167-181},
number = {2},
bibsource = {DBLP, http://dblp.uni-trier.de},
comment = {DBLP:journals/nc/Csuhaj-VarjuV08},
ee = {http://dx.doi.org/10.1007/s11047-007-9034-z},
owner = {ver},
timestamp = {2010.06.11},
url = {lensepNC.pdf}
}
@ARTICLE{CV10,
author = {E. Csuhaj-Varj{\'u} and S. Verlan},
title = {On Generalized Communicating {P} Systems with Minimal Interaction
Rules},
journal = {Theoretical Computer Science},
year = {2010},
note = {2010. In press.},
owner = {ver},
timestamp = {2010.06.11},
url = {min-int-revised-v8.pdf}
}
@INPROCEEDINGS{FKV09,
author = {Rudolf Freund and Marian Kogler and Sergey Verlan},
title = {P Automata with Controlled Use of Minimal Communication Rules},
booktitle = {Workshop on Non-Classical Models of Automata and Applications, NCMA
2009, Wroclaw, Poland},
year = {2009},
editor = {H. Bordihn and R. Freund and M. Holzer and M. Kutrib and F. Otto},
pages = {107--120},
publisher = {Oesterreichische Computer Gesellschaft},
owner = {ver},
timestamp = {2009.10.08},
url = {NCMAfreundetal.pdf}
}
@INPROCEEDINGS{FreundVerlan07,
author = {Rudolf Freund and Sergey Verlan},
title = {A Formal Framework for Static (Tissue) {P} Systems},
booktitle = {Membrane Computing, 8th International Workshop, WMC 2007, Thessaloniki,
Greece, June 25-28, 2007 Revised Selected and Invited Papers},
year = {2007},
editor = {George Eleftherakis and Petros Kefalas and Gheorghe P\u{a}un and
Grzegorz Rozenberg and Arto Salomaa},
volume = {4860},
series = {Lecture Notes in Computer Science},
pages = {271-284},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1007/978-3-540-77312-2_17},
isbn = {978-3-540-77311-5},
owner = {ver},
timestamp = {2009.11.18},
url = {formFrameworkLNCS.pdf}
}
@INPROCEEDINGS{FV08,
author = {R. Freund and S. Verlan},
title = {P Systems Working in the k-Restricted Minimally Parallel Mode},
booktitle = {International Workshop on Computing with Biomolecules, August 27th,
2008, Wien, Austria},
year = {2008},
editor = {Erzsébet Csuhaj-Varjú and Rudolf Freund and Marion Oswald and Kai
Salomaa},
volume = {244},
pages = {43--52},
publisher = {Oesterreichische Computer Gesellschaft},
owner = {ver},
timestamp = {2009.07.02},
url = {minmaxkfin.pdf}
}
@INPROCEEDINGS{KRV08,
author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan},
title = {Further Results on Insertion-Deletion Systems with One-Sided Contexts},
booktitle = {Language and Automata Theory and Applications, Second International
Conference, LATA 2008, Tarragona, Spain, March 13-19, 2008. Revised
Papers},
year = {2008},
editor = {Carlos Mart\'{\i}n-Vide and Friedrich Otto and Henning Fernau},
volume = {5196},
series = {Lecture Notes in Computer Science},
pages = {333-344},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
comment = {DBLP:conf/lata/KrassovitskiyRV08},
ee = {http://dx.doi.org/10.1007/978-3-540-88282-4_31},
isbn = {978-3-540-88281-7},
url = {furtherInsDelLNCS.pdf}
}
@INPROCEEDINGS{KRV08b,
author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan},
title = {One-Sided Insertion and Deletion: Traditional and {P} Systems Case},
booktitle = {International Workshop on Computing with Biomolecules, August 27th,
2008, Wien, Austria},
year = {2008},
editor = {Erzs\'ebet Csuhaj-Varj\'u and Rudolf Freund and Marion Oswald and
Kai Salomaa},
pages = {53--64},
publisher = {Druckerei Riegelnik},
comment = {http://www.emcc.at/CBM2008/CBM2008.pdf},
timestamp = {2009.07.02},
url = {insdelMemf1.pdf}
}
@INPROCEEDINGS{KRV08c,
author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan},
title = {Computational Power of {P} Systems with Small Size Insertion and
Deletion Rules},
booktitle = {Proceedings International Workshop on The Complexity of Simple Programs,
Cork, Ireland, 6-7th December 2008},
year = {2009},
editor = {Turlough Neary and Damien Woods and Anthony Karel Seda and Niall
Murphy},
volume = {1},
series = {EPTCS},
pages = {108-117},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://arxiv.org/abs/0906.3119},
owner = {ver},
timestamp = {2010.06.14},
url = {pinsdel-final.pdf}
}
@UNPUBLISHED{KRV09-NC,
author = {Alexander Krassovitskiy and Yurii Rogozhin and Sergey Verlan},
title = {Computational Power of Insertion-Deletion ({P}) Systems with Rules
of Size Two},
note = {Accepted to \emph{Natural Computing}. 2010, in publication.},
owner = {ver},
timestamp = {2009.10.28},
url = {insdel_110_nc-v6.pdf}
}
@ARTICLE{MPRV05,
author = {Maurice Margenstern and Gheorghe P\u{a}un and Yurii Rogozhin and
Sergey Verlan},
title = {Context-Free Insertion-Deletion Systems},
journal = TCS,
year = {2005},
volume = {330},
pages = {339-348},
number = {2},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1016/j.tcs.2004.06.031},
url = {cfInsDelTCS.pdf}
}
@INPROCEEDINGS{MRV07,
author = {Artiom Matveevici and Yurii Rogozhin and Sergey Verlan},
title = {Insertion-Deletion Systems with One-Sided Contexts},
booktitle = {Machines, Computations, and Universality, 5th International Conference,
MCU 2007, Orl{\'e}ans, France, September 10-13, 2007, Proceedings},
year = {2007},
editor = {J{\'e}r{\^o}me Olivier Durand-Lose and Maurice Margenstern},
volume = {4664},
series = {Lecture Notes in Computer Science},
pages = {205-217},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1007/978-3-540-74593-8_18},
url = {insdeloneM_LNCS.pdf}
}
@INPROCEEDINGS{RV05,
author = {Yurii Rogozhin and Sergey Verlan},
title = {On the Rule Complexity of Universal Tissue {P} Systems},
booktitle = {Membrane Computing, 6th International Workshop, WMC 2005, Vienna,
Austria, July 18-21, 2005, Revised Selected and Invited Papers},
year = {2005},
editor = {Rudolf Freund and Gheorghe P\u{a}un and Grzegorz Rozenberg and Arto
Salomaa},
volume = {3850},
series = {Lecture Notes in Computer Science},
pages = {356-362},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1007/11603047_24},
owner = {ver},
timestamp = {2010.06.11},
url = {ruleComplLNCS.pdf}
}
@INCOLLECTION{Verlan04a,
author = {Sergey Verlan},
title = {Communicating Distributed {H} Systems with Alternating Filters},
booktitle = {Aspects of Molecular Computing. Essays Dedicated to Tom Head on the
Occasion of His 70th Birthday},
publisher = {Springer},
year = {2004},
editor = {N. Jonoska and Gh. P\u{a}un and G. Rozenberg},
volume = {2950},
series = {Lecture Notes in Computer Science},
pages = {367--384},
doi = {http://dx.doi.org/10.1007/b94864},
url = {ttH_LNCS.pdf}
}
@ARTICLE{Verlan07,
author = {Sergey Verlan},
title = {On Minimal Context-Free Insertion-Deletion Systems},
journal = {Journal of Automata, Languages and Combinatorics},
year = {2007},
volume = {12},
pages = {317-328},
number = {1-2},
bibsource = {DBLP, http://dblp.uni-trier.de},
comment = {DBLP:journals/jalc/Verlan07},
url = {http://lacl.univ-paris12.fr/verlan/data/articles/insdel22_jalc2.pdf}
}
@PHDTHESIS{VerlanPhD,
author = {Sergey Verlan},
title = {Head Systems and Applications to Bioinformatics},
school = {University of Metz},
year = {2004},
owner = {ver},
timestamp = {2010.07.25},
url = {http://lacl.univ-paris12.fr/verlan/data/thesis-en.pdf}
}
@INPROCEEDINGS{VerlanWMC09,
author = {Sergey Verlan},
title = {Look-Ahead Evolution for {P} Systems},
booktitle = {Membrane Computing, 10th International Workshop, WMC 2009, Curtea
de Arges, Romania, August 24-27, 2009. Revised Selected and Invited
Papers},
year = {2009},
editor = {Gheorghe P\u{a}un and Mario J. P{\'e}rez-Jim{\'e}nez and Agustin
Riscos-N{\'u}{\~n}ez and Grzegorz Rozenberg and Arto Salomaa},
volume = {5957},
series = {Lecture Notes in Computer Science},
pages = {479-485},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1007/978-3-642-11467-0_32},
isbn = {978-3-642-11466-3},
owner = {ver},
timestamp = {2010.06.11},
url = {Look-aheadP.pdf}
}
@INPROCEEDINGS{VBGM06,
author = {Sergey Verlan and Francesco Bernardini and Marian Gheorghe and Maurice
Margenstern},
title = {Computational Completeness of Tissue {P} Systems with Conditional
Uniport},
booktitle = {Membrane Computing, 7th International Workshop, WMC 2006, Leiden,
The Netherlands, July 17-21, 2006, Revised, Selected, and Invited
Papers},
year = {2006},
editor = {Hendrik Jan Hoogeboom and Gheorghe P\u{a}un and Grzegorz Rozenberg
and Arto Salomaa},
volume = {4361},
series = {Lecture Notes in Computer Science},
pages = {521-535},
publisher = {Springer},
bibsource = {DBLP, http://dblp.uni-trier.de},
ee = {http://dx.doi.org/10.1007/11963516_33},
owner = {ver},
timestamp = {2010.06.11},
url = {condUniport.pdf}
}
@ARTICLE{VBGM08,
author = {Sergey Verlan and Francesco Bernardini and Marian Gheorghe and Maurice
Margenstern},
title = {Generalized Communicating {P} Systems},
journal = TCS,
year = {2008},
volume = {404},
pages = {170-184},
number = {1-2},
bibsource = {DBLP, http://dblp.uni-trier.de},
comment = {DBLP:journals/tcs/VerlanBGM08},
ee = {http://dx.doi.org/10.1016/j.tcs.2008.04.008},
owner = {ver},
timestamp = {2010.05.08},
url = {genComm.pdf}
}
@INPROCEEDINGS{VR09,
author = {Sergey Verlan and Yurii Rogozhin},
title = {New Choice for Small Universal Devices: Symport/Antiport {P} Systems},
booktitle = {Proceedings International Workshop on The Complexity of Simple Programs,
Cork, Ireland, 6-7th December 2008},
year = {2008},
editor = {Turlough Neary and Damien Woods and Anthony Karel Seda and Niall
Murphy},
volume = {1},
series = {EPTCS},
pages = {235-241},
bibsource = {DBLP, http://dblp.uni-trier.de},
owner = {ver},
timestamp = {2010.06.14},
url = {symantiov.pdf}
}
@comment{jabref-meta: selector_publisher:}
@comment{jabref-meta: selector_author:}
@comment{jabref-meta: selector_journal:}
@comment{jabref-meta: selector_keywords:}

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publisher={Springer Netherlands},
keywords={Insertion–deletion systems; P systems; Decidability; Universality; Computational completeness},
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year={2008},
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series={Lecture Notes in Computer Science},
editor={Mart\'in-Vide, Carlos and Otto, Friedrich and Fernau, Henning},
doi={10.1007/978-3-540-88282-4_31},
title={Further Results on Insertion-Deletion Systems with One-Sided Contexts},
url={http://dx.doi.org/10.1007/978-3-540-88282-4_31},
publisher={Springer Berlin Heidelberg},
keywords={Insertion-deletion systems; universality; computational non-completeness},
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@phdthesis{Krassovitskiy2011,
author = {Alexander Krassovitskiy},
title = {Complexity and Modeling Power of Insertion-Deletion Systems},
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year = {2011}
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% psystems.bib
%
% A reference database for P systems.
@String{j-jucs = "Journal of Universal Computer Science"}
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year={2006},
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booktitle={Applications of Membrane Computing},
series={Natural Computing Series},
editor={Ciobanu, Gabriel and P\u{a}un, Gheorghe and P\'{e}rez-Jim\{e}nez, Mario J.},
doi={10.1007/3-540-29937-8_1},
title={Introduction to Membrane Computing},
url={http://dx.doi.org/10.1007/3-540-29937-8_1},
publisher={Springer Berlin Heidelberg},
author={P\u{a}un, Gheorghe},
pages={1-42},
language={English}
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@ARTICLE{Paun98computingwith,
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@MISC{Freund_matrixlanguages,
author = {Rudolf Freund and Oscar H. Ibarra and Gheorghe P\u{a}un and Hsu-chen Yen},
title = {Matrix Languages, Register Machines, Vector Addition Systems},
year = {}
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@misc{ppage,
title = {The {P} systems web page},
howpublished = {\url{http://ppage.psystems.eu/}}
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title={Membrane Computing: An Introduction},
author={P{\u{a}}un, Gheorghe},
isbn={9783540436010},
lccn={2002075730},
series={Natural Computing Series Natural Computing},
url={https://encrypted.google.com/books?id=8CE3BZ7y\_kIC},
year={2002},
publisher={Springer}
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@Article{Dassow:jucs_5_2:on_the_power_of,
author = {J\"{u}rgen Dassow and Gheorghe P\u{a}un"},
title = "On the Power of Membrane Computing",
abstract = "
We continue the investigation of the power of the computability models introduced in [12] under the name of transition super-cell systems. We compare these systems with classic mechanisms in formal language theory, context-free and matrix grammars, E0L and ET0L systems, interpreted as generating mechanisms of number relations (we take the Parikh image of the usual language generated by these mecha- nisms rather than the language). Several open problems are also formulated.
",
journal = j-jucs,
year = "1999",
volume = "5",
number = "2",
pages = "33--49",
date = "1999-02-28",
month = "feb",
note = "\url|http://www.jucs.org/jucs_5_2/on_the_power_of|"}
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author = {P\u{a}un, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto},
title = {The Oxford Handbook of Membrane Computing},
year = {2010},
isbn = {0199556679, 9780199556670},
publisher = {Oxford University Press, Inc.},
address = {New York, NY, USA},
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year={2007},
isbn={978-3-540-77311-5},
booktitle={Membrane Computing},
volume={4860},
series={Lecture Notes in Computer Science},
editor={Eleftherakis, George and Kefalas, Petros and P\u{a}un, Gheorghe and Rozenberg, Grzegorz and Salomaa, Arto},
doi={10.1007/978-3-540-77312-2_17},
title={A Formal Framework for Static (Tissue) {P} Systems},
url={http://dx.doi.org/10.1007/978-3-540-77312-2_17},
publisher={Springer Berlin Heidelberg},
author={Freund, Rudolf and Verlan, Sergey},
pages={271-284}
}
@book{Rozenberg:1997:HFL:267871,
editor = {Rozenberg, Grzegorz and Salomaa, Arto},
title = {Handbook of Formal Languages, Vol. 3: Beyond Words},
year = {1997},
isbn = {3-540-60649-1},
publisher = {Springer-Verlag New York, Inc.},
address = {New York, NY, USA},
}
@article{Porreca:2011:PSA:1968992.1969023,
author = {Porreca, Antonio E. and Leporati, Alberto and Mauri, Giancarlo and Zandron, Claudio},
title = {P Systems with Active Membranes: Trading Time for Space},
issue_date = {March 2011},
volume = {10},
number = {1},
month = mar,
year = {2011},
issn = {1567-7818},
pages = {167--182},
numpages = {16},
url = {http://dx.doi.org/10.1007/s11047-010-9189-x},
doi = {10.1007/s11047-010-9189-x},
acmid = {1969023},
publisher = {Kluwer Academic Publishers},
address = {Hingham, MA, USA},
keywords = {Computational complexity, Membrane computing, Register machines}
}