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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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