From cb0ac419575fd74e9f92c00c5f028d67877a1490 Mon Sep 17 00:00:00 2001 From: Sergiu Ivanov Date: Sat, 22 Sep 2018 13:39:59 +0200 Subject: [PATCH] Force the encoding to UTF-8 on Sergey's files. The newer Biber uses a different file parser which is less tolerant with encodings. --- bib/hdr_noverlan.bib | 1346 +++++++++++++++++++++--------------------- bib/hdr_verlan.bib | 988 +++++++++++++++---------------- 2 files changed, 1167 insertions(+), 1167 deletions(-) diff --git a/bib/hdr_noverlan.bib b/bib/hdr_noverlan.bib index 8851723..52d628c 100644 --- a/bib/hdr_noverlan.bib +++ b/bib/hdr_noverlan.bib @@ -1,673 +1,673 @@ -% 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:} - +% 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:} + diff --git a/bib/hdr_verlan.bib b/bib/hdr_verlan.bib index b253243..7b33a11 100644 --- a/bib/hdr_verlan.bib +++ b/bib/hdr_verlan.bib @@ -1,494 +1,494 @@ -% 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. 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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 = {ErzsĂ©bet Csuhaj-VarjĂş 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:} +