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ORCIDIon Petre
Person information
- affiliation: Department of Mathematics and Statistics, University of Turku, Finland
- affiliation (former): Abo Akademi University, Turku, Finland
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2020 – today
- 2022
[j69]Nicoleta Siminea
, Victor-Bogdan Popescu, José Ángel Sánchez Martín, Daniela Florea, Georgiana Gavril, Ana Maria Gheorghe, Corina Itcus, Krishna Kanhaiya, Octavian Pacioglu, Laura Ioana Popa, Romica Trandafir, Maria Iris Tusa, Manuela Sidoroff, Mihaela Paun, Eugen Czeizler, Andrei Paun, Ion Petre:
Network analytics for drug repurposing in COVID-19. Briefings Bioinform. 23(1) (2022)- [e10]Ion Petre, Andrei Paun:
Computational Methods in Systems Biology - 20th International Conference, CMSB 2022, Bucharest, Romania, September 14-16, 2022, Proceedings. Lecture Notes in Computer Science 13447, Springer 2022, ISBN 978-3-031-15033-3 [contents] - 2021
- [j68]Victor-Bogdan Popescu, José Ángel Sánchez Martín, Daniela Schacherer, Sadra Safadoust, Negin Majidi, Andrei Andronescu, Alexandru Nedea, Diana Ion, Eduard Mititelu, Eugen Czeizler, Ion Petre:
NetControl4BioMed: a web-based platform for controllability analysis of protein-protein interaction networks. Bioinform. 37(21): 3976-3978 (2021) - [j67]Lila Kari, Ion Petre, Grzegorz Rozenberg, Arto Salomaa:
A fascinating rainbow of computation - Honoring Gheorghe Păun on the occasion of his 70th birthday. Theor. Comput. Sci. 862: 1-2 (2021) - [j66]Lukasz Mikulski, Ion Petre:
Preface: Special Issue on Reaction Systems. Theor. Comput. Sci. 881: 1-2 (2021) - [j65]Paola Bonizzoni, Lila Kari, Ion Petre, Grzegorz Rozenberg:
Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday. Theor. Comput. Sci. 894: 1-2 (2021) - [i6]Elio Nushi, Victor-Bogdan Popescu, José Ángel Sánchez Martín, Sergiu Ivanov, Eugen Czeizler, Ion Petre:
Network modeling methods for precision medicine. CoRR abs/2104.09206 (2021) - [i5]Usman Sanwal, Thai Son Hoang, Luigia Petre, Ion Petre:
Towards Scalable Modeling of Biology in Event-B. CoRR abs/2105.10344 (2021) - 2020
- [j64]Luigia Petre, Usman Sanwal, Gohar Shah, Charmi Panchal, Dwitiya Tyagi, Ion Petre:
A Computational Model for The Access to Medical Service in a Basic Prototype of a Healthcare System. Fundam. Informaticae 171(1-4): 331-343 (2020) - [j63]José Ángel Sánchez Martín, Ion Petre:
Network Controllability Analysis of Three Multiple-myeloma Patient Genetic Mutation Datasets. Fundam. Informaticae 175(1-4): 281-299 (2020) - [j62]Lukasz Mikulski, Ion Petre:
Preface. J. Membr. Comput. 2(3): 147-148 (2020) - [j61]Sergiu Ivanov, Ion Petre:
Controllability of reaction systems. J. Membr. Comput. 2(4): 290-302 (2020) - [i4]Victor-Bogdan Popescu, Krishna Kanhaiya, Iulian Nastac, Eugen Czeizler, Ion Petre:
Identifying efficient controls of complex interaction networks using genetic algorithms. CoRR abs/2007.04853 (2020) - [i3]Sergiu Ivanov, Ion Petre:
Controllability of reaction systems. CoRR abs/2007.09461 (2020)
2010 – 2019
- 2019
- [j60]Bogdan Iancu, Usman Sanwal, Cristian Gratie, Ion Petre:
Refinement-based modeling of the ErbB signaling pathway. Comput. Biol. Medicine 106: 91-96 (2019) - 2018
- [j59]Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre:
NetControl4BioMed: a pipeline for biomedical data acquisition and analysis of network controllability. BMC Bioinform. 19-S(7): 3-12 (2018) - [j58]Eugen Czeizler, Wu Kai Chiu, Cristian Gratie, Krishna Kanhaiya, Ion Petre:
Structural Target Controllability of Linear Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 15(4): 1217-1228 (2018) - [c38]Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre:
WEBRSIM: A Web-Based Reaction Systems Simulator. Enjoying Natural Computing 2018: 170-181 - 2017
- [j57]Usman Sanwal, Luigia Petre, Ion Petre:
Stepwise construction of a metabolic network in Event-B: The heat shock response. Comput. Biol. Medicine 91: 1-12 (2017) - [j56]Mikhail Barash, Ion Petre:
A Foundational Framework for Step-by-step Model Construction. Fundam. Informaticae 154(1-4): 15-24 (2017) - [j55]Sepinoud Azimi, Charmi Panchal, Andrzej Mizera, Ion Petre:
Multi-Stability, Limit Cycles, and Period-Doubling Bifurcation with Reaction Systems. Int. J. Found. Comput. Sci. 28(8): 1007-1020 (2017) - [j54]Gheorghe Paun, Ion Petre, Grzegorz Rozenberg, Arto Salomaa:
From finite state grammars to natural computing - In memory of Solomon Marcus. Theor. Comput. Sci. 701: 2-7 (2017) - [c37]Andrzej Ehrenfeucht, Ion Petre, Grzegorz Rozenberg:
Reaction Systems: A Model of Computation Inspired by the Functioning of the Living Cell. The Role of Theory in Computer Science 2017: 1-32 - [e9]Jarkko Kari, Florin Manea, Ion Petre:
Unveiling Dynamics and Complexity - 13th Conference on Computability in Europe, CiE 2017, Turku, Finland, June 12-16, 2017, Proceedings. Lecture Notes in Computer Science 10307, Springer 2017, ISBN 978-3-319-58740-0 [contents] - 2016
- [j53]Vladimir Rogojin, Ion Petre:
Large-scale executable biology using rapid integration of computational models. Comput. Sci. J. Moldova 24(1): 118-135 (2016) - [j52]Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Luca Manzoni, Ion Petre, Antonio E. Porreca:
Complexity of model checking for reaction systems. Theor. Comput. Sci. 623: 103-113 (2016) - [j51]Cristian Gratie, Ion Petre:
Complete characterization for the fit-preserving data refinement of mass-action reaction networks. Theor. Comput. Sci. 641: 11-24 (2016) - [c36]Charmi Panchal, Sepinoud Azimi, Ion Petre:
Generating the Logicome of a Biological Network. AlCoB 2016: 38-49 - [c35]Eugen Czeizler, Cristian Gratie, Wu Kai Chiu, Krishna Kanhaiya, Ion Petre:
Target Controllability of Linear Networks. CMSB 2016: 67-81 - [p3]Diana-Elena Gratie, Bogdan Iancu, Sepinoud Azimi, Ion Petre:
Quantitative Model Refinement in Four Different Frameworks, with Applications to the Heat Shock Response. From Action Systems to Distributed Systems 2016: 201-214 - 2015
- [j50]Vladimir Rogojin, Ion Petre:
The Structure of Elementary Strategies for Gene Assembly in Ciliates. Fundam. Informaticae 138(1-2): 145-158 (2015) - [j49]Sepinoud Azimi, Cristian Gratie, Sergiu Ivanov, Ion Petre:
Dependency graphs and mass conservation in reaction systems. Theor. Comput. Sci. 598: 23-39 (2015) - [j48]Emanuela Merelli, Ion Petre:
From Computer Science to Biology and Back. Theor. Comput. Sci. 608: 2-3 (2015) - [c34]Diana-Elena Gratie, Ion Petre:
Full structural model refinement as type refinement of colored Petri nets. BioPPN@Petri Nets 2015: 70-84 - [c33]Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana-Elena Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri:
An Excursion Through Quantitative Model Refinement. Int. Conf. on Membrane Computing 2015: 25-47 - 2014
- [j47]Sepinoud Azimi, Bogdan Iancu, Ion Petre:
Reaction System Models for the Heat Shock Response. Fundam. Informaticae 131(3-4): 299-312 (2014) - [c32]Bogdan Iancu, Diana-Elena Gratie, Sepinoud Azimi, Ion Petre:
On the Implementation of Quantitative Model Refinement. AlCoB 2014: 95-106 - [c31]Sepinoud Azimi, Ion Petre:
The Reduction Power of Simple Operations for Gene Assembly in Ciliates. Discrete Mathematics and Computer Science 2014: 23-36 - [c30]Cristian Gratie, Ion Petre:
Fit-Preserving Data Refinement of Mass-Action Reaction Networks. CiE 2014: 204-213 - [c29]Emanuela Merelli, Ion Petre:
Preface. CS2Bio 2014: 1-3 - [e8]Emanuela Merelli, Ion Petre:
Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology, CS2Bio 2014, Berlin, Germany, June 6, 2014. Electronic Notes in Theoretical Computer Science 306, Elsevier 2014 [contents] - 2013
- [c28]Diana-Elena Gratie, Bogdan Iancu, Ion Petre:
ODE Analysis of Biological Systems. SFM 2013: 29-62 - [e7]Ion Petre:
Proceedings Fourth International Workshop on Computational Models for Cell Processes, CompMod 2013, Turku, Finland, 11th June 2013. EPTCS 116, 2013 [contents] - 2012
- [j46]Elena Czeizler, Andrzej Mizera, Ion Petre:
A Boolean Approach for Disentangling the Roles of Submodules to the Global Properties of a Biomodel. Fundam. Informaticae 116(1-4): 51-63 (2012) - [j45]Bogdan Iancu, Elena Czeizler, Eugen Czeizler, Ion Petre:
Quantitative Refinement of Reaction Models. Int. J. Unconv. Comput. 8(5-6): 529-550 (2012) - [j44]Jarkko Kari, Ion Petre:
Preface. Nat. Comput. 11(4): 551-552 (2012) - [j43]Eugen Czeizler, Andrzej Mizera, Elena Czeizler, Ralph-Johan Back, John E. Eriksson, Ion Petre:
Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 885-898 (2012) - [j42]Eugen Czeizler, Vladimir Rogojin, Ion Petre:
The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. IEEE ACM Trans. Comput. Biol. Bioinform. 9(5): 1326-1337 (2012) - [j41]Giorgio Ausiello, Hendrik Jan Hoogeboom, Juhani Karhumäki, Ion Petre, Arto Salomaa:
Preface. Theor. Comput. Sci. 429: 1-20 (2012) - [j40]Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre:
Simple gene assembly as a rewriting of directed overlap-inclusion graphs. Theor. Comput. Sci. 454: 30-37 (2012) - [j39]Ion Petre, Sergey Verlan:
Matrix insertion-deletion systems. Theor. Comput. Sci. 456: 80-88 (2012) - [j38]Andrzej Mizera, Eugen Czeizler, Ion Petre:
Self-assembly Models of Variable Resolution. Trans. Comp. Sys. Biology 14: 181-203 (2012) - [p2]Robert Brijder, Mark Daley, Tero Harju, Natasa Jonoska, Ion Petre, Grzegorz Rozenberg:
Computational Nature of Gene Assembly in Ciliates. Handbook of Natural Computing 2012: 1233-1280 - [e6]Corrado Priami, Ion Petre, Erik P. de Vink:
Transactions on Computational Systems Biology XIV - Special Issue on Computational Models for Cell Processes. Lecture Notes in Computer Science 7625, Springer 2012, ISBN 978-3-642-35523-3 [contents] - 2011
- [j37]Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin:
Directed Overlap-inclusion Graphs as Representations of Ciliate Genes. Fundam. Informaticae 110(1-4): 29-44 (2011) - [j36]Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Ion Petre, José M. Sempere:
Complexity-preserving simulations among three variants of accepting networks of evolutionary processors. Nat. Comput. 10(1): 429-445 (2011) - [j35]Ion Petre, Andrzej Mizera, Claire L. Hyder, Annika Meinander, Andrey Mikhailov, Richard I. Morimoto, Lea Sistonen, John E. Eriksson, Ralph-Johan Back:
A simple mass-action model for the eukaryotic heat shock response and its mathematical validation. Nat. Comput. 10(1): 595-612 (2011) - [c27]Eugen Czeizler, Vladimir Rogojin, Ion Petre:
The phosphorylation of the heat shock factor as a modulator for the heat shock response. CMSB 2011: 9-23 - [c26]Elena Czeizler, Eugen Czeizler, Bogdan Iancu, Ion Petre:
Quantitative Model Refinement as a Solution to the Combinatorial Size Explosion of Biomodels. SASB 2011: 35-53 - [e5]Cristian S. Calude, Jarkko Kari, Ion Petre, Grzegorz Rozenberg:
Unconventional Computation - 10th International Conference, UC 2011, Turku, Finland, June 6-10, 2011. Proceedings. Lecture Notes in Computer Science 6714, Springer 2011, ISBN 978-3-642-21340-3 [contents] - [e4]Ion Petre, Erik P. de Vink:
Proceedings Third International Workshop on Computational Models for Cell Processes, CompMod 2011, Aachen, Germany, September 10, 2011. EPTCS 67, 2011 [contents] - [e3]Corrado Priami, Ralph-Johan Back, Ion Petre, Erik P. de Vink:
Transactions on Computational Systems Biology XIII. Lecture Notes in Computer Science 6575, Springer 2011, ISBN 978-3-642-19747-5 [contents] - [i2]Giancarlo Mauri, Ion Petre:
New Robustness Paradigms: from Nature to Computing. ERCIM News 2011(85): 33 (2011) - 2010
- [j34]Sergey Verlan, Artiom Alhazov, Ion Petre:
A sequence-based analysis of the pointer distribution of stichotrichous ciliates. Biosyst. 101(2): 109-116 (2010) - [j33]Miika Langille, Ion Petre, Vladimir Rogojin:
Three models for gene assembly in ciliates: a comparison. Comput. Sci. J. Moldova 18(1): 15-40 (2010) - [j32]Ion Petre, Grzegorz Rozenberg:
Gene assembly in Ciliates. Scholarpedia 5(1): 9269 (2010) - [j31]Robert Brijder, Miika Langille, Ion Petre:
Extended strings and graphs for simple gene assembly. Theor. Comput. Sci. 411(4-5): 730-738 (2010) - [j30]Artiom Alhazov, Chang Li, Ion Petre:
Computing the graph-based parallel complexity of gene assembly. Theor. Comput. Sci. 411(25): 2359-2367 (2010) - [j29]Victor Mitrana, Ion Petre, Vladimir Rogojin:
Accepting splicing systems. Theor. Comput. Sci. 411(25): 2414-2422 (2010) - [i1]Ion Petre, Sergey Verlan:
Matrix Insertion-Deletion Systems. CoRR abs/1012.5248 (2010)
2000 – 2009
- 2009
- [j28]Artiom Alhazov, Ion Petre, Vladimir Rogojin:
The parallel complexity of signed graphs: Decidability results and an improved algorithm. Theor. Comput. Sci. 410(24-25): 2308-2315 (2009) - [c25]Ion Petre, Andrzej Mizera, Claire L. Hyder, Andrey Mikhailov, John E. Eriksson, Lea Sistonen, Ralph-Johan Back:
A New Mathematical Model for the Heat Shock Response. Algorithmic Bioprocesses 2009: 411-425 - [c24]Ion Petre, Andrzej Mizera, Ralph-Johan Back:
Computational Heuristics for Simplifying a Biological Model. CiE 2009: 399-408 - [c23]Elena Czeizler, Eugen Czeizler, Ralph-Johan Back, Ion Petre:
Control Strategies for the Regulation of the Eukaryotic Heat Shock Response. CMSB 2009: 111-125 - [e2]Ralph-Johan Back, Ion Petre, Erik P. de Vink:
Proceedings Second International Workshop on Computational Models for Cell Processes, COMPMOD 2009, Eindhoven, the Netherlands, November 3, 2009. EPTCS 6, 2009 [contents] - [e1]Corrado Priami, Ralph-Johan Back, Ion Petre:
Transactions on Computational Systems Biology XI. Lecture Notes in Computer Science 5750, Springer 2009, ISBN 978-3-642-04185-3 [contents] - 2008
- [j27]Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg:
Patterns of simple gene assembly in ciliates. Discret. Appl. Math. 156(14): 2581-2597 (2008) - [j26]Tero Harju, Chang Li, Ion Petre:
Graph theoretic approach to parallel gene assembly. Discret. Appl. Math. 156(18): 3416-3429 (2008) - [j25]Tseren-Onolt Ishdorj, Remco Loos, Ion Petre:
Computational Efficiency of Intermolecular Gene Assembly. Fundam. Informaticae 84(3-4): 363-373 (2008) - [j24]Ion Petre, Vladimir Rogojin:
Decision problem for shuffled genes. Inf. Comput. 206(11): 1346-1352 (2008) - [j23]Tseren-Onolt Ishdorj, Ion Petre:
Gene Assembly Models and Boolean Circuits. Int. J. Found. Comput. Sci. 19(5): 1133-1145 (2008) - [j22]Artiom Alhazov, Ion Petre, Vladimir Rogojin:
Solutions to computational problems through gene assembly. Nat. Comput. 7(3): 385-401 (2008) - [j21]Tero Harju, Chang Li, Ion Petre:
Parallel complexity of signed graphs for gene assembly in ciliates. Soft Comput. 12(8): 731-737 (2008) - [j20]Adrian Atanasiu, Radu-Florian Atanasiu, Ion Petre:
Parikh matrices and amiable words. Theor. Comput. Sci. 390(1): 102-109 (2008) - [j19]Miika Langille, Ion Petre:
Sequential vs. parallel complexity in simple gene assembly. Theor. Comput. Sci. 395(1): 24-30 (2008) - [c22]Ion Petre:
Mathematics of gene assembly in ciliates (Abstract). AFL 2008: 54-55 - [c21]Miika Langille, Ion Petre, Vladimir Rogojin:
Three models for gene assembly in ciliates: a comparison. BIONETICS 2008: 23 - [c20]Ion Petre, Grzegorz Rozenberg:
Summary of the Workshop on Natural Computing and Graph Transformations. ICGT 2008: 470-472 - 2007
- [j18]Tseren-Onolt Ishdorj, Ion Petre, Vladimir Rogojin:
Computational Power of intramolecular gene Assembly. Int. J. Found. Comput. Sci. 18(5): 1123-1136 (2007) - [j17]Erzsébet Csuhaj-Varjú, Ion Petre, György Vaszil:
Self-assembly of strings and languages. Theor. Comput. Sci. 374(1-3): 74-81 (2007) - [c19]Artiom Alhazov, Ion Petre, Vladimir Rogojin:
Solutions to Computational Problems Through Gene Assembly. DNA 2007: 36-45 - [c18]Robert Brijder, Miika Langille, Ion Petre:
A String-Based Model for Simple Gene Assembly. FCT 2007: 161-172 - [c17]Tseren-Onolt Ishdorj, Ion Petre:
Computing Through Gene Assembly. UC 2007: 91-105 - 2006
- [j16]Miika Langille, Ion Petre:
Simple Gene Assembly Is Deterministic. Fundam. Informaticae 73(1-2): 179-190 (2006) - [j15]Lucian Ilie, Solomon Marcus, Ion Petre:
Periodic and Sturmian languages. Inf. Process. Lett. 98(6): 242-246 (2006) - [j14]Ion Petre:
Invariants of Gene-Assembly in Stichotrichous Ciliates (Invarianten der Gen-Assemblierung in Ciliaten der Unterklasse Stichotrichia). it Inf. Technol. 48(3): 161-167 (2006) - [j13]Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg:
Parallelism in Gene Assembly. Nat. Comput. 5(2): 203-223 (2006) - [c16]Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg:
Complexity Measures for Gene Assembly. KDECB 2006: 42-60 - [c15]Tero Harju, Ion Petre, Grzegorz Rozenberg:
Modelling Simple Operations for Gene Assembly. Nanotechnology: Science and Computation 2006: 361-373 - 2005
- [j12]Juhani Karhumäki, Michel Latteux, Ion Petre:
Commutation with Ternary Sets of Words. Theory Comput. Syst. 38(2): 161-169 (2005) - [j11]Juhani Karhumäki, Michel Latteux, Ion Petre:
Commutation with codes. Theor. Comput. Sci. 340(1): 322-333 (2005) - [c14]Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg:
Simple Operations for Gene Assembly. DNA 2005: 96-111 - 2004
- [j10]Tero Harju, Ion Petre, Grzegorz Rozenberg:
Gene Assembly in Celiates. Part I. Molecular Operations (Column: Natural Computing). Bull. EATCS 82: 227-241 (2004) - [c13]Tero Harju, Ion Petre, Grzegorz Rozenberg:
Two Models for Gene Assembly in Ciliates. Theory Is Forever 2004: 89-101 - [c12]Tero Harju, Ion Petre, Grzegorz Rozenberg:
Formal Properties of Gene Assembly: Equivalence Problem for Overlap Graphs. Aspects of Molecular Computing 2004: 202-212 - [c11]Tero Harju, Chang Li, Ion Petre, Grzegorz Rozenberg:
Parallelism in Gene Assembly. DNA 2004: 138-148 - [c10]Tero Harju, Ion Petre, Grzegorz Rozenberg:
Tutorial on DNA Computing and Graph Transformation. ICGT 2004: 434-436 - 2003
- [j9]Tero Harju, Ion Petre, Grzegorz Rozenberg:
Gene Assembly in Ciliates Part I. Molecular Operations. Bull. EATCS 81: 236-249 (2003) - [j8]Andrzej Ehrenfeucht, Tero Harju, Ion Petre, David M. Prescott, Grzegorz Rozenberg:
Formal systems for gene assembly in ciliates. Theor. Comput. Sci. 292(1): 199-219 (2003) - [c9]Ion Petre:
On the Difference Problem for Semilinear Power Series. Grammars and Automata for String Processing 2003: 317-326 - [c8]Juhani Karhumäki, Michel Latteux, Ion Petre:
The Commutation with Codes and Ternary Sets of Words. STACS 2003: 74-84 - 2002
- [j7]Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg:
String and Graph Reduction Systems for Gene Assembly in Ciliates. Math. Struct. Comput. Sci. 12(2): 113-134 (2002) - [j6]Andrzej Ehrenfeucht, Tero Harju, Ion Petre, Grzegorz Rozenberg:
Characterizing the Micronuclear Gene Patterns in Ciliates. Theory Comput. Syst. 35(5): 501-519 (2002) - [j5]Juhani Karhumäki, Ion Petre:
Conway's problem for three-word sets. Theor. Comput. Sci. 289(1): 705-725 (2002) - [c7]Juhani Karhumäki, Ion Petre:
The Branching Point Approach to Conway's Problem. Formal and Natural Computing 2002: 69-76 - [c6]Tero Harju, Ion Petre, Grzegorz Rozenberg:
Tutorial on DNA Computing and Graph Transformation - Computational Nature of Gene Assembly in Ciliates. ICGT 2002: 430-434 - 2001
- [j4]Juhani Karhumäki, Ion Petre:
Conway's Problem and the Communication of Languages. Bull. EATCS 74: 171-189 (2001) - [c5]