selected publications
-
chapter
- Reaction Systems: A Natural Computing Approach to the Functioning of Living Cells. 189-208. 2013
- Reaction Systems with Duration. Lecture Notes in Artificial Intelligence. 191-202. 2011
-
conference proceeding
- Processes Inspired by the Functioning of Living Cells: Natural Computing Approach. Lecture Notes in Artificial Intelligence. 3-5. 2013
- Reaction Systems: A Model of Computation Inspired by Biochemistry. Lecture Notes in Artificial Intelligence. 1-3. 2010
- Computational Nature of Processes Induced by Biochemical Reactions. Lecture Notes in Artificial Intelligence. 16-17. 2009
- Summary of the Workshop on Natural Computing and Graph Transformations. Lecture Notes in Artificial Intelligence. 470-+. 2008
- Biochemical reactions as computations. Lecture Notes in Artificial Intelligence. 672-+. 2007
- Theory inspired by gene assembly in ciliates. Lecture Notes in Artificial Intelligence. 10-10. 2006
- Complexity measures for gene assembly. Lecture Notes in Artificial Intelligence. 42-+. 2006
- The breakpoint graph in ciliates. Lecture Notes in Artificial Intelligence. 128-139. 2005
- Towards a Petri net semantics for membrane systems. Lecture Notes in Artificial Intelligence. 292-309. 2005
- Simple operations for gene assembly. Lecture Notes in Artificial Intelligence. 96-111. 2005
- Tutorial on DNA computing and graph transformation - Computational nature of gene assembly in ciliates. Lecture Notes in Artificial Intelligence. 430-434. 2002
- Computational processes in living cells: Gene assembly in ciliates. Lecture Notes in Artificial Intelligence. 1-20. 2002
- Modelling gene assembly in ciliates. Natural Computing Series. 105-124. 2002
- Computational aspects of gene (un)scrambling in ciliates. Natural Computing Series. 216-256. 1999
-
Computing by splicing.
Theoretical Computer Science.
321-336.
1995
-
journal article
-
Evolving reaction systems.
Theoretical Computer Science.
79-99.
2017
-
An overview of Tomography and Applications Preface.
Fundamenta Informaticae.
I-VII.
2017
- HARTMUT EHRIG (1944-2016). Bulletin- European Association for Theoretical Computer Science. 15-22. 2016
-
Standard and ordered zoom structures.
Theoretical Computer Science.
4-15.
2015
-
Model checking temporal properties of reaction systems.
Information Sciences.
22-42.
2015
-
Tomography and Applications Preface.
Fundamenta Informaticae.
I-XXI.
2015
-
ZOOM STRUCTURES AND REACTION SYSTEMS YIELD EXPLORATION SYSTEMS.
International Journal of Foundations of Computer Science.
275-305.
2014
-
Strategies for Tomography Preface.
Fundamenta Informaticae.
V-XXI.
2014
-
RESEARCH FRONTIERS OF MEMBRANE COMPUTING: OPEN PROBLEMS AND RESEARCH TOPICS.
International Journal of Foundations of Computer Science.
547-623.
2013
-
Step semantics of boolean nets.
Acta Informatica.
15-39.
2013
-
Strategies for Tomography Preface.
Fundamenta Informaticae.
I-XVIII.
2013
-
STABILITY AND CHAOS IN REACTION SYSTEMS.
International Journal of Foundations of Computer Science.
1173-1184.
2012
-
A TOUR OF REACTION SYSTEMS.
International Journal of Foundations of Computer Science.
1499-1517.
2011
-
FUNCTIONS DEFINED BY REACTION SYSTEMS.
International Journal of Foundations of Computer Science.
167-178.
2011
-
COMBINATORICS OF LIFE AND DEATH FOR REACTION SYSTEMS.
International Journal of Foundations of Computer Science.
345-356.
2010
-
Introducing time in reaction systems.
Theoretical Computer Science.
310-322.
2009
-
The Many Facets of Natural Computing.
Communications of the ACM.
72-83.
2008
-
Computing morphisms by spiking neural P systems.
International Journal of Foundations of Computer Science.
1371-1382.
2007
-
Events and modules in reaction systems.
Theoretical Computer Science.
3-16.
2007
-
A model for the origin of internal eliminated segments (IESs) and gene rearrangement in stichotrichous ciliates.
Journal of Theoretical Biology.
108-114.
2007
-
Finite metrics in switching classes.
Discrete Applied Mathematics.
68-73.
2007
- Multiset-based self-assembly of graphs. Fundamenta Informaticae. 49-75. 2007
- Reaction systems. Fundamenta Informaticae. 263-280. 2007
- The embedding problem for switching classes of graphs. Fundamenta Informaticae. 115-134. 2006
- Interpreted trajectories. Fundamenta Informaticae. 81-97. 2006
-
Spike trains in spiking neural P systems.
International Journal of Foundations of Computer Science.
975-1002.
2006
-
Reducibility of gene patterns in ciliates using the breakpoint graph.
Theoretical Computer Science.
26-45.
2006
-
Covers from templates.
International Journal of Foundations of Computer Science.
475-488.
2006
-
Embedding linear orders in grids.
Acta Informatica.
419-428.
2006
- Computational nature of biochemical reactions. Lecture Notes in Artificial Intelligence. 36-36. 2006
- Parallelism in gene assembly. Lecture Notes in Artificial Intelligence. 138-148. 2005
-
Zebra factorizations in free semigroups.
Semigroup Forum.
365-372.
2004
-
Transitivity of local complementation and switching on graphs.
Discrete Mathematics.
45-60.
2004
- Basic notions of reaction systems. Lecture Notes in Artificial Intelligence. 27-29. 2004
- Embedding in switching classes with skew gains. Lecture Notes in Artificial Intelligence. 257-270. 2004
- Formal properties of gene assembly: Equivalence problem for overlap graphs. Lecture Notes in Artificial Intelligence. 202-212. 2004
-
Template-guided recombination for IES elimination and unscrambling of genes in stichotrichous ciliates.
Journal of Theoretical Biology.
323-330.
2003
-
DNA computing by blocking.
Theoretical Computer Science.
653-665.
2003
-
Forbidding-enforcing systems.
Theoretical Computer Science.
611-638.
2003
-
Formal systems for gene assembly in ciliates.
Theoretical Computer Science.
199-219.
2003
-
A guide to membrane computing.
Theoretical Computer Science.
73-100.
2002
-
Topics in the theory of DNA computing.
Theoretical Computer Science.
3-38.
2002
-
Characterizing the micronuclear gene patterns in ciliates.
Theory of Computing Systems.
501-519.
2002
-
Membrane systems with promoters/inhibitors.
Acta Informatica.
695-720.
2002
-
Gene assembly through cyclic graph decomposition.
Theoretical Computer Science.
325-349.
2002
-
ICALP, EATCS and Maurice Nivat.
Theoretical Computer Science.
25-30.
2002
-
Membrane systems with carriers.
Theoretical Computer Science.
779-796.
2002
- Membrane systems with coupled transport: Universality and normal forms. Fundamenta Informaticae. 1-15. 2002
-
Models of molecular computing based on molecular reactions.
New Generation Computing: computing paradigms and computational intelligence.
237-249.
2002
-
Molecular operations for DNA processing in hypotrichous ciliates.
European Journal of Protistology.
241-260.
2001
-
On strongly context-free languages.
Discrete Applied Mathematics.
153-165.
2000
-
Pancyclicity in switching classes.
Information Processing Letters.
153-156.
2000
-
A characterization of poly-slender context-free languages.
RAIRO: Theoretical Informatics and Applications.
77-86.
2000
- Complexity issues in switching of graphs. Lecture Notes in Artificial Intelligence. 59-70. 2000
-
On representing recursively enumerable languages by internal contextual languages.
Theoretical Computer Science.
61-83.
1998
-
Permutations, parenthesis words, and Schroder numbers.
Discrete Mathematics.
259-264.
1998
-
Simple splicing systems.
Discrete Applied Mathematics.
145-163.
1998
-
Characterizations of RE languages starting from internal contextual languages.
International Journal of Computer Mathematics.
179-197.
1998
-
The linear landscape of external contextual languages.
Acta Informatica.
571-593.
1996
-
A note on binary grammatical codes of trees.
Theoretical Computer Science.
425-438.
1996
-
Characterization and complexity of uniformly nonprimitive labeled 2-structures.
Theoretical Computer Science.
247-282.
1996
-
Finite languages for the representation of finite graphs.
Journal of Computer and System Sciences.
170-184.
1996
-
Restricted use of the splicing operation.
International Journal of Computer Mathematics.
17-32.
1996
- Theory of 2-structures. Lecture Notes in Artificial Intelligence. 1-14. 1995
-
COMBINATORIAL PROPERTIES OF DEPENDENCE GRAPHS.
Information and Computation.
315-328.
1994
-
CLANS AND REGIONS IN 2-STRUCTURES.
Theoretical Computer Science.
207-262.
1994
-
HYPEREDGE CHANNELS ARE ABELIAN.
Theoretical Computer Science.
387-393.
1994
-
INCREMENTAL CONSTRUCTION OF 2-STRUCTURES.
Discrete Mathematics.
113-141.
1994
-
PROPERTIES OF GRAMMATICAL CODES OF TREES.
Theoretical Computer Science.
259-293.
1994
-
SEMANTICS OF TREES.
Mathematical Systems Theory.
159-181.
1994
-
CONTEXT-FREE TEXT GRAMMARS.
Acta Informatica.
161-206.
1994
-
T-STRUCTURES, T-FUNCTIONS, AND TEXTS.
Theoretical Computer Science.
227-290.
1993
-
COMBINATORIAL PROPERTIES OF TEXTS.
RAIRO: Theoretical Informatics and Applications.
433-464.
1993
-
ON THE STRUCTURE OF RECOGNIZABLE LANGUAGES OF DEPENDENCE GRAPHS.
RAIRO: Theoretical Informatics and Applications.
7-22.
1993
-
PERMUTABLE TRANSFORMATION SEMIGROUPS.
Semigroup Forum.
123-125.
1993
-
ANGULAR 2-STRUCTURES.
Theoretical Computer Science.
227-248.
1992
-
GRAMMATICAL CODES OF TREES.
Discrete Applied Mathematics.
103-129.
1991
- LABELED 2-STRUCTURES. Lecture Notes in Artificial Intelligence. 268-282. 1991
-
EDGE-LABEL CONTROLLED GRAPH-GRAMMARS.
Journal of Computer and System Sciences.
188-228.
1990
-
PRIMITIVITY IS HEREDITARY FOR 2-STRUCTURES.
Theoretical Computer Science.
343-358.
1990
-
THEORY OF 2-STRUCTURES .1. CLANS, BASIC SUBCLASSES, AND MORPHISMS.
Theoretical Computer Science.
277-303.
1990
-
THEORY OF 2-STRUCTURES .2. REPRESENTATION THROUGH LABELED TREE FAMILIES.
Theoretical Computer Science.
305-342.
1990
-
A CHARACTERIZATION OF SET REPRESENTABLE LABELED PARTIAL 2-STRUCTURES THROUGH DECOMPOSITIONS.
Acta Informatica.
83-94.
1990
-
PARTIAL (SET) 2-STRUCTURES .1. BASIC NOTIONS AND THE REPRESENTATION PROBLEM.
Acta Informatica.
315-342.
1990
-
PARTIAL (SET) 2-STRUCTURES .2. STATE-SPACES OF CONCURRENT SYSTEMS.
Acta Informatica.
343-368.
1990
-
RECORDING THE USE OF MEMORY IN RIGHT-BOUNDARY GRAMMARS AND PUSH-DOWN AUTOMATA.
Acta Informatica.
203-231.
1988
-
HANDLE NLC GRAMMARS AND RE LANGUAGES.
Journal of Computer and System Sciences.
192-205.
1987
- BEHAVIOR OF ELEMENTARY NET SYSTEMS. Lecture Notes in Artificial Intelligence. 60-94. 1987
- FUNDAMENTALS OF EDGE-LABEL CONTROLLED GRAPH-GRAMMARS. Lecture Notes in Artificial Intelligence. 411-426. 1987
-
COORDINATED PAIR SYSTEMS .1. DYCK WORKS AND CLASSICAL PUMPING.
RAIRO: Theoretical Informatics and Applications.
405-424.
1986
-
COORDINATED PAIR SYSTEMS .2. SPARSE STRUCTURE OF DYCK WORDS AND OGDENS LEMMA.
RAIRO: Theoretical Informatics and Applications.
425-439.
1986
-
EACH REGULAR CODE IS INCLUDED IN A MAXIMAL REGULAR CODE.
RAIRO: Theoretical Informatics and Applications.
89-96.
1986
-
ON THE ACTIVE AND FULL USE OF MEMORY IN RIGHT-BOUNDARY GRAMMARS AND PUSH-DOWN AUTOMATA.
Theoretical Computer Science.
201-228.
1986
-
ON THE MEMBERSHIP PROBLEM FOR REGULAR DNLC GRAMMARS.
Discrete Applied Mathematics.
79-85.
1986
-
ADDING GLOBAL FORBIDDING CONTEXT TO CONTEXT-FREE GRAMMARS.
Theoretical Computer Science.
337-360.
1985
-
A COMBINATORIAL PROPERTY OF EOL LANGUAGES.
Mathematical Systems Theory.
207-235.
1985
-
A MORPHIC REPRESENTATION OF EOL LANGUAGES AND OTHER ETOL LANGUAGES.
Discrete Applied Mathematics.
115-122.
1985
- ON COORDINATED REWRITING. Lecture Notes in Artificial Intelligence. 100-111. 1985
-
ON COORDINATED SELECTIVE SUBSTITUTIONS - TOWARDS A UNIFIED THEORY OF GRAMMARS AND MACHINES.
Theoretical Computer Science.
31-50.
1985
- STRONG ITERATIVE PAIRS AND THE REGULARITY OF CONTEXT-FREE LANGUAGES. RAIRO: Theoretical Informatics and Applications. 43-56. 1985
-
AN EASY PROOF OF GREIBACH NORMAL-FORM.
Information and Control.
190-199.
1984
- ON AMBIGUITY IN DOS SYSTEMS. RAIRO: Theoretical Informatics and Applications. 279-295. 1984
-
ON DOS LANGUAGES AND DOS MAPPINGS.
Semigroup Forum.
123-148.
1984
- ON INHERENTLY AMBIGUOUS E0L LANGUAGES. Theoretical Computer Science. 197-214. 1984
-
ON REGULARITY OF LANGUAGES GENERATED BY COPYING SYSTEMS.
Discrete Applied Mathematics.
313-317.
1984
-
RESTRICTIONS ON NLC GRAPH-GRAMMARS.
Theoretical Computer Science.
211-223.
1984
-
CONTEXT FREE NORMAL SYSTEMS AND ETOL SYSTEMS.
Journal of Computer and System Sciences.
34-46.
1983
-
ON BINARY EQUALITY SETS AND A SOLUTION TO THE TEST SET CONJECTURE IN THE BINARY CASE.
Journal of Algebra.
76-85.
1983
-
ON REGULARITY OF CONTEXT-FREE LANGUAGES.
Theoretical Computer Science.
311-332.
1983
- ON THE SEPARATING POWER OF EOL SYSTEMS. RAIRO: Theoretical Informatics and Applications. 13-22. 1983
-
ON THE SIZE OF THE ALPHABET AND THE SUBWORD COMPLEXITY OF SQUARE-FREE DOL LANGUAGES.
Semigroup Forum.
215-223.
1983
-
ON THE SUBWORD COMPLEXITY OF LOCALLY CATENATIVE DOL LANGUAGES.
Information Processing Letters.
7-9.
1983
-
ON THE SUBWORD COMPLEXITY OF M-FREE D0L LANGUAGES.
Information Processing Letters.
121-124.
1983
-
REPETITION OF SUBWORDS IN DOL LANGUAGES.
Information and Control.
13-35.
1983
-
BASIC FORMULAS AND LANGUAGES .2. APPLICATIONS TO E0L SYSTEMS AND FORMS.
Discrete Applied Mathematics.
11-22.
1982
- CONDITIONS ENFORCING REGULARITY OF CONTEXT-FREE LANGUAGES. Lecture Notes in Artificial Intelligence. 187-191. 1982
- ON SUBWORD COMPLEXITIES OF HOMOMORPHIC IMAGES OF LANGUAGES. RAIRO: Theoretical Informatics and Applications. 303-316. 1982
- REPETITIONS IN HOMOMORPHISMS AND LANGUAGES. Lecture Notes in Artificial Intelligence. 192-196. 1982
-
REPRESENTATION THEOREMS USING DOS LANGUAGES.
Theoretical Computer Science.
75-90.
1982
-
THE (GENERALIZED) POST CORRESPONDENCE PROBLEM WITH LISTS CONSISTING OF 2 WORDS IS DECIDABLE.
Theoretical Computer Science.
119-144.
1982
-
A MORPHIC REPRESENTATION OF COMPLEMENTS OF RECURSIVELY-ENUMERABLE SETS.
Journal- ACM.
706-714.
1981
-
BASIC FORMULAS AND LANGUAGES .1. THE THEORY.
Discrete Applied Mathematics.
235-255.
1981
- FPOL SYSTEMS GENERATING COUNTING LANGUAGES. RAIRO: Theoretical Informatics and Applications. 161-173. 1981
-
ON ETOL SYSTEMS WITH FINITE TREE-RANK.
SIAM Journal on Computing.
40-58.
1981
-
ON THE SUBWORD COMPLEXITY OF DOL LANGUAGES WITH A CONSTANT DISTRIBUTION.
Information Processing Letters.
108-113.
1981
-
ON THE SUBWORD COMPLEXITY OF SQUARE-FREE D0L LANGUAGES.
Theoretical Computer Science.
25-32.
1981
-
PUMPING LEMMAS FOR REGULAR SETS.
SIAM Journal on Computing.
536-541.
1981
-
CONTINUOUS GRAMMARS.
Information and Control.
71-91.
1980
-
EVERY 2 EQUIVALENT D0L SYSTEMS HAVE A REGULAR TRUE ENVELOPE.
Theoretical Computer Science.
45-52.
1980
-
MANY-TO-ONE SIMULATION IN EOL FORMS IS DECIDABLE.
Discrete Applied Mathematics.
73-76.
1980
-
ON A BOUND FOR THE D0L SEQUENCE EQUIVALENCE PROBLEM.
Theoretical Computer Science.
339-342.
1980
-
ON AMBIGUITY IN E0L SYSTEMS.
Theoretical Computer Science.
127-134.
1980
-
ON BASIC PROPERTIES OF DOS SYSTEMS AND LANGUAGES.
Information and Control.
137-153.
1980
-
ON THE EMPTINESS OF THE INTERSECTION OF 2 DOS LANGUAGES PROBLEM.
Information Processing Letters.
223-225.
1980
-
THE SEQUENCE EQUIVALENCE PROBLEM IS DECIDABLE FOR 0S SYSTEMS.
Journal- ACM.
656-663.
1980
-
ETOL SYSTEMS WITH RANK.
Journal of Computer and System Sciences.
237-255.
1979
-
FINDING A HOMOMORPHISM BETWEEN 2 WORDS IS NP-COMPLETE.
Information Processing Letters.
86-88.
1979
-
OBSERVATION ON SCATTERED GRAMMARS.
Information Processing Letters.
84-85.
1979
-
NOTE ON DOL LENGTH SETS.
Discrete Mathematics.
233-242.
1978
-
SIMPLIFICATIONS OF HOMOMORPHISMS.
Information and Control.
298-309.
1978
-
STRUCTURE OF DERIVATIONS IN DETERMINISTIC ETOL SYSTEMS.
Journal of Computer and System Sciences.
331-347.
1978
- SOME CONTEXT FREE LANGUAGES THAT ARE NOT DETERMINISTIC ETOL LANGUAGES. Technique et Science Informatiques. 273-291. 1977
- SOME CONTEXT FREE LANGUAGES THAT ARE NOT DETERMINISTIC ETOL LANGUAGES. Technique et Science Informatiques. 273-291. 1977
-
NUMBER OF SUB-WORDS OF EVERYWHERE GROWING DTOL LANGUAGES.
Discrete Mathematics.
223-234.
1976
-
PROVING THAT CERTAIN LANGUAGES ARE NOT ETOL.
Acta Informatica.
407-415.
1976
-
SUBWORD COMPLEXITIES OF VARIOUS CLASSES OF DETERMINISTIC DEVELOPMENTAL LANGUAGES WITH INTERACTIONS.
International Journal of Parallel Programming.
219-236.
1975
-
Evolving reaction systems.
Theoretical Computer Science.
79-99.
2017