all publications coauthors

2010

F. Bernardini, R Brijder, M. Cavaliere, G. Franco, H.J. Hoogeboom, G. Rozenberg.

On aggregation in multiset-based self-assembly of graphs.
|natcomp| (2010).
doi:10.1007/s11047-010-9183-3

R. Brijder, H.J. Hoogeboom.

Combining Overlap and Containment for Gene Assembly in Ciliates.
Theoretical Computer Science 411 (2010) 897-905.
doi:10.1016/j.tcs.2009.07.047

R. Brijder, M. Langille, I. Petre.

Extended Strings and Graphs for Simple Gene Assembly.
Theoretical Computer Science 411 (2010) 730-738.
doi:10.1016/j.tcs.2009.10.011

J. Kleijn, M. Koutny.

Petri nets and membrane computing (Chapter 15).
In: The Oxford Handbook of Membrane Computing (G. Paun, G. Rozenberg, A. Salomaa, eds.), Oxford University Press, 389-412, 2010.

J. Kleijn, M. Koutny.

Applying Step Coverability Trees to Communicating Component-Based Systems.
In: Fundamentals of Software Engineering (FSEN 2009) (F. Arbab, M. Sirjani, eds.), Lecture Notes in Computer Science, v. 5961, 178-193, 2010.
doi:10.1007/978-3-642-11623-0_10

G. Paun, G. Rozenberg.

An introduction to and an overview of membrane computing.
In: The Oxford Handbook of Membrane Computing (G. Paun, G. Rozenberg, A. Salomaa, eds.), Oxford University Press, 2010.

G. Paun, G. Rozenberg.

Computability elements for membrane computing.
In: The Oxford Handbook of Membrane Computing (G. Paun, G. Rozenberg, A. Salomaa, eds.), Oxford University Press, 2010.

G. Rozenberg, T. Bäck, J.N. Kok (eds.).

Handbook of Natural Computing. Springer, May 2010.

2009

M.H. ter Beek, J. Kleijn.

Associativity of Infinite Synchronized Shuffles and Team Automata.
Fundamenta Informaticae 91 (2009) 437-461.
doi:10.3233/FI-2009-0051

L.M.F. Bertens, H.J. Jansen, J. Kleijn, M. Koutny, F.J. Verbeek.

Using Petri Nets in Higher Level Developmental Biology: A case study on the AP axis development in Xenopus laevis - Extended Abstract -.
LIACS Technical Report 2009-03, 2009.

H. Blockeel, R. Brijder.

Learning Non-Confluent NLC Graph Grammar Rules.
In: 5th Conference on Computability in Europe (CiE 2009), Mathematical Theory and Computational Practice (K. Ambos-Spies, B. Löwe, W. Merkle, eds.), Abstract Booklet, University of Heidelberg, 60-69, 2009.
Abstracts .

R. Brijder, H.J. Hoogeboom.

Perfectly Quilted Rectangular Snake Tilings.
Theoretical Computer Science 410 (2009) 1486-1494.
doi:10.1016/j.tcs.2008.12.010
Workshop on Tilings and Self-Assembly, Turku 2007 .

R. Brijder, H.J. Hoogeboom.

Reality-and-Desire in Ciliates.
In: Algorithmic Bioprocesses (A. Condon, D. Harel, J.N. Kok, A. Salomaa, E. Winfree, eds.), Natural Computing Series, 99-115, 2009.
doi:10.1007/978-3-540-88869-7_7
google books .

R. Brijder, H.J. Hoogeboom, G. Rozenberg.

Reduction Graphs from Overlap Graphs for Gene Assembly in Ciliates.
International Journal of Foundations of Computer Science 20 (2009) 271-291.
doi:10.1142/S0129054109006553

C.S. Calude, J.F. Costa, N. Dershowitz, E. Freire, G. Rozenberg (eds.).

Unconventional Computation, 8th International Conference, UC 2009, Portugal. volume 5715, Springer, 2009.
doi:978-3-642-03745-0

D.W. Corne, P. Frisco, G. Paun, G. Rozenberg, A. Salomaa (eds.).

Membrane Computing - 9th International Workshop, WMC 2008, Edinburgh, UK. Lecture Notes in Computer Science, volume 5391, Springer, 2009.
doi:10.1007/978-3-540-95885-7

A. Ehrenfeucht, G. Rozenberg.

Introducing time in reaction systems.
Theoretical Computer Science 410 (2009) 310-322.
doi:10.1016/j.tcs.2008.09.043

J. Engelfriet.

The time complexity of typechecking tree-walking tree transducers.
Acta Informatica 46 (2009) 139-154.
doi:10.1007/s00236-008-0087-y

J. Engelfriet, E. Lilin, A. Maletti.

Extended multi bottom-up tree transducers -- Composition and decomposition.
Acta Informatica 46 (2009) 561-590.
doi:10.1007/s00236-009-0105-8

J. Engelfriet, S. Maneth, H. Seidl.

Deciding equivalence of top-down XML transformations in polynomial time.
Journal of Computer and System Sciences 75 (2009) 271-286.
doi:10.1016/j.jcss.2009.01.001

H.J. Hoogeboom.

Automata walking over trees and graphs.
In: Workshop on Non-Classical Models for Automata and Applications (NCMA) (H. Bordihn, R. Freund, M. Holzer, M. Kutrib, F. Otto, eds.), v. Band 256, Österreichische Computer Gesellschaft, Vienna, Austria, 11-14, September 2009.

T.-O. Ishdorj, A. Leporati, L. Pan, J. Wang.

Solving NP-complete Problems by Spiking Neural P Systems with Budding Rules.
In: Proceedings of the Tenth Workshop on Membrane Computing (WMC10) (G. Paun, M.J. Pérez-Jiménez, A. Riscos-Núñez, eds.), University of Seville, RGNC Report 3/2009, 317-336, 2009.
online proceedings .

J. Kleijn, M. Koutny.

Applying Step Coverability Trees to Communicating Component-Based Systems.
School of Computing Science, Newcastle University, Jan 2009.
Technical Report CS-TR No 1134 .

J. Kleijn, M. Koutny.

A Petri net model for membrane systems with dynamic structure.
Natural Computing 8 (2009) 781-796.
doi:10.1007/s11047-008-9101-0

J. Wang, H.J. Hoogeboom, L. Pan, Gh. Paun.

Spiking Neural P Systems with Weights and Thresholds.
In: Proceedings of the Tenth Workshop on Membrane Computing (WMC10) (G. Paun, M.J. Pérez-Jiménez, A. Riscos-Núñez, eds.), University of Seville, RGNC Report 3/2009, 514-533, 2009.

2008

R. Brijder.

Models of Natural Computation: Gene Assembly and Membrane Systems.
Ph.D. Thesis, Universiteit Leiden, december 2008.
VIEWS . Leiden University repository .

R. Brijder, M. Cavaliere, A. Riscos-Núñez, G. Rozenberg, D. Sburlan.

Membrane Systems with Proteins Embedded in Membranes.
Theoretical Computer Science 404 (2008) 26-39.
doi:10.1016/j.tcs.2008.04.002
VIEWS .

R. Brijder, H.J. Hoogeboom.

The Fibers and Range of Reduction Graphs in Ciliates.
Acta Informatica 45 (2008) 383-402.
doi:10.1007/s00236-008-0074-3
VIEWS . arXiv.org/abs/cs/0702041 .

R. Brijder, H.J. Hoogeboom.

Extending the Overlap Graph for Gene Assembly in Ciliates.
In: Language and Automata Theory and Applications, 2nd International Conference, LATA 2008 (C. Martín-Vide, F. Otto, H. Fernau, eds.), Lecture Notes in Computer Science, v. 5196, 137-148, 2008.
doi:10.1007/978-3-540-88282-4_14
VIEWS . arXiv.org/abs/0712.3380 .

R. Brijder, H.J. Hoogeboom, M. Muskulus.

Strategies of Loop Recombination in Ciliates.
Discrete Applied Mathematics 156 (2008) 1736-1753.
doi:10.1016/j.dam.2007.08.032
VIEWS . arXiv.org/abs/cs/0601135 .

C.S. Calude, J.F. Costa, R. Freund, M. Oswald, G. Rozenberg (eds.).

Unconventional Computation, 7th International Conference, UC 2008. Lecture Notes in Computer Science, volume 5204, 2008.

J. Engelfriet.

The complexity of typechecking tree-walking tree transducers.
LIACS Technical Report 2008-01, January 2008.
ps-file .

J. Engelfriet, E. Lilin, A. Maletti.

Extended Multi Bottom-Up Tree Transducers.
In: Developments in Language Theory, 12th International Conference, DLT 2008, Kyoto, Japan (M. Ito, M. Toyama, eds.), Lecture Notes in Computer Science, v. 5257, 2008.
doi:10.1007/978-3-540-85780-8

T. Harju, I. Petre, V. Rogojin, G. Rozenberg.

Patterns of simple gene assembly in ciliates.
Discrete Applied Mathematics 156 (2008) 2581-2597.
doi:10.1016/j.dam.2007.09.026
presented at DNA11 .

H.J. Hoogeboom, J.F.J. Laros, W.A. Kosters.

Selection of DNA Markers.
IEEE Transactions on Systems, Man, and Cybernetics - Part C: Applications and Reviews 38 (2008) 26-32.
doi:10.1109/TSMCC.2007.906060

L. Kari, G. Rozenberg.

The many facets of natural computing.
Communications of the ACM 51 (October 2008) 72-83.
doi:10.1145/1400181.1400200

J. Kleijn, M. Koutny (eds.).

CHINA 2008 (Concurrency metHods: Issues aNd Applications). Proceedings of Workshop held at Xidian University, Xi'an, China, June 2008.
also published as Technical Report CS-TR-1102, School of Computing Science, University of Newcastle, June 2008 .

J. Kleijn, M. Koutny.

Formal Languages and Concurrent Behaviours.
In: New Developments in Formal Languages and Applications (G. Bel-Enguix, M.D. Jiménez-López, C. Martín-Vide, eds.), Studies in Computational Intelligence, v. 113, Springer, 125-182, 2008.
doi:10.1007/978-3-540-78291-9_5
also Technical Report CS-TR No 1049, School of Computing Science, Newcastle University, Sep 2007 .

J. Kleijn, M. Koutny.

Processes of membrane systems with promoters and inhibitors.
Theoretical Computer Science 404 (2008) 112-126.
doi:10.1016/j.tcs.2008.04.006

J. Kleijn, M. Koutny.

Steps and Coverability in Inhibitor Nets.
In: Perspectives in Concurrency Theory, (K. Lodaya, M. Mukund, R Ramanujam, eds.), Universities Press, Hyderabad, India, 264-295, 2008.
also Technical Report CS-TR No 1118, School of Computing Science, Newcastle University, Sep 2008 .

J. Kleijn, M. Koutny.

A Petri net model for membrane systems with dynamic structure.
Natural Computing (2008).
doi:10.1007/s11047-008-9101-0
online October 01, 2008, to appear in print . also Technical Report CS-TR No 1119, School of Computing Science, Newcastle University, Sep 2008 .

J. Kleijn, M. Koutny.

Petri Nets and Membrane Computing.
School of Computing Science, Newcastle University, Sep 2008.
Technical Report CS-TR No 1117 .

J. Kleijn, A. Yakovlev (eds.).

Special Issue: Petri Nets 2007. Fundamenta Informaticae, volume 88(3), 2008.

H.-J. Kreowski, S. Kuske, G. Rozenberg.

Graph Transformation Units - An Overview.
In: Concurrency, Graphs and Models (P. Degano, R. De Nicola, J. Meseguer, eds.), Lecture Notes in Computer Science, v. 5065, 57-75, 2008.
doi:10.1007/978-3-540-68679-8_5

M. Möllenbeck, Y. Zhou, A.R.O. Cavalcanti, F. Jönsson, B.P. Higgins, W.-J. Chang, S. Juranek, T.G. Doak, G. Rozenberg, H.J. Lipps, L.F. Landweber.

The Pathway to Detangle a Scrambled Gene.
PLoS ONE 3 (2008) e2330.
doi:10.1371/journal.pone.0002330