|
Robert Brijder
Member of the research group lead by Hendrik Blockeel at the Leiden Institute of
Advanced Computer Science (LIACS) at Leiden University.
Former member of the research group Theoretical Computer
Science, lead by G.
Rozenberg, at LIACS.
Available in PDF: CV (including publication list).
Dr. R. Brijder
Leiden Institute of Advanced Computer Science
(LIACS)
P.O. Box 9512,
2300 RA Leiden
The
Netherlands
Room 156a
Niels Bohrweg 1, 2333 CA Leiden, The
Netherlands
Phone: +31-71-5277143
Fax: +31-71-5276985
E-mail: rbrijder {at} liacs.nl
- Received PhD in December 2008. PhD Thesis. Former PhD student and member of the VIEWS project, funded by NWO.
- Finished Master's Thesis titled "Characterizing Reducibility of Gene Patterns in Ciliates" in March 2004.
- Internship at Philips Medical Systems from Januari 2003 until June 2003 as part of the Science Based Business program.
Other sources: LIACS DB and DBLP.
Principal Pivot Transform
- Nullity Invariance for Pivot and the Interlace Polynomial.
R. Brijder, and H.J. Hoogeboom
arXiv preprint 0912.0878.
- The Group Structure of Pivot and Loop Complementation on Graphs and Set Systems.
R. Brijder, and H.J. Hoogeboom
arXiv preprint 0909.4004.
- Maximal Pivots on Graphs with an Application to Gene Assembly.
R. Brijder, and H.J. Hoogeboom
Submitted. arXiv preprint 0909.3789.
- Pivots, Determinants, and Perfect Matchings of Graphs.
R. Brijder, T. Harju, and H.J. Hoogeboom
Submitted. arXiv preprint 0811.3500.
Graph Grammars
- Non-Confluent NLC Graph Grammar Inference by Compressing Disjoint Subgraphs.
H. Blockeel, and R. Brijder
Submitted.
- Learning Non-Confluent NLC Graph Grammar Rules.
H. Blockeel, and R. Brijder
5th Conference on Computability in Europe (CiE 2009), Mathematical Theory and Computational Practice (K. Ambos-Spies, B. Lowe, W. Merkle, eds.), Abstract Booklet, 60-69, 2009.
Gene Assembly in Ciliates
The topic of Principal Pivot Transform above is highly relevant for (the formal study of) Gene Assembly in Ciliates.
- Computational Nature of Gene Assembly in Ciliates.
R. Brijder, M. Daley, T. Harju, N. Jonoska, I. Petre, and G. Rozenberg
Handbook of Natural Computing (G. Rozenberg, T.H.W. Bäck, J.N. Kok, eds.), Springer, 2010.
- Combining Overlap and Containment for Gene Assembly in Ciliates.
R. Brijder and H.J. Hoogeboom
Theoretical Computer Science, v. 411, 897-905, 2010.
- Extended Strings and Graphs for Simple Gene Assembly.
R. Brijder, M. Langille, and I. Petre
Theoretical Computer Science, v. 411, 730-738, 2010.
- Reality-and-Desire in Ciliates.
R. Brijder and H.J. Hoogeboom
Algorithmic Bioprocesses (A. Condon, D. Harel, J.N. Kok, A. Salomaa, E. Winfree, eds.), Natural Computing Series, Springer, 99-115, 2009.
- Reduction Graphs from Overlap Graphs for Gene Assembly in Ciliates.
R. Brijder, H.J. Hoogeboom, and G. Rozenberg
International Journal of Foundations of Computer Science, v. 20, no. 2, 271-291, 2009. arXiv preprint cs.LO/0702171 (older version).
- Extending the Overlap Graph for Gene Assembly in Ciliates.
R. Brijder and H.J. Hoogeboom
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. arXiv preprint 0712.3380.
- The Fibers and Range of Reduction Graphs in Ciliates.
R. Brijder and H.J. Hoogeboom
Acta Informatica, v. 45, 383-402, 2008. arXiv preprint cs.LO/0702041.
- Strategies of Loop Recombination in Ciliates.
R. Brijder, H.J. Hoogeboom, and M. Muskulus
Discrete Applied Mathematics, v. 156, 1736-1753, 2008. arXiv preprint cs.LO/0601135 (older version).
- Using Sorting by Reversal: Breakpoint Graph for Gene Assembly in Ciliates.
R. Brijder and H.J. Hoogeboom
CompLife 2007 (M.R. Berthold et al., eds.), AIP Conference Proceedings, v. 940, 50-59, 2007.
- A String-Based Model for Simple Gene Assembly.
R. Brijder, M. Langille, and I. Petre
16th International Symposium on Fundamentals of Computation Theory, FCT 2007 (E. Csuhaj-Varjú and Z. Ésik, eds.), Lecture Notes in Computer Science, v. 4639, 161-172, 2007.
- From Micro to Macro: How the Overlap Graph Determines the Reduction Graph in Ciliates.
R. Brijder, H.J. Hoogeboom, and G. Rozenberg
16th International Symposium on Fundamentals of Computation Theory, FCT 2007 (E. Csuhaj-Varjú and Z. Ésik, eds.), Lecture Notes in Computer Science, v. 4639, 149-160, 2007.
- Characterizing Reduction Graphs for Gene Assembly in Ciliates.
R. Brijder and H.J. Hoogeboom
11th International Conference on Developments in Language Theory, DLT 2007 (T. Harju, J. Karhumäki, A. Lepistö, eds.), Lecture Notes in Computer Science, v. 4588, 120-131, 2007.
- Applicability of Loop Recombination in Ciliates using the Breakpoint Graph.
R. Brijder, H.J. Hoogeboom, and M. Muskulus
CompLife 2006 (M.R. Berthold et al., eds.), Lecture Notes in Bioinformatics, v. 4216, 97-106, 2006.
- Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph.
R. Brijder, H.J. Hoogeboom, and G. Rozenberg
Theoretical Computer Science, v. 356, 26-45, 2006. arXiv preprint cs.LO/0601122 (older version).
- The Breakpoint Graph in Ciliates.
R. Brijder, H.J. Hoogeboom, and G. Rozenberg
CompLife 2005 (M.R. Berthold et al., eds.), Lecture Notes in Bioinformatics, v. 3695, 128-139, 2005.
Self-Assembly
- On Aggregation in Multiset-Based Self-Assembly of Graphs.
F. Bernardini, R. Brijder, M. Cavaliere, G. Franco, H.J. Hoogeboom, and G. Rozenberg
Accepted for Natural Computing, 2010.
- Perfectly Quilted Rectangular Snake Tilings.
R. Brijder, and H.J. Hoogeboom
Theoretical Computer Science, v. 410, 1486-1494, 2009.
- Perfectly Quilted Rectangular Snake Tilings.
R. Brijder, and H.J. Hoogeboom
Proceedings of the Satellite Workshops of DLT 2007, Part 3: Workshop on Tilings and Self-Assembly (J. Kari, ed.), TUCS General Publication No 45, June 2007.
- Multiset-Based Self-Assembly of Graphs.
F. Bernardini, R. Brijder, G. Rozenberg, and C. Zandron
Fundamenta Informaticae, v. 75, 49-75, 2007.
Membrane Computing
- Membrane Systems with Proteins Embedded in Membranes.
R. Brijder, M. Cavaliere, A. Riscos-Núñez, G. Rozenberg, and D. Sburlan
Theoretical Computer Science, v. 404, 26-39, 2008.
- Cycles and Communicating Classes in Membrane Systems and Molecular Dynamics.
M. Muskulus, D. Besozzi, R. Brijder, P. Cazzaniga, S. Houweling, D. Pescini, and G. Rozenberg
Theoretical Computer Science, v. 372, 242-266, 2007.
- Membrane Systems with Marked Membranes.
R. Brijder, M. Cavaliere, A. Riscos-Núñez, G. Rozenberg, and D. Sburlan
Workshop on Membrane Computing and Biologically Inspired Process Calculi (MeCBIC 2006). Electronic Notes in Theoretical Computer Science (ENTCS), v. 171, 25-36, 2007.
- Membrane Systems with External Control.
R. Brijder, M. Cavaliere, A. Riscos-Núñez, G. Rozenberg, and D. Sburlan
Seventh Workshop on Membrane Computing (H.J. Hoogeboom et al., eds.), Lecture Notes in Computer Science, v. 4361, 215-232, 2006.
- Communication Membrane Systems with Active Symports.
R. Brijder, M. Cavaliere, A. Riscos-Núñez, G. Rozenberg, and D. Sburlan
Journal of Automata, Languages and Combinatorics (JALC), v. 11, no. 3, 2006.
- Reaction Cycles in Membrane Systems and Molecular Dynamics.
M. Muskulus, S. Houweling, G. Rozenberg, D. Besozzi, P. Cazzaniga, D. Pescini, and R. Brijder
Proceedings of the Fourth Brainstorming Week on Membrane Computing (C. Graciani Diaz, G. Paun, A. Romero-Jimenez, F. Sancho-Caparrini, eds.), vol2, 185-208, 2006.
- Complexity of Biocomputation: Symbolic Dynamics in Membrane Systems.
M. Muskulus, and R. Brijder
International Journal of Foundations of Computer Science, v. 17, no. 1, 147-165, 2006.
- First Steps towards a Geometry of Computation.
M. Muskulus, and R. Brijder
Proceedings of the Third Brainstorming Week on Membrane Computing (M.A. Gutiérrez-Naranjo, A. Riscos-Núñez, F.J. Romero-Campero, D. Sburlan, eds.), 197-218, 2005.
- High angular resolution diffusion weighted MRI.
F.G.C. Hoogenraad, R.F.J. Holthuizen, and R. Brijder
International Patent WO2005076030 EP1714164 CN1918481 (2005).
|
