Robert Brijder

Available in PDF: CV (including publication list).

Contact information

Room C257, Phone: +32-11-268260
E-mail: robert.brijder {at} uhasselt.be

Current Projects

• Member of the research group Database and Theoretical Computer Sciences at Hasselt University.

Finished Projects

• Former member of the research group lead by Hendrik Blockeel at the Leiden Institute of Advanced Computer Science (LIACS) at Leiden University. Project Annotated Graph Mining funded by NWO.
• Former PhD student and member of the research group Theoretical Computer Science, lead by G. Rozenberg, at LIACS. Received PhD from Leiden University in December 2008. PhD Thesis. Project VIEWS funded by NWO.
• Finished Master's Thesis at Leiden University in March 2004.
• Internship at Philips Medical Systems from Januari 2003 until June 2003 as part of the Science Based Business program.

Publications

Self-Assembly

• Graph-Theoretic Formalization of Hybridization in DNA Sticker Complexes.
  R. Brijder, J.J.M. Gillis, and J. Van den Bussche
  DNA Computing and Molecular Programming - 17th International Conference, DNA 17 (L. Cardelli and W.M. Shih, eds.), Lecture Notes in Computer Science, v. 6937, 49-63, 2011.
   
• On Aggregation in Multiset-Based Self-Assembly of Graphs.
  F. Bernardini, R. Brijder, M. Cavaliere, G. Franco, H.J. Hoogeboom, and G. Rozenberg
  Natural Computing, v. 10, 17-38, 2011.
   
• 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.
  

Principal Pivot Transform

• The adjacency matroid of a graph.
  R. Brijder, and L. Traldi
  arXiv preprint 1107.5493.
   
• Interlace Polynomials for Delta-Matroids.
  R. Brijder, and H.J. Hoogeboom
  arXiv preprint 1010.4678.
   
• Nullity and Loop Complementation for Delta-Matroids.
  R. Brijder, and H.J. Hoogeboom
  arXiv preprint 1010.4497.
   
• The Group Structure of Pivot and Loop Complementation on Graphs and Set Systems.
  R. Brijder, and H.J. Hoogeboom
  European Journal of Combinatorics, v. 32, 1353-1367, 2011. arXiv preprint 0909.4004.
   
• Nullity Invariance for Pivot and the Interlace Polynomial.
  R. Brijder, and H.J. Hoogeboom
  Linear Algebra and its Applications, v. 435, 277-288, 2011. arXiv preprint 0912.0878.
   
• Pivot and Loop Complementation on Graphs and Set Systems.
  R. Brijder, and H.J. Hoogeboom
  7th Annual Conference on Theory and Applications of Models of Computation, TAMC 2010 (J. Kratochvil and A. Li, eds.), Lecture Notes in Computer Science, v. 6108, 151-162, 2010.
   
• Maximal Pivots on Graphs with an Application to Gene Assembly.
  R. Brijder, and H.J. Hoogeboom
  Discrete Applied Mathematics, v. 158, 1977-1985, 2010. 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

• On the Inference of Non-Confluent NLC Graph Grammars.
  R. Brijder, and H. Blockeel
  To appear in Journal of Logic and Computation. arXiv preprint 0901.4876 (older version with different title).
   
• Characterizing Compressibility of Disjoint Subgraphs with NLC Grammars.
  R. Brijder, and H. Blockeel
  Language and Automata Theory and Applications, 5th International Conference, LATA 2011 (A.-H. Dediu, S. Inenaga, C. Martín-Vide, eds.), Lecture Notes in Computer Science, v. 6638, 167-178, 2011.
   
• 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.
  

Reaction Systems

• Representing Reaction Systems by Trees.
  R. Brijder, A. Ehrenfeucht, and G. Rozenberg
  Submitted.
   
• A Tour of reaction Systems.
  R. Brijder, A. Ehrenfeucht, and G. Rozenberg
  International Journal of Foundations of Computer Science, v. 22, 1499-1517, 2011.
   
• Reaction Systems with Duration.
  R. Brijder, A. Ehrenfeucht, and G. Rozenberg
  In: Computation, Cooperation, and Life. Lecture Notes in Computer Science, v. 6610, 191-202, 2011.
   
• A Note on Causalities in Reaction Systems.
  R. Brijder, A. Ehrenfeucht, and G. Rozenberg
  Electronic Communications of the EASST, v. 30, 2010.
  

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, 2011.
   
• 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.
  

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.
  

Patents

• High angular resolution diffusion weighted MRI.
  F.G.C. Hoogenraad, R.F.J. Holthuizen, and R. Brijder
  International Patent WO2005076030 EP1714164 CN1918481 (2005).
  

Teaching

• Topics on Parsing and Formal Languages in fall of 2010.

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Last edited by: Robert Brijder