Hendrik Jan Hoogeboom
Associate professor
- Name
- Dr. H.J. Hoogeboom
- Telephone
- +31 71 527 7062
- h.j.hoogeboom@liacs.leidenuniv.nl
- ORCID iD
- 0000-0002-6673-0124
Hendrik Jan Hoogeboom's research interest is theoretical computer science (formal languages, algorithms). In particular: formal models of natural computation, infinitary languages, logic & automata, tree-walking automata, patterns in strings, graph polynomials.
More information about Hendrik Jan Hoogeboom
Former PhD candidates
Associate professor
- Science
- Leiden Inst of Advanced Computer Science
- Engelfriet J., Hoogeboom H.J. & Samwel B. (2021), XML navigation and transformation by tree-walking automata and transducers with visible and invisible pebbles, Theoretical Computer Science 850: 40-97.
- Genova D., Hoogeboom H.J. & Klein H.C.M. (2021), Comparing reactions in reaction systems, Theoretical Computer Science 881: 83-96.
- Genova D., Hoogeboom H.J. & Prodanoff Z. (2020), Extracting reaction systems from function behavior, Journal of Membrane Computing 2(3): 194-206.
- Genova D. & Hoogeboom H.J. (2017), Enforcing Regular Languages, Fundamenta Informaticae 154(1-4): 131-144.
- Genova D. & Hoogeboom H.J. (2017), Finite Language Forbidding-Enforcing Systems. Kari J., Manea F. & Petre I. (Eds.), Unveiling Dynamics and Complexity. CiE 2017. CiE 2017: Unveiling Dynamics and Complexity 12 June 2017 - 16 June 2017 no. LNCS Volume 10307. Cham: Springer. 258-269.
- Genova D., Hoogeboom H.J. & Jonoska N. (2017), A graph isomorphism condition and equivalence of reaction systems, Theoretical Computer Science 701: 109-119.
- Hoogeboom H.J., Kleijn H.C.M., Nat M. van der, Petre I. & Salomaa A. (Eds.) (2017), A Magician in Science. Liber Amicorum Grzegorz Rozenberg. Turku, Finland: TUCS.
- Hoogeboom H.J., Kosters W.A., Rijn J.N. van & Vis J.K. (2014), Acyclic Constraint Logic and Games, ICGA Journal 37(1): 3-16.
- Brijder R. & Hoogeboom H.J. (2014), Graph Polynomials Motivated by Gene Rearrangements in Ciliates. Beckmann A., Csuhaj-Varju E. & Meer K. (Eds.), Language, Life, Limits, 10th Conference on Computability in Europe (CiE 2014). no. 8493 63-72.
- Brijder R. & Hoogeboom H.J. (2014), The Algebra of Gene Assembly in Ciliates. In: Jonoska N. & Saito M. (Eds.), Discrete and Topological Models in Molecular Biology. Natural Computing Series. Berlin Heidelberg: Springer. 289-307.
- Brijder Robert & Hoogeboom Hendrik Jan (2014), Interlace polynomials for multimatroids and delta-matroids, European Journal of Combinatorics 40: 142-167.
- Vliet R. van & Hoogeboom H.J. (2013), A Minimal Normal Form for DNA Expressions, Fundamenta Informaticae 123: 227-243.
- Traldi L., Brijder R. & Hoogeboom H.J. (2013), The Adjacency Matroid of a Graph, The Electronic Journal of Combinatorics 20(3): P27.
- Vliet R. van & Hoogeboom H.J. (2013), Making DNA Expressions Minimal, Fundamenta Informaticae 123: 199-226.
- Brijder R. & Hoogeboom H.J. (2013), Nullity and Loop Complementation for Delta-Matroids, SIAM Journal on Discrete Mathematics 27: 492-506.
- Ausiello G., Hoogeboom H.J., Karhumäki J., Petre I. & Salomaa A. (Eds.) (2012), Magic in Science. Amsterdam: Elsevier.
- Ausiello Giorgio, Hoogeboom Hendrik Jan, Karhumaki Juhani, Petre Ion & Salomaa Arto (2012), Magic in Science Preface, 429: 1-20.
- Brijder R., Harju T. & Hoogeboom H.J. (2012), Pivots, determinants, and perfect matchings of graphs, 454: 64-71.
- Pan L., Wang Jun & Hoogeboom H.J. (2012), Spiking Neural P Systems with Astrocytes, Neural Computation 24: 805-825.
- Pan L., Wang Jun & Hoogeboom H.J. (2012), Asynchronous extended spiking neural P systems with Astrocytes. Gheorghe M., Paun G., Rozenberg G., Salomaa A. & Verlan S. (Eds.), Membrane Computing, 12th International Conference, CMC 2011. : Springer Verlag. 243-246.
- Brijder Robert & Hoogeboom Hendrik Jan (2012), Binary Symmetric Matrix Inversion Through Local Complementation, Fundamenta Informaticae 116(1-4): 15-23.
- Schraagen M.P. & Hoogeboom H.J. (2011), Predicting record linkage potential in a family reconstruction graph. De Causmaecker P. (Ed.), Proceedings of 23rd Benelux Conference on Artificial Intelligence (BNAIC 2011). 199-206.
- Frisco P. & Hoogeboom H.J. (2011), P systems and topology: some suggestions for research, International Journal of Foundations of Computer Science 22: 179-190.
- Pan L., Wang Jun & Hoogeboom H.J. (2011), Limited Asynchronous Spiking Neural P Systems, Fundamenta Informaticae 110: 271-293.
- Brijder R. & Hoogeboom H.J. (2011), Nullity Invariance for Pivot and the Interlace Polynomial, Linear Algebra and Its Applications 435: 277-288.
- Bernardini F., Brijder R., Cavaliere M., Franco G., Hoogeboom H.J. & Rozenberg G. (2011), On aggregation in multiset-based self-assembly of graphs, Natural computing 10: 17-38.
- Brijder R. & Hoogeboom H.J. (2011), The Group Structure of Pivot and Loop Complementation on Graphs and Set Systems, European Journal of Combinatorics 32: 1353-1367.
- Brijder R. & Hoogeboom H.J. (2010), Combining Overlap and Containment for Gene Assembly in Ciliates, 411: 897-905.
- Wang Jun, Hoogeboom H.J., Pan L., Paun G. & Pérez-Jiménez A.J. (2010), Spiking Neural P Systems with Weights, Neural Computation 22: 2615-2646.
- Brijder R. & Hoogeboom H.J. (2010), Pivot and Loop Complementation on Graphs and Set Systems. Kratochvil J. & Li A. (Eds.), 7th Annual Conference on Theory and Applications of Models of Computation (TAMC 2010). : Springer Verlag. 151-162.
- Wang Jun, Hoogeboom H.J. & Pan L. (2010), Spiking Neural P Systems with Neuron Division. Hinze T., Paun G., Gheorghe M., Rozenberg G. & Salomaa A. (Eds.), Membrane Computing, 11th International Conference (CMC 2010). : Springer. 361-376.
- Brijder R. & Hoogeboom H.J. (2010), Maximal Pivots on Graphs with an Application to Gene Assembly, Discrete Applied Mathematics 158: 1977-1985.
- Wang Jun, Hoogeboom H.J., Pan L. & Paun G. (2009), Spiking Neural P Systems with Weights and Thresholds. Paun G., Pérez-Jiménez M.J. & Riscos-Núñez A. (Eds.), Proceedings of the Tenth Workshop on Membrane Computing (WMC10). : University of Seville. 514-533.
- Brijder R., Hoogeboom H.J. & Rozenberg G. (2009), Reduction Graphs from Overlap Graphs for Gene Assembly in Ciliates, International Journal of Foundations of Computer Science 20: 271-291.
- Brijder R. & Hoogeboom H.J. (2009), Perfectly Quilted Rectangular Snake Tilings, 410: 1486-1494.
- Brijder R. & Hoogeboom H.J. (2009), Reality-and-Desire in Ciliates. In: Condon A., Harel D., Kok J.N., Salomaa A. & Winfree E. (Eds.), Algorithmic Bioprocesses: Springer.
- Hoogeboom H.J. (2009), Automata walking over trees and graphs. Bordihn H., Freund R., Holzer M., Kutrib M. & Otto F. (Eds.), Workshop on Non-Classical Models for Automata and Applications (NCMA). NCMA. Vienna, Austria: Oesterreichische Computer Gesellschaft. 11-14.
- Brijder R., Hoogeboom H.J. & Muskulus M. (2008), Strategies of Loop Recombination in Ciliates, Discrete Applied Mathematics 156: 1736-1753.
- Brijder R. & Hoogeboom H.J. (2008), Extending the Overlap Graph for Gene Assembly in Ciliates. Martín-Vide C., Otto F. & Fernau H. (Eds.), Language and Automata Theory and Applications. 137-148.
- Hoogeboom H.J., Kosters W.A. & Laros J.F.J. (2008), Selection of DNA Markers, IEEE Transactions on Systems, Man, and Cybernetics 38(1): 26-32.
- Brijder R. & Hoogeboom H.J. (2008), The Fibers and Range of Reduction Graphs in Ciliates, Acta Informatica 45: 383-402.
- Brijder R. & Hoogeboom H.J. (2007), Using Sorting by Reversal: Breakpoint Graph for Gene Assembly in Ciliates. Siebes A.P.J.M., Berthold M.R., Glen R.C. & Feelders A.J. (Eds.), CompLife 2007: The Third International Symposium on Computational Life Sciences. AIP Conference Proceedings 50-59.
- Brijder R. & Hoogeboom H.J. (2007), Perfectly Quilted Rectangular Snake Tilings. Kari J. (Ed.), Proceedings of the Workshop on Tilings and Self-Assembly. : TUCS General Publication.
- Deutz Andre, Vliet Rudy van & Hoogeboom Hendrik Jan (2007), High spies (or how to win a programming contest), 4475: 93-107.
- Engelfriet J. & Hoogeboom H.J. (2007), Finitary Compositions of Two-way Finite-State Transductions, Fundamenta Informaticae 80: 111-113.
- Deutz A.H., Vliet R. van & Hoogeboom H.J. (2007), High Spies, or How to win a programming contest. Crescenzi P., Prencipe G. & Pucci G. (Eds.), Fun with Algorithms, FUN 2007. 93-107.
- Brijder R. & Hoogeboom H.J. (2007), Characterizing Reduction Graphs for Gene Assembly in Ciliates. Harju T., Karhumäki J. & Lepistö A. (Eds.), 11th International Conference on Developments in Language Theory, DLT 2007. 120-131.
- Brijder R., Hoogeboom H.J. & Rozenberg G. (2007), From Micro to Macro: How the Overlap Graph Determines the Reduction Graph in Ciliates. Csuhaj-Varjú E. & Ésik Z. (Eds.), Fundamentals of Computation Theory, 16th International Symposium, FCT 2007. 149-160.
- Gao Y. & Hoogeboom H.J. (2007), P Systems with Single Passenger, International Journal of Foundations of Computer Science 17: 1227-1235.
- Engelfriet J., Hoogeboom H.J. & Samwel H. (2007), XML Transformation by Tree-Walking Transducers with Invisible Pebbles. Libkin L. (Ed.), Proceedings of the twenty-sixth ACM Symposium on Principles of Database Systems, PODS 2007. : ACM Press. 63-72.
- Engelfriet J. & Hoogeboom H.J. (2007), Automata with nested pebbles capture first-order logic with transitive closure, Logical Methods in Computer Science 3(2-3): 1-27.
- Vliet R. van, Hoogeboom H.J. & Rozenberg G. (2006), The construction of minimal DNA expressions, Natural computing 5: 127-149.
- Engelfriet J. & Hoogeboom H.J. (2006), Nested Pebbles and Transitive Closure. Durand B. & Thomas W. (Eds.), STACS 2006, 23rd Annual Symposium on Theoretical Aspects of Computer Science. : Springer Verlag. 477-488.
- Hoogeboom H.J., Paun G., Rozenberg G. & Salomaa A. (Eds.) (2006), Membrane Computing, Seventh International Workshop, WMC7. Heidelberg-Berlin: Springer.
- Brijder R., Hoogeboom H.J. & Muskulus M. (2006), Strategies of Loop Recombination in Ciliates, LIACS Technical Report 2006-01: .
- Cavaliere M., Frisco P. & Hoogeboom H.J. (2006), Computing by Only Observing. Dang Z. & Ibarra O.H. (Eds.), Developments in Language Theory: 10th International Conference, DLT 2006. : Springer Verlag. 304-314.
- Brijder R., Hoogeboom H.J. & Rozenberg G. (2006), Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph, 356: 26-45.
- Brijder R., Hoogeboom H.J. & Muskulus M. (2006), Applicability of Loop Recombination in Ciliates using the Breakpoint Graph. Berthold M.R. & et al. (Eds.), CompLife 2006. . Lecture Notes in Computer Science: Springer Verlag. 97-106.
- Hoogeboom H.J. & Kosters W.A. (2005), The Theory of Tetris, Nieuwsbrief van de Nederlandse Vereniging voor Theoretische Informatica 9: 14-21.
- Hoogeboom H.J. (2005), Klein Duimpje, Eureka! : 18-19.
- Halava V., Harju T., Hoogeboom H.J. & Latteux M. (2005), Equality sets for recursively enumerable languages, RAIRO-INFORMATIQUE THEORIQUE ET APPLICATIONS-THEORETICAL INFORMATICS AND APPLICATIONS 39: 661-675.
- Vliet R. van, Hoogeboom H.J. & Rozenberg G. (2005), Combinatorial aspects of minimal DNA expressions. Feretti C., Mauri G. & Zandron C. (Eds.), 10th International meeting on DNA computing, DNA10, June 7-10, 2004, Milan, Italy -- Revised selected papers. International Conference on DNA Computing and Molecular Programming 7 June 2004 - 10 June 2004 no. LNCS 3384. Berlin, Heidelberg: Springer. 375-388.
- Brijder R., Hoogeboom H.J. & Rozenberg G. (2005), The Breakpoint Graph in Ciliates. Berthold M.R., Glen R.C., Diederichs K., Kohlbacher O. & Fischer I. (Eds.), CompLife 2005. . Lecture Notes in Computer Science: Springer Verlag. 128-139.
- Breukelaar R., Demaine E.D., Hohenberger S., Hoogeboom H.J., Kosters W.A. & Liben-Nowell D. (2004), Tetris is hard, even to approximate, International Journal of Computational Geometry & Applications 14(1-2): 41-68.
- Hoogeboom H.J. & Engelfriet J. (2004), Pushdown Automata. In: Martín-Vide C., Mitrana V. & Paun G. (Eds.), Formal Languages and Applications. Studies in Fuzziness and Soft Computing no. 148. Berlin: Springer. 117-138.
- Hoogeboom H.J. & Rozenberg G. (2004), DNA Computing - Computer in de Reageerbuis. In: Heesterbeek J.A.P., Diekmann O. & Metz J.A.J. (Eds.), De wiskundige kat, de biologische muis en de jacht op inzicht no. 55. Utrecht: Epsilon.
- Frisco P. & Hoogeboom H.J. (2004), P systems with symport/antiport simulating counter automata, Acta Informatica 41(2-3): 145-170.
- Hoogeboom H.J. & Kosters W.A. (2004), Tetris and Decidability, Information Processing Letters 89: 267-272.
- Halava V., Harju T., Hoogeboom H.J. & Latteux M. (2004), Valence Languages Generated by Equality Sets, Journal of Automata, Languages and Combinatorics 9: 339-406.
- Hoogeboom H.J. & Kosters W.A. (2004), How to Construct Tetris Configurations, International Journal of Intelligent Games and Simulation 3: 94-102.
- Hoogeboom H.J. (2003), Carriers and counters - P systems with carriers vs. (Blind) counter automata, DEVELOPMENTS IN LANGUAGE THEORY 2450: 140-151.
- Halava V., Harju T., Hoogeboom H.J. & Latteux M. (2003), Languages defined by generalized equality sets, FUNDAMENTALS OF COMPUTATION THEORY, PROCEEDINGS 2751: 355-363.
- Hoogeboom H.J. & Vugt N. van (2002), Upper Bounds for Restricted Splicing. In: Brauer W., Ehrig H., Karhumaki J. & Salomaa A. (Eds.), Formal and Natural Computing - Essays Dedicated to Grzegorz Rozenberg: Springer Verlag. 361-375.
- Frisco P., Hoogeboom H.J. & Sant P. van 't (2002), A Direct Construction of a Universal P, Fundamenta Informaticae 49: 103-122.
- Frisco P. & Hoogeboom H.J. (2002), Simulating counter automata by P systems with symport/antiport. Paun Gh. & Zandron C. (Eds.), Proc. of Second Workshop on Membrane Computing. .
- Hoogeboom H.J. (2002), Context-Free Valence Grammars - Revisited. Kuich W., Rozenberg G. & Salomaa A. (Eds.), Developments in Language Theory. 293-303.
- Hoogeboom H.J. (2002), Carriers and Counters: P systems with Carriers vs. (Blind) Counter Automata. Ito M. & Toyama M. (Eds.), Developements in Language Theory. 255-268.
- Hoogeboom H.J. & Vugt N. van (2000), Fair sticker languages, Acta Informatica 37(3): 213-225.
- Hoogeboom H.J. & Vugt N. van (1998), The power of H systems: does representation matter?. In: Paun G. (Ed.), Computing with bio-molecules. Singapore: Springer-Verlag. 255-268.
- Engelfriet J. & Hoogeboom H.J. (1998), MSO Definable String Transductions and Two-Way Finite State Transducers. onbekend: LIACS.
- Hoogeboom H.J. & Muscholl A. (1997), The code problem for traces - Improving the boundaries, Theoretical Computer Science 172(1-2): 309-321.
- Hoogeboom H.J. & Pas P. ten (1997), Monadic second-order definable text languages, Theory of Computing Systems 30(4): 335-354.
- Ehrenfeucht A., Hoogeboom H.J. & Rozenberg G. (1994), Combinatorial properties of dependence graphs, Information and Computation 114(2): 315-328.
- Engelfriet J. & Hoogeboom H.J. (1993), X-Automata on Omega-words, 110(1): 1-51.
- Ehrenfeucht A., Hoogeboom H.J. & Rozenberg G. (1993), On the structure of recognizable languages of dependence graphs, RAIRO-INFORMATIQUE THEORIQUE ET APPLICATIONS-THEORETICAL INFORMATICS AND APPLICATIONS 27(1): 7-22.
- Engelfriet J. & Hoogeboom H.J. (1989), Automata with storage on infinite words, Lecture Notes in Computer Science 372: 289-303.
- Hoogeboom H.J. & Aalbersberg IJ.J. (1989), Characterization of the decidability of some problems for regular trace languages, Mathematical Systems Theory 22(1): 1-19.
- Ehrenfeucht A., Hoogeboom H.J. & Rozenberg G. (1988), Recording the use of memory in right-boundary grammars and push-down automata, Acta Informatica 25(2): 203-231.
- Engelfriet J. & Hoogeboom H.J. (1988), Prefix and equality languages of rational functions are co-context-free, Information Processing Letters 28(2): 77-79.
- Ehrenfeucht A., Hoogeboom H.J. & Rozenberg G. (1986), On the active and full use of memory in right-boundary grammars and push-down automata, Theoretical Computer Science 48(2-3): 201-228.
- Ehrenfeucht A., Hoogeboom H.J. & Rozenberg G. (1986), Coordinated pair systems .1. Dyck works and classical pumping, RAIRO-INFORMATIQUE THEORIQUE ET APPLICATIONS-THEORETICAL INFORMATICS AND APPLICATIONS 20(4): 405-424.
- Hoogeboom H.J. & Rozenberg G. (1986), INFINITARY LANGUAGES - BASIC THEORY AND APPLICATIONS TO CONCURRENT SYSTEMS, 224: 266-342.
- Ehrenfeucht A., Hoogeboom H.J. & Rozenberg G. (1986), Coordinated pair systems .2. sparse structure of Dyck words and Ogdens lemma, RAIRO-INFORMATIQUE THEORIQUE ET APPLICATIONS-THEORETICAL INFORMATICS AND APPLICATIONS 20(4): 425-439.
- Ehrenfeucht A., Hoogeboom H.J. & Rozenberg G. (1985), On coordinated rewriting, FUNDAMENTALS OF COMPUTATION THEORY, PROCEEDINGS 199: 100-111.