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Click on a project in the table below for all publications registered to that project.
Project AFM2: Algorithms and Processes in Life Sciences
2009
- A. Zagaris, A. Doelman, N. N. Pham Thi, and B. P. Sommeijer, Blooming in a Nonlocal, Coupled Phytoplankton-Nutrient Model, SIAM J. Appl. Math. 69, 2009, 1174-1204.
- Acuña, V., Chierichetti, F., Lacroix, V., Marchetti Spaccamela, A., Sagot, M.F., Stougie, L. Modes and cuts in metabolic networks : complexity and algorithms. {\em BioSystems 95}, 2009, 51--60.
- L. van Iersel, J. Keijsper, S. Kelk, L. Stougie, F. Hagen and T. Boekhout. Constructing level-2 phylogenetic networks from triplets. In IEEE/ACM Trans. Comput. Biol. Bioinformatics, http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.22, 2009.
- L. van Iersel, S. Kelk and M. Mnich. Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks. In Journal of Bioinformatics and Computational Biology, 2009.
- J. Byrka, P. Gawrychowski, K. Huber, S. Kelk. Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, doi:10.1016/j.jda.2009.01.004, 2009.
- L. van Iersel and M. Mnich. Computing rooted and unrooted maximum consistent supertrees. arXiv:0901.3299v1, 2009.
- L. van Iersel. Algorithms, Haplotypes and phylogenetic networks. Ph.D. Thesis, Eindhoven University of Technology, January 29, 2009, 1st Supervisor L. Stougie, Co-supervisor J. Keijsper, 2nd Supervisor Gerhard Woeginger.
2008
- M. Ashyraliyev, J. Jaeger, J. G. Blom, (2008), Parameter Estimation And Determinability Analysis Applied To Drosophila Gap Gene Circuits, BMC Systems Biology, 2, 83.
- K. D. Joehnk, J. Huisman, J. Sharples, B. P. Sommeijer, P. M. Visser, J. M. Stroom, (2008), Summer Heatwaves Promote Blooms Of Harmful Cyanobacteria, Global Change Biology, 14, 3, 495-512.
- W. Koolen. Temporary unavailability logic and general modification logic. ILLC Prepublication Series, 2008.
- W.M. Koolen and S. de Rooij. Combining expert advice efficiently. CoRR, abs/0802.2015, Feb 2008.
- W.M. Koolen and S. de Rooij. Combining expert advice efficiently. In Rocco Servedio and Tong Zang, editors, Proceeding of the 21st Annual Conference on Learning Theory, pages 275-286, 2008.
- W.M. Koolen and S. de Rooij. Combining expert advice efficiently. In Anton Nijholt, Maja Pantic, Mannes Poel, and Hendri Hondorp, editors, Proceedings of the twentieth Belgian-Dutch Conference on Artificial Intelligence, pages 323-324, 2008.
- E.G. Daylight, W.M. Koolen, and P.M.B. Vitányi. On time-bounded incompressibility of compressible strings. CoRR, abs/0809.2965, 2008.
- E.G. Daylight, W.M. Koolen, and P.M.B. Vitányi. On time-bounded incompressibility of compressible strings. Preprint submitted to Elsevier, 2008.
- M. Ziegler and W.M. Koolen. Kolmogorov complexity theory over the reals. CoRR, abs/0802.2027, 2008.
- M. Ziegler and W.M. Koolen. Kolmogorov complexity theory over the reals. Electronic Notes in Theoretical Computer Science, 221:153-169, 2008.
- J. van den Berg, Y. Peres, V. Sidoravicius and M.E. Vares, Random spatial growth with paralyzing obstacles, {\em Ann.Inst. H. Poincaré (probab. and stat.)}, {\bf 44}, 1173--1187 (2008).
- J. van den Berg, Approximate zero-one laws and sharpness of the percolation transition in a class of models including 2D Ising percolation, {\it Ann. Probab.} {\bf 36}, 1880-1903 (2008).
- J. van den Berg, R. Brouwer and B. Vágvölgyi, Box-crossings and continuity results for self-destructive percolation in the plane, {\it In and out of equilibrium 2}, Series: Progress in probability vol. 60, V. Sidoravicius and M. Vares (Eds.), Birkhäuser, pp. 117--136 (2008).
- L. Cottret, P.V. Milreu, V. Acuna, A. Machetti Spaccamela, F. Viduani Martinez, M-F. Sagot, L. Stougie, Enumerating precursor sets of target metabolites in a metabolic network, In Proceedings of the 8th International Workshop on Algorithms in Bioinformatics (WABI), Karlsruhe,Germany, September 15--17, 2008,{\em Lecture Notes in Computer Science}, {\bf 5151}, Springer Verlag, Berlin, 2008, pp. 233--244.
- M. Ashyraliyev, J. G. Blom, J. G. Verwer, (2008), On The Numerical Solution Of Diffusion-Reaction Equations With Singular Source Terms, Journal of Computational and Applied Mathematics, 216, 1, 20 -- 38.
- L. van Iersel, J. Keijsper, S. Kelk, and L. Stougie. Shorelines of islands of tractability: Algorithms for parsimony and perfect phylogeny haplotyping problems. In IEEE/ACM Trans. Comput. Biol. Bioinformatics, 5(2), pp. 301-312, 2008.
- L. van Iersel, J. Keijsper, S. Kelk, L. Stougie, F. Hagen and T. Boekhout. Constructing level-2 phylogenetic networks from triplets. In Research in Computational Molecular Biology (RECOMB), Lecture Notes in Bioinformatics 4955, pp. 464-476, 2008.
- L. van Iersel and S. Kelk. Constructing the simplest possible phylogenetic network from triplets. In Proceedings of the 19th International Symposium on Algorithms and Computation (ISAAC 2008), LNCS 5369, pp. 472-483, 2008.
- L. van Iersel and S. Kelk, Constructing the simplest possible phylogenetic network from triplets. arXiv:0805.1859v2 [q-bio.PE], 2008.
2007
- Cor Hurkens, Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, and John Tromp. Prefix Reversals on Binary and Ternary Strings. In: Algebraic Biology (volume 4545, pages 292-306), July 2007
- Adriaans and P.M.B. Vitanyi. The power and perils of MDL. In: Proc. IEEE Intn'l Symp. Information Theory (ISIT) (pages 2216-2220), June 24-29, 2007, Nice, France
- Maciej Dobrzynski, Jordi Vidal Rodríguez, Jaap A. Kaandorp, and Joke G. Blom. Computational methods for diffusion-influenced biochemical reactions. In: Bioinformatics (volume 23, number 15, pages 1969-1977), 2007
- N. Chater, P. Vitanyi. `Ideal learning' of natural language: positive results about learning from positive evidence. In: Journal Mathematical Psychology, 2007 Note: To appear
- J. van den Berg, Y. Peres and, V. Sidoravicius, and M.E. Vares. Random spatial growth with paralyzing obstacles. 2007 Note: preprint at http://front.math.ucdavis.edu/0706.0219
- J. van den Berg. Approximate zero-one laws and sharpness of the percolation transition in a class of models including 2D Ising percolation. 2007 Note: preprint at http://front.math.ucdavis.edu/0707.2077
- J. Bruggeman, H. Burchard, B. Kooi, and B. Sommeijer. A second-order, unconditionally positive, mass-conserving integration scheme for biochemical systems. In: Applied Numerical Mathematics (volume 57, pages 36-58), 2007
- P.M.B. Vitanyi. Analysis of Sorting Algorithms by Kolmogorov Complexity (A Survey). In: Entropy, Search, Complexity: Bolyai Society Mathematical Studies (volume 16, pages 209-232), 2007
- Cor Hurkens, Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, and John Tromp. Prefix reversals on binary and ternary strings. In: SIAM Journal on Discrete Mathematics (volume 21, number 3, pages 592-611), 2007
- Yves Fomekong Nanfack, Jaap Kaandorp, and Joke Blom. Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster. In: accepted for publication in Bioinformatics, 2007
- R.L. Cilibrasi, P.M.B. Vitanyi. The Google Similarity Distance. In: IEEE Trans. Knowledge and Data Engineering (volume 19, number 3, pages 370-383), 2007
- Flavio Chierichetti, Vincent Lacroix, Alberto Marchetti-Spaccamela, Marie-France Sagot, and Leen Stougie. Modes and Cuts in Metabolic Networks: Complexity and Algorithms. (Technische Universiteit Eindhoven technical report SPOR-Report 2007-01), 2007
- B.P. Sommeijer and J.G. Verwer. On stabilized integration for time-dependent PDES. In: to appear in Journal of Computational Physics, 2007 Note: Report MAS-E0616, CWI, Amsterdam
- Leo van Iersel, Judith Keijsper, Steven Kelk, and Leen Stougie. Constructing level-2 phylogenetic networks from triplets. 2007 Note: preprint at http://arxiv.org/abs/0707.2890v1
- B.P. Sommeijer and J.G. Verwer. On stabilized integration for time-dependent PDEs. In: J. Comput. Phys. (volume 224, pages 3-16), 2007
- A. Zagaris, A. Doelman, N.N. Pham Thi, and B.P. Sommeijer. Blooming in a non-local, coupled phytoplankton-nutrient model. (CWI technical report MAS-E0708), 2007, Amsterdam, Note: submitted to SIAM. J. Appl. Math.
- K.D. Joehnk, J. Huisman, J. Sharples, B. Sommeijer, P.M. Visser, and J. Stroom. Summer heatwaves promote blooms of harmful cyanobacteria. In: to appear in: Global Change Biology, 2007
- Ming Li and Paul M.B. Vitanyi. Applications of Algorithmic Information Theory. In: Scholarpedia (pages 12407), Scholarpedia, 2007
- S. de Rooij, P. Vitanyi. Approximating rate-distortion graphs of individual data: Experiments in lossy compression and denoising. In: IEEE Trans. Inform. Th., 2007 Note: Submitted
- Leo van Iersel, Judith Keijsper, Steven Kelk, and Leen Stougie. Shorelines of islands of tractability: Algorithms for parsimony and perfect phylogeny haplotyping problems. In: IEEE/ACM Trans. Comput. Biol. Bioinformatics (volume to appear), 2007
- M. Ashyraliyev, J.G. Blom, and J.G. Verwer. On the Numerical Solution of Diffusion-Reaction Equations with Singular Source Terms. In: J. Comp. Appl. Math. (volume doi:10.1016/j.cam.2007.04.017), 2007
2006
- P. Vitanyi. Asshuku ni Motozuita Hanyou na ruijido sokuteihou. In: Surikagaku (volume 519, pages 54-59), September 2006 Note: Japanese, translated by O. Watanabe, English title: universal similarity based on compression
- L.F. Shampine, B.P. Sommeijer, and J.G. Verwer. IRKC: an IMEX Solver for Stiff Diffusion-Reaction PDEs. In: Journal of Apllied Mathematics (volume 196, pages 485-497), 2006
- N.K. Vereshchagin and P.M.B. Vitanyi. Algorithmic rate-distortion function. In: Proc. IEEE Intn'l Symp. Information Theory (ISIT) (pages 798-802), 2006, Seattle, Wash. USA
- C. Costa Santos, J. Bernardes, P.M.B. Vitanyi, and L. Antunes. Clustering fetal heart rate tracings by compression. In: Proc. 19th IEEE Symp. Computer-based Medical Systems (pages 685-690), 2006
- L. van Iersel, J. Keijsper, S. Kelk, and L. Stougie. Beaches of Islands of tractability: Algorithms for parsimony and minimum perfect phylogeny haplotyping problems. In: In Proceedings of the 6th International Workshop on Algorithms in Bioinformatics (WABI) (volume 4175, pages 80-91), Lecture Notes in Computer Science, Springer Verlag, Zürich, Switzerland, 2006
- J. Huisman, N.N. Pham Thi, D.M. Karl, and B.P. Sommeijer. Reduced mixing generates oscillations and chaos in the oceanic deep chlorophyll maximum. In: Nature (volume 439, pages 322-325), 2006
- S. de Rooij and P. Vitanyi. Approximating rate-distortion graphs of individual data: Experiments in lossy compression and denoising. In: IEEE Trans. Inform. Th., 2006 Note: Submitted
- P. Vitanyi. Meaningful information. In: IEEE Trans. Inform. Th. (volume 52, number 10, pages 4617 - 4626), 2006
- J. van den Berg, Olle Haggstrom, and J. Kahn. Proof of a conjecture of N. Konno for the 1D contact process. In: Dynamic and stochastics, Festschrift in honor of M.S. Keane (volume 48, pages 16-23), 2006
- Margaret A. Beck, Arjen Doelman, and Tasso J. Kaper. A geometric construction of traveling waves in a bioremediation model. In: Journal of Nonlinear Science (volume 16, number 4, pages 329-349), 2006 Note: Based on TR MAS-E0519
- R.L. Cilibrasi and P.M.B. Vitanyi. The Google Similarity Distance. In: IEEE Trans. Knowledge and Data Engineering, 2006 Note: To appear
- R. Cilibrasi and P.M.B. Vitanyi. Automatic extraction of meaning from the Web. In: Proc. IEEE Intn'l Symp. Information Theory (ISIT) (pages 2309-2313), 2006, Seattle, Wash. USA
- R. Cilibrasi and P.M.B. Vitanyi. Similarity of objects and the meaning of words. In: Proc. 3rd Conf. Theory and Applications of Models of Computation (tamc) (Edited by J.-Y. Cai, S. B. Cooper, and and A. Li) (volume 3959, pages 21-45), Lecture notes in computer science, Springer-Verlag, Berlin, 2006
- R. Cilibrasi, L. van Iersel, S. Kelk, and J. Tromp. On the complexity of the single individual SNP haplotyping problem. In: Algorithmica, 2006
- Jordi Vidal Rodríguez, Jaap A. Kaandorp, Maciej Dobrzynski, and Joke G. Blom. Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. In: Bioinformatics (volume 22, number 15, pages 1895-1901), 2006
- C. Hurkens, L. van Iersel, J. Keijsper, S. Kelk, L. Stougie, and J. Tromp. Prefix reversals on binary and ternary strings. (Technische Universiteit Eindhoven technical report SPOR-Report 2006-10), 2006
- J. van den Berg and R. Brouwer. Self-organized forest-fires near the critical time. In: Communications of Mathematical Physics (volume 67, pages 265-277), 2006
2005
- J. van den Berg, O. Häggström, and J. Kahn. Some conditional correlation inequalities for percolation and related processes. In: Random Structures and Algorithms, December 12, 2005 Note: published online, DOI: 10.1002/rsa.20102
- P.M.B. Vitanyi. Universal Similarity. In: Proceedings ITW2005 - IEEE ITSOC Information Theory Workshop 2005 on Coding and Complexity, August 29 - September 1, 2005, Rotorua, New Zealand
- van de Wiel, Mark A., Smeets, Serge J., Brakenhoff, Ruud H., and Ylstra, Bauke. CGHMultiArray: exact P-values for multi-array comparative genomic hybridization data. In: Bioinformatics (volume 21, number 14, pages 3193-3194), July 2005
- R. Cilibrasi, P.M.B. Vitanyi. A New Quartet Tree Heuristic for Hierarchical Clustering. In: EU-PASCAL Statistics and Optimization of Clustering Workshop, July 5-6, 2005, London, UK
- P.M.B. Vitanyi. Algorithmic statistics and Kolmogorov's Structure Functions. In: Advances in Minimum Description Length: Theory and Applications (Edited by P.D. Grunwald, I.J. Myung, and M.A. Pitt) (pages 151-174), MIT Press, 2005
- R. Cilibrasi and P.M.B. Vitanyi. Clustering by compression. In: IEEE Trans. Information Theory (volume 51, number 4, pages 1523-1545), 2005 Note: Also: http://xxx.lanl.gov/abs/cs.CV/031204 (2003).
- R. Cilibrasi and P.M.B. Vitanyi. Automatic meaning discovery using Google. e-print. 2005
- P.D. Grunwald and P.M.B. Vitanyi. Shannon Information and Kolmogorov complexity. In: IEEE Trans. Information Theory, Submitted, 2005
- M.A. van de Wiel, J.L. Costa, K. Smid, C.B.M. Oudejans, A.M. Bergman, G.A. Meijer, G.J. Peters, and B. Ylstra. Expression microarray analysis and oligo array CGH of acquired gemcitabine resistance in mouse colon reveals selection for chromosomal aberrations. In: Cancer research (volume 65, pages 10208-10213), 2005
- Joke Blom and Annette Kik. Modelling a Living Cell - Mathematics to Model Metabolic Pathways. In: ERCIM News (volume 60), 2005
- T.Roos, T.Heikki, R.Cilibrasi, and P.Myllymaki. Compression-based Stemmatology: A Study of the Legend of St. Henry of Finland. (Helsinki Institute for Information Technology (HIIT) technical report HIIT-2005-3), 2005
- L.F. Shampine, B.P. Sommeijer, and J.G. Verwer. IRKC: an IMEX Solver for Stiff Diffusion-Reaction PDEs. (CWI technical report MAS-E0513), 2005 Note: to appear in J. Comput. Applied Math
- J. van den Berg, O. Häggström, and J. Kahn. Proof of a conjecture of N. Konno for the 1D contact process. to appear in Festschrift for Mike Keane. 2005
- Rudi Cilibrasi, Leo van Iersel, Steven Kelk, and John Tromp. On the Complexity of Several Haplotyping Problems. In: Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings (Edited by Rita Casadio and Gene Myers) (volume 3692, pages 128-139), Lecture Notes in Computer Science, Springer, 2005
- N.N. Pham Thi, J. Huisman, B.P. Sommeijer. Simulation of 3D phytoplankton dynamics: competition in light-limited environments. In: J. Comput. Appl. Math. (volume 174, pages 57-77), 2005
- M. Ashyraliyev, J.G. Blom, and J.G. Verwer. On the Numerical Solution of Diffusion-Reaction Equations with Singular Source Terms. (CWI technical report MAS-E0512), 2005
- Margaret A. Beck, Arjen Doelman, and Tasso J. Kaper. A geometric construction of traveling waves in a bioremediation model. (CWI technical report MAS-E0519), 2005 Note: to appear in the Journal of Nonlinear Science
- J. van den Berg and A. Jarai. On the asymptotic density in a one-dimensional critical forest-fire model. In: Comm. Math. Phys. (volume 253, pages 633-644), 2005
- N.N. Pham Thi, W. Hundsdorfer, and B.P. Sommeijer. Positivity for explicit two-step methods in linear multistep and one-leg form. (CWI technical report MAS-E0522), 2005
2004
- N.J. Armstrong and M.A. van de Wiel. Microarray data analysis: from hypotheses to conclusions using gene expression data. In: Cellular Oncology (volume 26, pages 279-290), 2004
- J. Huisman, J. Sharples, J. Stroom, P.M. Visser, W.E.A. Kardinaal, J.M.H. Verspagen, and B.P. Sommeijer. Changes in turbulent mixing shift competition for light between phytoplankton species. In: Ecology (volume 85, pages 2960-2970), 2004
- Nikolai K. Vereshchagin and Paul M.B. Vitanyi. Kolmogorov's Structure functions and model selection. In: IEEE Transactions on Information Theory (volume 50, number 12, pages 3265-3290), 2004
- Uri Keich, Ming Li, Bin Ma, and John Tromp. Computing optimally spaced seeds. In: Discrete Applied Mathematics (volume 138, number 3, pages 253-263), 2004
- R. Cilibrasi, R. de Wolf, and P.M.B. Vitanyi. Algorithmic Clustering of Music. In: Computer Music Journal (volume 28, number 4, pages 49-67), 2004
- P.D. Grunwald and P.M.B. Vitanyi. Shannon information and Kolmogorov complexity. Computing Research Repository Archive: http://de.arxiv.org/abs/cs.IT/0410002. 2004
- Ming Li, Bin Ma, Derek Kisman, and John Tromp. PatternHunter II: Highly Sensitive and Fast Homology Search. In: Journal of Bioinformatics and Computational Biology (volume 2, number 3, pages 417-439), 2004
- J.G. Verwer, B.P. Sommeijer, and W. Hundsdorfer. RKC time-stepping for advection-diffusion-reaction problems. In: J. Comput. Phys. (volume 201, pages 61-79), 2004
- K. Johnk, J. Huisman, J. Sharples, B.P. Sommeijer, P.M. Visser, and J. Stroom. Summer heatwaves promote blooms of harmful cyanobacteria. 2004 Note: Submitted
- Ming Li, Xin Chen, Xin Li, Bin Ma, and Paul Vitanyi. The similarity metric. In: IEEE Transactions on Information Theory (volume 50, number 12, pages 3250-3264), 2004
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