Publications of the CSL group

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2011

• Article
  H. Tahir, A. G. Hoekstra, E. Lorenz, P. V. Lawford, D. R. Hose, J. Gunn, and D. J. W. Evans. Multi-scale simulations of the dynamics of in-stent restenosis: impact of stent deployment and design. Interface Focus 1(3), pp. 365-373.
  Abstract Citation Links
• PhD Thesis
  L. A. Naumov. Modelling with cellular automata: problem solving environments and multidimensional applications. ISBN 9789057762253. Supervised by P. M. A. Sloot and A. G. Hoekstra.
  Abstract Citation Links
• Article
  C. Tamulonis, M. Postma, and J. Kaandorp. Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure. PLoS ONE 6(7).
  Abstract Citation Links
• Article
  A. L. Pyayt, I. I. Mokhov, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer. Machine learning methods for environmental monitoring and flood protection. World Academy of Science, Engineering and Technology. Proceedings 78, pp. 118-123.
  Abstract Citation Links
• Proceedings
  A. L. Pyayt, I. I. Mokhov, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer. Machine Learning Methods for Environmental Monitoring and Flood Protection. World Academy of Science, Engineering and Technology 78, pp. 118-123.
  Citation Links
• Article
  A. Mei Shan, R. Quax, D. van de Vijver, Y. Zhu, and P. M. A. Sloot. Increasing risk behaviour can outweigh the benefits of antiretroviral drug treatment on the HIV incidence among men-having-sex-with-men in Amsterdam. BMC Infectious Diseases 11(118).
  Abstract Citation Links
• Proceedings
  M. Gerhards, V. Sander, A. Belloum, D. Vasunin, and A. Benabdelkader. HisT/PLIER: A two-fold Provenance Approach for Grid-enabled Scientific Workflows using WS-VLAM. In: 2011 12th IEEE/ACM International Conference on Grid Computing : Grid 2011. ISBN 9780769545721, 9780769545726. pp. 224-225.
  Abstract Citation Links
• Article
  E. Lorenz and A. G. Hoekstra. Heterogeneous multiscale simulations of suspension flow. Multiscale Modeling & Simulation 9(4), pp. 1301-1326.
  Abstract Citation Links
• Article
  C. A. D. Leguy, E. M. H. Bosboom, A. S. Z. Belloum, A. P. G. Hoeks, and F. N. van de Vosse. Global sensitivity analysis of a wave propagation model for arm arteries. Medical Engineering & Physics 33(8), pp. 1008-1016.
  Abstract Citation Links
• Proceedings
  B. Pengel, G. S. Shirshov, V. V. Krzhizhanovskaya, A. R. Koelewijn, I. I. Mokhov, A. L. Pyayt, and N. B. Melnikova. Flood early warning system: sensors and internet. In: Abstract proceedings: 5th International CConference on Flood Management (ICFM5): Floods: from Risk to Opportunity: 27 to 29 September 2011, Tokyo-Japan. pp. 212-221.
  Citation Links
• Article
  V. V. Krzhizhanovskaya, G. S. Shirshov, N. B. Melnikova, R. G. Belleman, F. I. Rusadi, B. J. Broekhuijsen, B. P. Gouldby, J. Lhomme, B. Balis, M. Bubak, A. L. Pyayt, I. I. Mokhov, A. V. Ozhigin, B. Lang, and R. J. Meijer. Flood early warning system: design, implementation and computational modules. Procedia Computer Science 4, pp. 106-115.
  Abstract Citation Links
• Proceedings
  P. Ramos-Silva, C. Combet, F. Marin, and J. A. Kaandorp. Finding patterns and differences on biomineralization-related proteins from Metazoans. In: Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application. ISBN 9788890580505. p. 21.
  Citation Links
• Proceedings
  Q. C. Bui and P. M. A. Sloot. Extracting biological events from text using simple syntactic patterns. In: Proceedings of BioNLP Shared Task 2011 Workshop: Portland, Oregon, USA, 24 June, 2011. ISBN 9781937284091. pp. 143-146.
  Abstract Citation Links
• MSc Thesis
  J. Jänes. Efficient integration of multiscale N-body systems. Supervised by F. I. Pelupessy and S. F. Portegies Zwart.
  Citation Links
• Proceedings
  R. Cushing, S. Koulouzis, A. Belloum, and M. Bubak. Dynamic handling for cooperating scientific web services. In: Proceedings 2011 IEEE Seventh International Conference on eScience: 5-8 December 2011, Stockholm, Sweden. ISBN 9780769545974. pp. 232-239.
  Abstract Citation Links
• Other: misc
  M. C. F. Prosperi, M. Rosen-Zvi, A. Altmann, M. Zazzi, S. Di Giambenedetto, R. Kaiser, E. Schülter, D. Struck, P. M. A. Sloot, D. A. M. C. van de Vijver, A.-M. Vandamme, and A. Sönnerborg. Correction: Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models. PLoS ONE 6(4).
  Citation Links
• Article
  M. C. F. Prosperi, M. Rosen-Zvi, A. Altmann, M. Zazzi, S. Di Giambenedetto, R. Kaiser, E. Schülter, D. Struck, P. Sloot, D. A. van de Vijver, A.-M. Vandamme, and A. Sönnerborg. Correction: Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models. PLoS ONE 6(4).
  Citation Links
• MSc Thesis
  H. Þorsdottir. Conservation Properties of the Hamiltonian Particle-Mesh method for the Quasi-Geostrophic Equations on a sphere. Supervised by J. Frank.
  Citation Links
• PhD Thesis
  İ. Altıntaş. Collaborative provenance for workflow-driven science and engineering. ISBN 9789090259796. Supervised by P. M. A. Sloot and B. Ludäscher.
  Abstract Citation Links
• Article
  A. Belloum, M. A. Inda, D. Vasunin, V. Korkhov, Z. Zhao, H. Rauwerda, T. M. Breit, M. Bubak, and L. O. Hertzberger. Collaborative e-Science Experiments and Scientific Workflows. IEEE Internet Computing 15(4), pp. 39-47.
  Abstract Citation Links
• Article
  S. Murtaza, A. G. Hoekstra, and P. M. A. Sloot. Cellular automata simulations on a FPGA cluster. International Journal of High Performance Computing Applications 25(2), pp. 193-204.
  Abstract Citation Links
• Article
  L. Naumov, A. Hoekstra, and P. Sloot. Cellular automata models of tumour natural shrinkage. Physica A : Statistical Mechanics and its Applications 390(12), pp. 2283-2290.
  Abstract Citation Links
• Article
  V. V. Krzhizhanovskaya. Better Flood Protection thanks to SARA's HPC Cloud. "High Performance Computing E-Science Support", SARA Annual Report 2010 pp. 39-39.
  Citation Links
• Proceedings
  A. L. Pyayt, I. I. Mokhov, A. Kozionov, V. Kusherbaeva, N. B. Melnikova, V. V. Krzhizhanovskaya, and R. J. Meijer. Artificial intelligence and finite element modelling for monitoring flood defence structures. In: EESMS 2011 proceedings . ISBN 9781457706080.
  Abstract Citation Links
• Proceedings
  A. L. Pyayt, I. I. Mokhov, A. Kozionov, V. Kusherbaeva, N. B. Melnikova, V. V. Krzhizhanovskaya, and R. J. Meijer. Artificial Intelligence and Finite Element Modelling for Monitoring Flood Defence Structures.
  Citation Links
• Proceedings
  D. Botman and J. A. Kaandorp. An integrated approach to infer the gene network in early development of the cnidarian Nematostella vectensis..
  Citation Links
• Proceedings
  F. Berretz, S. Skorupa, V. Sander, A. Belloum, and M. Bubak. Actor-driven workflow execution in distributed environments. In: Euro-Par 2010 Parallel Processing Workshops. ISBN 9783642218781. pp. 287-294.
  Abstract Citation Links
• Proceedings
  J. A. Kaandorp, C. Cronemberger, and L. Huisman. A spatial model of calcification in scleractinian corals. In: Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application. ISBN 9788890580505. p. 14.
  Abstract Citation Links
• Article
  A. Bankhead, E. Mancini, A. C. Sims, R. S. Baric, S. McWeeney, and P. M. A. Sloot. A simulation framework to investigate in vitro viral infection dynamics. Procedia Computer Science 4, pp. 1798-1807.
  Abstract Citation Links
• Proceedings
  J. Borgdorff, J.-L. Falcone, E. Lorenz, B. Chopard, and A. G. Hoekstra. A principled approach to distributed multiscale computing, from formalization to execution. In: Workshop Proceedings, 7th IEEE International Conference on eScience. ISBN 9781467300261. pp. 97-104.
  Abstract Citation Links
• PhD Thesis
  G. Ertaylan. A multi-scale approach for deciphering HIV infection. Supervised by P. M. A. Sloot.
  Abstract Citation Links
• Article
  Q. C. Bui, S. Katrenko, and P. M. A. Sloot. A hybrid approach to extract protein-protein interactions. Bioinformatics 27(2), pp. 259-265.
  Abstract Citation Links
• Proceedings
  B. Chopard, J.-L. Falcone, A. G. Hoekstra, and J. Borgdorff. A framework for multiscale and multiscience modeling and numerical simulations. In: Unconventional Computation. ISBN 9783642213410. pp. 2-8.
  Abstract Citation Links
• Article
  I. Altintas, M. K. Anand, T. N. Vuong, S. Bowers, B. Ludäscher, and P. M. A. Sloot. A data model for analyzing user collaborations in workflow-driven e-Science. The International Journal of Computers and Their Applications (IJCA) 18(3), pp. 160-179.
  Abstract Citation Links
• Article
  C. Tamulonis, M. Postma, H. Q. Marlow, C. R. Magie, J. de Jong, and J. Kaandorp. A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering. Developmental Biology 351(1), pp. 217-228.
  Abstract Citation Links
• Proceedings
  N. Javaheri, C. M. Cronemberger, and J. Kaandorp. A Particle-Based Model for Aggregate Formation in Biomineralization. In: Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application. ISBN 9788890580505. p. 23.
  Citation Links
• Article
  I. Altintas, M. K. Anand, T. Vuong, S. Bowers, B. Ludäscher, and P. M. A. Sloot. A Data Model for Analyzing User Collaborations in Workflow-Driven eScience. The International Journal of Computers and Their Applications (IJCA) 18(3), pp. 160-179.
  Citation Links
• Article
  A. Caiazzo, D. Evans, J.-L. Falcone, J. Hegewald, E. Lorenz, B. Stahl, D. Wang, J. Bernsdorf, B. Chopard, J. Gunn, R. Hose, M. Krafczyk, P. Lawford, R. Smallwood, D. Walker, and A. Hoekstra. A Complex Automata approach for in-stent restenosis: two-dimensional multiscale modelling and simulations. Journal of Computational Science 2(1), pp. 9-17.
  Abstract Citation Links

2010

• Article
  R. G. Belleman. Visualization in computational science. Procedia Computer Science 1(1), pp. 1689-1690.
  Abstract Citation Links
• Proceedings
  A. Lunzer, R. Belleman, P. Melis, J. Pukacki, P. Spychala, and G. Stamatakos. Validating the ACGT Oncosimulator with a Grid-Supported Visualisation Environment. In: 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation.
  Abstract Citation Links
• Proceedings
  I. Altintas, M. K. Anand, D. Crawl, S. Bowers, A. Belloum, P. Missier, B. Ludäscher, C. A. Goble, and P. M. A. Sloot. Understanding collaborative studies through interoperable workflow provenance. In: Provenance and Annotation of Data and Processes. ISBN 9783642178191. pp. 42-58.
  Abstract Citation Links
• Proceedings
  A. G. Hoekstra and P. Coveney. Towards distributed multiscale computing for the VPH. In: Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference. pp. 198-200.
  Abstract Citation Links
• Proceedings
  F. Berretz, S. Skorupa, V. Sander, and A. Belloum. Towards an actor-driven workflow management system for Grids. In: The 2010 International Symposium on Collaborative Technologies and Systems : CTS 2010. ISBN 9781424466191. pp. 611-616.
  Abstract Citation Links
• Article
  D. Groen, S. Harfst, and S. Portegies Zwart. The living application: A self-organizing system for complex grid tasks. International Journal of High Performance Computing Applications 24(2), pp. 185-193.
  Abstract Citation Links
• Article
  L. Naumov, A. Hoekstra, and P. Sloot. The influence of mitoses rate on growth dynamics of a cellular automata model of tumour growth. Procedia Computer Science 1(1), pp. 971-978.
  Abstract Citation Links
• Article
  P. M. A. Sloot. The cross-disciplinary road to true computational science. Journal of Computational Science 1(3), p. 131.
  Citation Links
• Proceedings
  G. Stamatakos, D. Dionysiou, E. Georgiadi, E. Kolokotroni, S. Giatili, A. Hoppe, C. Desmedt, A. Lunzer, M. Erdt, J. Jacques, J. Pukacki, R. Belleman, P. Melis, A. d'Onofrio, F. M. Buffa, B. Claerhout, S. Rueping, K. Marias, M. Tsiknakis, and N. Graf. The ACGT Oncosimulator: from conceptualization to development via multiscale cancer modeling. In: 4th International Advanced Research Workshop on In Silico Oncology and Cancer Investigation - The ContraCancrum Workshop. pp. 54-57.
  Abstract Citation Links
• Article
  V. Krzhizhanovskaya. Simulation of Multiphysics Multiscale Systems, 7th International Workshop. Procedia Computer Science 1(1), pp. 603-605.
  Abstract Citation Links
• Article
  S. Portegies Zwart, T. Ishiyama, D. Groen, K. Nitadori, J. Makino, C. de Laat, S. McMillan, K. Hiraki, S. Harfst, and P. Grosso. Simulating the universe on an intercontinental grid. Computer 43(8), pp. 63-70.
  Abstract Citation Links
• Book
  A. G. Hoekstra, J. Kroc, and P. M. A. Sloot. Simulating complex systems by cellular automata. ISBN 9783642122033.
  Abstract Citation Links
• Chapter
  J. Cui, J. A. Kaandorp, P. M. A. Sloot, and P. S. Thiagarajan. Simulating Calcineurin-Centered Calcium Signaling Network in Cardiac Myocytes. In: Congestive heart failure: symptoms, causes and treatment. ISBN 9781608766772. pp. 111-127.
  Citation Links
• Article
  P. R. Frade, M. C. Reyes-Nivia, J. Faria, J. A. Kaandorp, P. C. Luttikhuizen, and R. P. M. Bak. Semi-permeable species boundaries in the coral genus Madracis: Introgression in a brooding coral system. Molecular Phylogenetics and Evolution 57(3), pp. 1072-1090.
  Abstract Citation Links
• Article
  S. Mei, D. van de Vijver, L. Xuan, Y. Zhu, and P. M. A. Sloot. Quantitatively evaluating interventions in the influenza A (H1N1) epidemic on China campus grounded on individual-based simulations. Procedia Computer Science 1(1), pp. 1675-1682.
  Abstract Citation Links
• Article
  G. J. Streekstra, J. G. G. Dobbe, and A. G. Hoekstra. Quantification of the fraction poorly deformable red blood cells using ektacytometry. Optics Express 18(13), pp. 14173-14182.
  Abstract Citation Links
• Proceedings
  A. Lunzer, R. Belleman, P. Melis, and G. Stamatakos. Preparing, exploring and comparing cancer simulation results within a large parameter space. In: 14th International Conference Information Visualisation. ISBN 9780769541655. pp. 258-264.
  Abstract Citation Links
• Article
  P. M. A. Sloot, G. D. van Albada, and J. Dongarra. Preface. Procedia Computer Science 1(1), pp. 1-2.
  Citation Links
• Proceedings
  A. G. Hoekstra, J. Kroc, and P. M. A. Sloot. Preface. In: Simulating Complex Systems by Cellular Automata. ISBN 9783642122033. pp. xi-xiii.
  Citation Links
• Article
  U. Schwiegelshohn, R. M. Badia, M. T. Bubak, M. Danelutto, S. Dustdar, F. Gagliardi, A. Geiger, L. Hluchy, D. Kranzlmüller, E. Laure, T. Priol, A. Reinefeld, M. Resch, A. Reuter, O. Rienhoff, T. Rüter, P. Sloot, D. Talia, K. Ullmann, R. Yahyapour, and G. von Voigt. Perspectives on grid computing. Future Generation Computer Systems 26(8), pp. 1104-1115.
  Abstract Citation Links
• Article
  E. van der Pol, A. G. Hoekstra, A. Sturk, C. Otto, T. G. van Leeuwen, and R. Nieuwland. Optical and non-optical methods for detection and characterization of microparticles and exosomes. Journal of Thrombosis and Haemostasis 8(12), pp. 2596-2607.
  Abstract Citation Links
• Proceedings
  B. P. Gouldby, V. V. Krzhizhanovskaya, and J. Simm. Multiscale modelling in real-time flood forecasting systems: From sand grain to dike failure and inundation. In: ICCS 2010. Procedia Computer Science 1(1), pp. 809 - 809.
  Abstract Citation Links
• Article
  B. Gouldby, V. Krzhizhanovskaya, and J. Simm. Multiscale modelling in real-time flood forecasting systems: From sand grain to dike failure and inundation. Procedia Computer Science 1(1), p. 809.
  Citation Links
• Proceedings
  A. G. Hoekstra. Multiscale coupling of a Lattice Boltzmann simulation of blood flow to cell- and tissue-level processes: the case of in-stent restenosis. In: Proceedings of the V European Conference on Computational Fluid Dynamics (ECCOMAS CFD 2010), Lisbon, Portugal.
  Abstract Citation Links
• Proceedings
  V. Krzhizhanovskaya, D. Ivanov, Y. Gorbachev, and A. Smirnov. Multiphysics multi-model simulation of large-area plasma chemical reactors. In: Proceedings of the ASME 2009 International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE 2009), San Diego, CA, USA: Volume 2: 29th Computers and Information in Engineering Conference. ISBN 9780791848999. pp. 1195-1196 (DETC2009-87039).
  Abstract Citation Links
• PhD Thesis
  E. Lorenz. Multi-scale simulations with complex automata: in-stent restenosis and suspension flow. Supervised by P. M. A. Sloot and A. G. Hoekstra.
  Citation Links
• Article
  P. M. A. Sloot and A. G. Hoekstra. Multi-scale modelling in computational biomedicine. Briefings in Bioinformatics 11(1), pp. 142-152.
  Abstract Citation Links
• Proceedings
  A. G. Hoekstra, P. Lawford, and R. Hose. Modelling and simulating in-stent restenosis with complex automata. In: Conference abstracts VPH 2010, 1st Virtual Physiological Human Conference. pp. 222-224.
  Abstract Citation Links
• Article
  G. Qiu, D. Kandhai, and P. M. A. Sloot. Modeling options markets by focusing on active tradersr. Procedia Computer Science 1(1), pp. 2457-2462.
  Abstract Citation Links
• Article
  N. Zarrabi, E. Mancini, J. Tay, S. Shahand, and P. M. A. Sloot. Modeling HIV-1 intracellular replication: two simulation approaches. Procedia Computer Science 1(1), pp. 555-564.
  Abstract Citation Links
• Article
  A. Hoekstra, L.-S. Luo, and M. Krafczyk. Mesoscopic methods in engineering and science. Computers & Mathematics with Applications 59(7), pp. 2139-2140.
  Citation Links
• Article
  J.-L. Falcone, B. Chopard, and A. Hoekstra. MML: towards a Multiscale Modeling Language. Procedia Computer Science 1(1), pp. 819-826.
  Abstract Citation Links
• Chapter
  J. L. Guisado, F. Jiménez-Morales, J. M. Guerra, F. Fernández de Vega, K. A. Iskra, P. M. A. Sloot, and D. Lombraña González. Laser dynamics modelling and simulation: An application of dynamic load balancing of parallel cellular automata. In: Parallel and Distributed Computational Intelligence. ISBN 9783642106750. pp. 321-347.
  Abstract Citation Links
• Chapter
  A. G. Hoekstra, J. Kroc, and P. M. A. Sloot. Introduction to modeling of complex systems using cellular automata. In: Simulating complex systems by cellular automata. ISBN 9783642122033. pp. 1-16.
  Abstract Citation Links
• Book
  P. M. A. Sloot, G. D. van Albada, and J. Dongarra. International Conference on Computational Science, ICCS 2010.
  Citation Links
• Article
  S. Jaeger, G. Ertaylan, D. van Dijk, U. Leser, and P. Sloot. Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PLoS ONE 5(10), p. e13139.
  Abstract Citation Links
• Article
  D. van Dijk, P. M. A. Sloot, J. C. Tay, and M. C. Schut. Individual-based simulation of sexual selection: A quantitative genetic approach. Procedia Computer Science 1(1), pp. 2003-2011.
  Abstract Citation Links
• Article
  D. van Dijk, G. Ertaylan, C. A. B. Boucher, and P. M. A. Sloot. Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks. BMC Systems Biology 4, p. 96.
  Abstract Citation Links
• PhD Thesis
  S. Murtaza. High performance reconfigurable computing with cellular automata. Supervised by P. M. A. Sloot and A. G. Hoekstra.
  Citation Links
• PhD Thesis
  D. J. Groen. High performance N-body simulation on computational grids. Supervised by S. F. Portegies Zwart, P. M. A. Sloot, and E. P. J. van den Heuvel.
  Abstract Citation Links
• PhD Thesis
  Y. Fomekong Nanfack. Genetic regulatory networks inference : modeling, parameters estimation & model validation. Supervised by P. M. A. Sloot and J. A. Kaandorp.
  Citation Links
• Article
  Q. C. Bui, B. Ó Nualláin, C. A. Boucher, and P. M. A. Sloot. Extracting causal relations on HIV drug resistance from literature. BMC Bioinformatics 11, p. 101.
  Abstract Citation Links
• Article
  E. Zudilova-Seinstra, B. van Schooten, A. Suinesiaputra, R. van der Geest, B. van Dijk, J. Reiber, and P. Sloot. Exploring individual user differences in the 2D/3D interaction with medical image data. Virtual Reality 14(2), pp. 105-118.
  Abstract Citation Links
• Article
  A. Sottoriva, P. M. A. Sloot, J. P. Medema, and L. Vermeulen. Exploring cancer stem cell niche directed tumor growth. Cell Cycle 9(8), pp. 1472-1479.
  Abstract Citation Links
• Article
  E. V. Zudilova-Seinstra, P. J. H. de Koning, A. Suinesiaputra, B. W. van Schooten, R. J. van der Geest, J. H. C. Reiber, and P. M. A. Sloot. Evaluation of 2D and 3D glove input applied to medical image analysis. International Journal of Human-Computer Studies 68(6), pp. 355-369.
  Abstract Citation Links
• Book
  J. A. Kaandorp, E. Meesters, R. Osinga, J. Verreth, and T. Wijgerde. Euro ISRS symposium 2010: reefs in a changing environment: book of abstracts.
  Citation Links
• Article
  S. Koulouzis, E. Zudilova-Seinstra, and A. Belloum. Data transport between visualization web services for medical image analysis. Procedia Computer Science 1(1), pp. 1721-1730.
  Abstract Citation Links
• Proceedings
  D. Ivanov, I. Marinov, Y. Gorbachev, A. Smirnov, and V. Krzhizhanovskaya. Computer simulation of laser annealing of a nanostructured surface. In: Proceedings of the ASME 2009 International Design Engineering Technical Conferences & Computers and Information in Engineering Conference (IDETC/CIE 2009), San Diego, CA, USA: Volume 2: 29th Computers and Information in Engineering Conference. ISBN 9780791848999. pp. 1197-1198 (DETC2009-87087).
  Abstract Citation Links
• Article
  P. M. A. Sloot. Computational science: A kaleidoscopic view into science. Journal of Computational Science 1(4), p. 189.
  Citation Links
• Article
  S. Mei, P. M. A. Sloot, R. Quax, Y. Zhu, and W. Wang. Complex agent networks explaining the HIV epidemic among homosexual men in Amsterdam. Mathematics and Computers in Simulation 80(5), pp. 1018-1030.
  Abstract Citation Links
• Chapter
  A. G. Hoekstra, A. Caiazzo, E. Lorenz, J.-L. Falcone, and B. Chopard. Complex Automata: Multi-scale Modeling with Coupled Cellular Automata. In: Simulating complex systems by cellular automata. ISBN 9783642122026. pp. 29-57.
  Abstract Citation Links
• Article
  D. Frentz, C. A. B. Boucher, M. Assel, A. De Luca, M. Fabbiani, F. Incardona, P. Libin, N. Manca, V. Müller, B. Ó Nualláin, R. Paredes, M. Prosperi, E. Quiros-Roldan, L. Ruiz, P. M. A. Sloot, C. Torti, A.-M. Vandamme, K. Van Laethem, M. Zazzi, and D. A. M. C. van de Vijver. Comparison of HIV-1 genotypic resistance test interpretation systems in predicting virological outcomes over time. PLoS ONE 5(7), p. e11505.
  Abstract Citation Links
• Article
  A. Sottoriva, J. J. C. Verhoeff, T. Borovski, S. K. McWeeney, L. Naumov, J. P. Medema, P. M. A. Sloot, and L. Vermeulen. Cancer stem cell tumor model reveals invasive morphology and increased phenotypical heterogeneity. Cancer Research 70(1), pp. 46-56.
  Abstract Citation Links
• MSc Thesis
  T. Wood. Applications of GPUs in Computational Finance. Supervised by R. G. Belleman and B. D. Kandhai.
  Citation Links
• Article
  M. A. Yurkin, M. Min, and A. G. Hoekstra. Application of the discrete dipole approximation to very large refractive indices: Filtered coupled dipoles revived. Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 82(3), p. 036703.
  Abstract Citation Links
• Article
  M. C. F. Prosperi, M. Rosen-Zvi, A. Altman, M. Zazzi, S. Di Giambenedetto, R. Kaiser, E. Schülter, D. Struck, P. Sloot, D. A. van de Vijver, A.-M. Vandamme, and A. Sönnerborg. Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models. PLoS ONE 5(10), p. e13753.
  Abstract Citation Links
• Book
  P. Bellavista, R.-S. Chang, H.-C. Chao, S.-F. Lin, and P. M. A. Sloot. Advances in Grid and Pervasive Computing: 5th International Conference, GPC 2010, Hualien, Taiwan, May 10-13, 2010: Proceedings. ISBN 9783642130663.
  Abstract Citation Links
• Article
  M. A. Yurkin, D. de Kanter, and A. G. Hoekstra. Accuracy of the discrete dipole approximation for simulation of optical properties of gold nanoparticles. Journal of Nanophotonics 4(1), p. 041585.
  Abstract Citation Links
• Article
  D. Groen, S. Rieder, P. Grosso, C. de Laat, and S. Portegies Zwart. A platform independent communication library for distributed computing. Procedia Computer Science 1(1), pp. 2693-2700.
  Abstract Citation Links
• Proceedings
  M. Gerhards, A. Belloum, F. Berretz, V. Sander, and S. Skorupa. A history-tracing XML-based provenance framework for workflows. In: 2010 5th Workshop on Workflows in Support of Large-Scale Science (WORKS). ISBN 9781424489909.
  Abstract Citation Links
• Article
  M. V. Filatov, J. A. Kaandorp, M. Postma, R. van Liere, K. J. Kruszyński, M. J. A. Vermeij, G. J. Streekstra, and R. P. M. Bak. A comparison between coral colonies of the genus Madracis and simulated forms. Proceedings of the Royal Society B-Biological Sciences 277(1700), pp. 3555-3561.
  Abstract Citation Links
• MSc Thesis
  J. Daub. A cell-based model of extracellular-matrix-guided endothelial cell migration during angiogenesis. Supervised by R. M. H. Merks and J. A. Kaandorp.
  Citation Links

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