Publications of the CSL group

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2012

• Proceedings
  A. Mordvintsev, V. Krzhizhanovskaya, M. Lees, and P. Sloot. Simulation of city evacuation coupled to flood dynamics. In: PED 2012: accompanying booklet: abstracts of all presentations and posters: 6th International Conference on Pedestrian and Evacuation Dynamics. pp. [156-158].
  Citation Links
• Proceedings
  A. L. Pyayt, I. I. Mokhov, A. P. Kozionov, V. T. Kusherbaeva, V. V. Krzhizhanovskaya, B. J. Broekhuijsen, and R. J. Meijer. Signal Processing Methods for Flood Early Warning Systems. In: Proceedings of 10th International Conference on Hydroinformatics 2012: Hamburg, Germany. ISBN 9783941492455.
  Abstract Citation Links
• Proceedings
  R. Cushing, S. Koulouzis, R. Strijkers, A. S. Z. Belloum, and M. Bubak. Service Level Management for executable papers. In: Euro-Par 2011: Parallel Processing Workshops. ISBN 9783642297403. 2, pp. 116-123.
  Abstract Citation Links
• PhD Thesis
  Q. C. Bui. Relation extraction methods for biomedical literature. ISBN 9789064645785. Supervised by P. M. A. Sloot.
  Abstract Citation Links
• Book
  H. Ali, Y. Shi, D. Khazanchi, M. Lees, G. D. van Albada, J. Dongarra, and P. M. A. Sloot. Proceedings of the International Conference on Computational Science, ICCS 2012.
  Citation Links
• Chapter
  A. Adamatzky, M. Lees, and P. M. A. Sloot. Physarum in the Netherlands: responding to the flood. In: Bioevaluation of world transport networks. ISBN 9789814407038. pp. 213-234.
  Citation Links
• Proceedings
  S. Varma, M. C. Villa Uriol, P. Lamata, E. Schileo, B. Ó Nualláin, J. Fenner, N. S. H. Smith, and D. R. Hose. Patient-Centred Multi-scale Computational Workflows. In: VPH Conference 2012, London.
  Citation
• Proceedings
  T. Szepieniec, J. Kocot, T. Schaaf, O. Appleton, M. Heikkurinen, A. S. Z. Belloum, J. Serrat-Fernández, and M. Metzker. On importance of Service Level Management in Grids. In: Euro-Par 2011: Parallel Processing Workshops. ISBN 9783642297403. 2, pp. 64-75.
  Abstract Citation Links
• Article
  P. Ramos-Silva, S. Benhamada, N. Le Roy, B. Marie, N. Guichard, I. Zannella-Cléon, L. Plasseraud, M. Corneillat, G. Alcaraz, J. Kaandorp, and F. Marin. Novel molluskan biomineralization proteins retrieved from proteomics: a case study with Upsalin. ChemBioChem 13(7), pp. 1067-1078.
  Abstract Citation Links
• Article
  J. Borgdorff, D. Groen, S. Ferlin, I. Saverchenko, J. Suter, A. G. Hoekstra, and P. V. Coveney. Multiscale Simulations on Distributed European e-Infrastructures. Inside 10(1), pp. 72-77.
  Citation Links
• Proceedings
  J. A. Kaandorp, D. Botman, C. Tamulonis, and R Dries. Multi-scale modeling of gene regulation of morphogenesis. In: How the World Computes. ISBN 9783642308703. pp. 355-362.
  Abstract Citation Links
• Proceedings
  V. V. Krzhizhanovskaya and N. B. Melnikova. Modeling earthen dikes: sensitivity analysis and calibration of soil properties based on sensor data. In: Proceedings of the 12th International Conference on Computational and Mathematical Methods in Science and Engineering: Murcia, Spain, July 2-5, 2012: CMMSE. - Vol. 4. ISBN 9788461553921. pp. 1414-1424.
  Citation Links
• Article
  R. Quax, A. Apolloni, and P. M. A. Sloot. Information processing reveals how microscopic components affect the macroscopic system-state in complex networks. Scientific Reports .
  Citation Links
• Article
  P. M. A. Sloot and R. Quax. Information processing as a paradigm to model and simulate complex systems. Journal of Computational Science 3(5), pp. 247-249.
  Citation Links
• Article
  E. Mancini, F. Gastiglione, M. Bernaschi, A. de Luca, and P. M. A. Sloot. HIV reservoirs and immune surveillance evasion cause the failure of structured treatment interruptions: a computational study. PLoS ONE 7(4), e36108.
  Abstract Citation Links
• Article
  Y. Kim, R. Sinclair, N. Chindapol, J. A. Kaandorp, and E. De Schutter. Geometric theory predicts bifurcations in minimal wiring cost trees in biology are flat. PLoS Computational Biology 8(4), p. e1002474.
  Abstract Citation Links
• Article
  X. Wang, H. C. Schröder, K. Wang, J. A. Kaandorp, and W. E. G. Müller. Genetic, biological and structural hierarchies during sponge spicule formation: From soft sol-gels to solid 3D silica composite structures. Soft Matter 8(37), pp. 9501-9518.
  Abstract Citation Links
• Article
  B. Pengel, G. S. Shirshov, V. V. Krzhizhanovskaya, N. B. Melnikova, A. Koelewijn, A. L. Pyayt, and I. I. Mokhov. Flood Early Warning System: Sensors and Internet. Journal of Flood Risk Management .
  Citation
• MSc Thesis
  K. W. Kongsgård. Expertise Modeling on cQA Sites -- News Feed Optimization. Supervised by E. Meij.
  Citation Links
• MSc Thesis
  P. Firmpas Nisantzis. Evolving collective and single cell motility in a computational model of tumor invasion. Supervised by R. M. H. Merks and J. A. Kaandorp.
  Citation Links
• Article
  S. Koulouzis, R. Cushing, K. A. Karasavvas, A. Belloum, and M. Bubak. Enabling web services to consume and produce large datasets. IEEE Internet Computing 16(1), pp. 52-60.
  Abstract Citation Links
• Article
  H. Ali, Y. Shi, D. Khazanchi, M. Lees, G. D. van Albada, J. Dongarra, and P. M. A. Sloot. Empowering Science through Computing, preface for ICCS 2012. Procedia Computer Science 9, pp. 1-6.
  Citation Links
• Proceedings
  S. Varma, C. Pedronaci, D. Kalra, M. C. Villa Uriol, P. Lamata, E. Schileo, B. Ó Nualláin, N. S. H. Smith, S. Wood, and D. R. Hose. Embodying a Patient Avatar for Computational Workflows. In: VPH Conference 2012, London.
  Citation
• Proceedings
  S. J. Zasada, M. Mamonski, D. Groen, J. Borgdorff, I. Saverchenko, T. Piontek, K. Kurowski, and P. V. Coveney. Distributed infrastructure for multiscale computing. In: 2012 IEEE/ACM 16th International Symposium on Distributed Simulation and Real Time Applications: DS-RET 2012: Proceedings. ISBN 9781467329545. pp. 65-74.
  Abstract Citation Links
• Proceedings
  A. L. Pyayt, I. I. Mokhov, A. P. Kozionov, V. T. Kusherbaeva, B. Lang, V. V. Krzhizhanovskaya, and R. J. Meijer. Data-driven modelling for flood defence structure analysis. In: Comprehensive flood risk management: research for policy and practice. ISBN 9780415621441. pp. 301-306.
  Abstract Citation Links
• Proceedings
  A. L. Pyayt, I. I. Mokhov, A. Kozionov, and V. Kusherbaeva. Data-driven methods in UrbanFlood project for flood defence structure measurements analysis.
  Citation
• Proceedings
  C. D. Erdbrink, V. V. Krzhizhanovskaya, and P. M. A. Sloot. Controlling flow-induced vibrations of flood barrier gates with data-driven and finite-element modelling. In: Comprehensive flood risk management: research for policy and practice. ISBN 9780415621441. pp. 425-434.
  Abstract Citation Links
• Proceedings
  V. V. Krzhizhanovskaya, N. B. Melnikova, G. S. Shirshov, F. I. Rusadi, R. G. Belleman, J. Lhomme, B. P. Gouldby, A. Topple, and J. Simm. Computational models in flood early warning systems. In: Comprehensive flood risk management: research for policy and practice. ISBN 9780415621441. p. 1533.
  Citation Links
• Article
  N. Zarrabi, M. Prosperi, R. G. Belleman, M. Colafigli, A. De Luca, and P. M. A. Sloot. Combining epidemiological and genetic networks signifies the importance of early treatment in HIV-1 transmission. PLoS ONE 7(9), p. e46156.
  Abstract Citation Links
• Chapter
  A. Adamatzky, S. Akl, R. Alonso-Sanz, W. van Dessel, Z. Ibrahim, A. Ilachinski, J. Jones, A. V. D. M. Kayem, G. J. Martínez, P. de Oliveira, M. Prokopenko, T. Schubert, P. Sloot, E. Strano, and X.-S. Yang. Biorationality of motorways. In: Bioevaluation of world transport networks. ISBN 9789814407038. pp. 309-325.
  Citation Links
• Article
  Q. C. Bui and P. M. A. Sloot. A robust approach to extract biomedical events from literature. Bioinformatics 28(20), pp. 2654-2661.
  Abstract Citation Links
• Article
  J. Borgdorff, C. Bona-Casas, M. Mamonski, K. Kurowski, T. Piontek, B. Bosak, K. Rycerz, E. Ciepiela, T. Gubala, D. Harezlak, M. Bubak, E. Lorenz, and A. G. Hoekstra. A distributed multiscale computation of a tightly coupled model using the Multiscale Modeling Language. Procedia Computer Science 9, pp. 596-605.
  Abstract Citation Links
• MSc Thesis
  R. Dries. 3D mass-spring model for studying early development of the starlet sea anemone nematostella vectensis. Supervised by C. Tamulonis and J. A. Kaandorp.
  Citation

2011

• Proceedings
  S. A. Konakov and V. V. Krzhizhanovskaya. Сравнение двух моделей плазмохимических процессов при осаждении нитрида Кемния. In: ХL Неделя науки СПбГПУ. 6, pp. 132-134.
  Citation Links
• Proceedings
  A. S. Afanasieva, S. A. Ponyaev, and V. V. Krzhizhanovskaya. Подготовка задачи численного моделирования синтеза фуллеренов в углеродсодержащей плазме дугового разряда. In: ХL Неделя науки СПбГПУ. 6, pp. 129-131.
  Citation Links
• Proceedings
  V. S. Lebanin and V. V. Krzhizhanovskaya. Обзор плазмохимических методов получения нитрида Кремния. In: ХL Неделя науки СПбГПУ. 6, pp. 131-132.
  Citation Links
• Proceedings
  I. S. Kiseleva and V. V. Krzhizhanovskaya. Моделирование аргоновой плазмы в установке плазмохимического осаждения с помощью пакета ESI CFD-ACE+. In: ХL Неделя науки СПбГПУ. 6, pp. 126-128.
  Citation Links
• Proceedings
  S. A. Konakov and V. V. Krzhizhanovskaya. Компьютерное моделирование процесса осаждения многослойных структур на основе нитрида кремния методом РЕСVD. In: Наука и инновации в технических университетах : Материалы пятого всероссийского форума студентов, аспирантов и молодых ученых. pp. 12-13.
  Citation Links
• Article
  N. B. Melnikova, G. S. Shirshov, and V. V. Krzhizhanovskaya. Virtual Dike: multiscale simulation of dike stability. Procedia Computer Science 4, pp. 791-800.
  Abstract Citation Links
• Proceedings
  N. B. Melnikova, G. S. Shirshov, V. V. Krzhizhanovskaya, and N. N. Shabrov. Virtual Dike and Flood Simulator: Parallel distributed computing for flood early warning systems. In: Параллельные вычислительные технологии (ПаВТ’2011). ISBN 9785696040905. pp. 365-373.
  Abstract Citation Links
• PhD Thesis
  G. Qiu. Understanding the complex dynamics of financial markets through microsimulation. ISBN 9789491211010. Supervised by P. M. A. Sloot and D. Kandhai.
  Abstract Citation Links
• PhD Thesis
  J. T. Mościcki. Understanding and mastering dynamics in computing grids: processing moldable tasks with user-level overlay. Supervised by M. T. Bubak and P. M. A. Sloot.
  Abstract Citation Links
• Proceedings
  J. Bernsdorf, G. Berti, B. Chopard, J. Hegewald, M. Krafczyk, D. Wang, E. Lorenz, and A. Hoekstra. Towards distributed multiscale simulation of biological processes. In: The Seventh IEEE International Conference on e-Science. Workshops: eScienceW 2011: proceedings: Stockholm, Sweden, 5-8 December 2011. ISBN 9781467300261. pp. 89-96.
  Abstract Citation Links
• MSc Thesis
  I. Niculescu. Towards a cell-based model of Neointimal Hyperplasia with Cellular Potts Model. Supervised by A. G. Hoekstra and R. M. H. Merks.
  Citation Links
• Article
  R. Strijkers, R. Cushing, D. Vasyunin, C. de Laat, A. S. Z. Belloum, and R. Meijer. Toward executable scientific publications. Procedia Computer Science 4, pp. 707-715.
  Abstract Citation Links
• Proceedings
  B. Pengel, L. Wentholt, V. V. Krzhizhanovskaya, G. Shirshov, N. Melnikova, B. Gouldby, A. Koelewijn, A. Pyayt, I. Mokhov, N. Pals, R. Meijer, and J. Broekhuijsen. The urbanflood early warning system: sensors and coastal flood safety. In: Proceedings of the CoastGIS 2011 Conference. ISBN 9788889405246. 4, pp. 20-27.
  Citation Links
• Article
  M. A. Yurkin and A. G. Hoekstra. The discrete-dipole-approximation code ADDA: capabilities and known limitations. Journal of Quantitative Spectroscopy & Radiative Transfer 112(13), pp. 2234-2247.
  Abstract Citation Links
• Chapter
  J. A. Kaandorp, M. Filatov, and N. Chindapol. Simulating and quantifying the environmental influence on coral colony growth and form. In: Coral reefs: An ecosystem in transition. ISBN 9789400701137. pp. 177-185.
  Abstract Citation Links
• Proceedings
  R. S. Cushing, S. Koulouzis, A. S. Z. Belloum, R. J. Strijkers, and M. T. Bubak. Service Level Management for Executable Papers. In: 7th International European Conference on Parallel and Distributed Computing (Euro-Par 2011), workshop MDGS2011.
  Citation Links
• Article
  R. Quax, D. A. Bader, and P. M. A. Sloot. SEECN: simulating complex systems using dynamic complex networks. International Journal for Multiscale Computational Engineering 9(2), pp. 201-214.
  Abstract Citation Links
• Article
  J. T. Mościcki, M. Lamanna, M. Bubak, and P. M. A. Sloot. Processing moldable tasks on the grid: late job binding with lightweight user-level overlay. Future Generation Computer Systems 27(6), pp. 725-736.
  Abstract Citation Links
• Book
  M. Sato, S. Matsuoka, P. M. A. Sloot, G. D. van Albada, and J. Dongarra. Proceedings of the International Conference on Computational Science, ICCS 2011.
  Citation Links
• Article
  M. Sato, S. Matsuoka, G. D. van Albada, J. Dongarra, and P. M. A. Sloot. Preface. Procedia Computer Science 4, pp. 1-6.
  Citation Links
• Proceedings
  R. Cushing, S. Koulouzis, A. S. Z. Belloum, and M. Bubak. Prediction-based auto-scaling of scientific workflows. In: Proceedings of the 9th International Workshop on Middleware for Grids, Clouds and e-Science: MGC 2011, co-located with ACM/IFIP/USENIX 12th International Middleware Conference, December 12-16, 2011, Lisbon, Portugal. ISBN 9781450310680. p. 1.
  Abstract Citation Links
• MSc Thesis
  F. Speelman. Position-Based Quantum Cryptography and the Garden-Hose Game. Supervised by H. Buhrman and C. Schaffner.
  Citation Links
• MSc Thesis
  J. Teunissen. Particle based 3D modeling of positive streamer inception. Supervised by U. Ebert.
  Citation Links
• Article
  V. V. Krzhizhanovskaya. Overstromingsrisico's in Kaart Brenger met de HPC Cloud. "High Performance Computing E-Science Support", SARA Jaarverslag 2010 pp. 38-38.
  Citation Links
• Chapter
  V. P. Maltsev, A. G. Hoekstra, and M. A. Yurkin. Optics of white blood cells: optical models, simulations, and experiments. In: Advanced optical flow cytometry: methods and disease diagnoses. ISBN 9783527409341. pp. 63-93.
  Citation Links
• 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

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