Publications of the CSL group

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2014

• Article
  J. Borgdorff, M. Mamonski, B. Bosak, K. Kurowski, M. Ben Belgacem, B. Chopard, D. Groen, P. V. Coveney, and A. G. Hoekstra. Distributed multiscale computing with MUSCLE 2, the Multiscale Coupling Library and Environment. Journal of Computational Science 5(5), pp. 719-731.
  Abstract Citation Links
• PhD Thesis
  J. Borgdorff. Distributed multiscale computing. ISBN 9789462592353. Supervised by P. M. A. Sloot and A. G. Hoekstra.
  Abstract Citation
• PhD Thesis
  A. L. Pyayt. Data-driven methods in application to flood defence systems monitoring and analysis. ISBN 9789064648052. Supervised by P. M. A. Sloot and V. V. Krzhizhanovskaya.
  Abstract Citation
• Article
  D. Abramson, M. Lees, V. V. Krzhizhanovskaya, J. Dongarra, and P. M. A. Sloot. Big Data Meets Computational Science: preface for ICCS 2014. Procedia Computer Science 29, pp. 1-7.
  Citation Links
• Proceedings
  J. Zhong, L. Luo, W. Cai, and M. Lees. Automatic Rule Identification for Agent-Based Crowd Models Through Gene Expression Programming. In: AAMAS '14: proceedings of the 2014 International Conference on Autonomous Agents & Multiagent Systems. ISBN 9781450327381. pp. 1125-1132.
  Abstract Citation Links
• Article
  T. I. Jung, F. Vogiatzian, O. Har-Shemesh, C. P. Fitzsimons, and R. Quax. Applying Information Theory to Neuronal Networks: From Theory to Experiments. Entropy 16(11), pp. 5721-5737.
  Abstract Citation Links
• Article
  Y. H. A. Teo, V. Viswanathan, M. Lees, and W. Cai. Analysing the Effectiveness of Wearable Wireless Sensors in Controlling Crowd Disasters. Procedia Computer Science 29, pp. 1590-1599.
  Abstract Citation Links
• PhD Thesis
  E. Mancini. Agent based modeling of viral infections: an investigation across several spatio-temporal scales. Supervised by P. M. A. Sloot.
  Citation Links
• Article
  Q. C. Bui, P. M. A. Sloot, E. M. van Mulligen, and J. A. Kors. A novel feature-based approach to extract drug-drug interactions from biomedical text. Bioinformatics 30(23), pp. 3365-3371.
  Abstract Citation Links
• Article
  C. Tamulonis and J. Kaandorp. A model of filamentous cyanobacteria leading to reticulate pattern formation. Life (Basel) 4(3), pp. 433-456.
  Abstract Citation Links
• Article
  B. Chopard, J. Borgdorff, and A. G. Hoekstra. A framework for multi-scale modelling. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 372(2021), 2013037813.
  Abstract Citation Links
• Article
  D. Botman, E. Röttinger, M. Q. Martindale, J. de Jong, and J. A. Kaandorp. A computational approach towards a gene regulatory network for the developing Nematostella vectensis gut. PLoS ONE 9(7), e103341.
  Abstract Citation Links
• Book
  D. Abramson, M. Lees, V. Krzhizhanovskaya, J. Dongarra, and P. M. A. Sloot. 2014 International Conference on Computational Science.
  Citation Links

2013

• Article
  A. L. Pyayt, I. I. Mokhov, and A. P. Kozionov. Интеллектуальная система мониторинга состояния объектов критической инфраструктуры. Integral 2013(4), pp. 84-86.
  Abstract Citation Links
• Article
  L. Mountrakis, E. Lorenz, and A. G. Hoekstra. Where do the platelets go? A simulation study of fully resolved blood flow through aneurysmal vessels. Interface Focus 3(2), p. 20120089.
  Abstract Citation Links
• Proceedings
  E. R. Dugundji and L. Gulyás. Understanding Emergence in a Fully-Specified Nested Logit Model.
  Citation
• Article
  R. Quax, A. Apolloni, and P. M. A. Sloot. Towards understanding the behavior of physical systems using information theory. The European Physical Journal - Special Topics 222(6), pp. 1389-1401.
  Abstract Citation Links
• PhD Thesis
  D. van Dijk. The symphony of gene regulation. Supervised by P. M. A. Sloot and J. A. Kaandorp.
  Abstract Citation
• Article
  P. Ramos-Silva, J. Kaandorp, L. Huisman, B. Marie, I. Zanella-Cléon, N. Guichard, D. J. Miller, and F. Marin. The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling. Molecular Biology and evolution 30(9), pp. 2099-2112.
  Abstract Citation Links
• Article
  B. Marie, D. J. Jackson, P. Ramos-Silva, I. Zanella-Cléon, N. Guichard, and F. Marin. The shell-forming proteome of Lottia gigantea reveals both deep conservations and lineage-specific novelties. The FEBS Journal 280(1), pp. 214-232.
  Abstract Citation Links
• Article
  N. Toth, L. Gulyas, R. O. Legendi, P. Duijn, P. M. A. Sloot, and G. Kampis. The importance of centralities in dark network value chains. The European Physical Journal - Special Topics 222(6), pp. 1413-1439.
  Abstract Citation Links
• Article
  R. Quax, A. Apolloni, and P. M. A. Sloot. The diminishing role of hubs in dynamical processes on complex networks. Journal of the Royal Society Interface 10(88), 20130568.
  Abstract Citation Links
• Article
  V. S. Lebanin, V. V. Krzhizhanovskaya, and S. E. Alexandrov. The dependence of the rate constant of the interaction between two excited particles on the excitation energy and temperature. Verification of the model with examples transfer of electronic excitation energy of the argon atom and the nitrogen molecule in the reaction of dissociation of nitrogen atom of argon. Technical Physics Letters .
  Citation
• PhD Thesis
  P. Sequeira dos Ramos Silva. The biocalcification of mollusk shells and coral skeletons: Integrating molecular, proteomics and bioinformatics methods. ISBN 9789810785635. Supervised by P. M. A. Sloot, J. A. Kaandorp, and F. G. Marin.
  Abstract Citation
• Article
  T. Ishiyama, S. Rieder, J. Makino, S. Portegies Zwart, D. Groen, K. Nitadori, C. de Laat, S. McMillan, K. Hiraki, and S. Harfst. The Cosmogrid simulation: Statistical properties of small dark matter halos. Astrophysical Journal 767(2), 146.
  Abstract Citation Links
• Article
  I. Bartha, M. Assel, P. M. A. Sloot, M. Zazzi, C. Torti, E. Schülter, A. De Luca, A. Sönnerborg, A. B. Abecasis, K. Van Laethem, A. Rosi, J. Svärd, R. Paredes, D. A. M. C. van de Vijver, A.-M. Vandamme, and V. Müller. Superinfection with drug-resistant HIV is rare and does not contribute substantially to therapy failure in a large European cohort. BMC Infectious Diseases 13, p. 537.
  Abstract Citation Links
• Article
  A. Czaplicka, J. A. Hołyst, and P. M. A. Sloot. Stochastic resonance for information flows on hierarchical networks. The European Physical Journal - Special Topics 222(6), pp. 1335-1345.
  Abstract Citation Links
• MSc Thesis
  J. Hofman. SPVAs: Grid GPU Implementation \& Risk Assessment of Investment Strategies. Supervised by B. D. Kandhai, D. Schrager, and V. Sergeev.
  Citation
• Article
  J. T. I. Tanzil, B. E. Brown, R. P. Dunne, J. N. Lee, J. A. Kaandorp, and P. A. Todd. Regional decline in growth rates of massive Porites corals in Southeast Asia. Global Change Biology 19(10), pp. 3011-3023.
  Abstract Citation Links
• Article
  P. Libin, G. Beheydt, K. Deforche, S. Imbrechts, F. Ferreira, K. Van Laethem, K. Theys, A. P. Carvalho, J. Cavaco-Silva, G. Lapadula, C. Torti, M. Assel, S. Wesner, J. Snoeck, J. Ruelle, A. de Bel, P. Lacor, P. de Munter, E. van Wijngaerden, M. Zazzi, R. Kaiser, A. Ayouba, M. Peeters, T. de Oliveira, L. C. J. Alcantara, Z. Grossman, P. Sloot, D. Otelea, S. Paraschiv, C. Boucher, R. J. Camacho, and A.-M. Vandamme. RegaDB: Community-driven data management and analysis for infectious diseases. Bioinformatics 29(11), pp. 1477-1480.
  Abstract Citation Links
• Article
  L. B. Carey, D. van Dijk, P. M. A. Sloot, J. A. Kaandorp, and E. Segal. Promoter sequence determines the relationship between expression level and noise. PLoS Biology 11(4), e1001528.
  Abstract Citation Links
• Proceedings
  V. Alexandrov, M. Lees, V. Krzhizhanovskaya, J. Dongarra, and P. M. A. Sloot. Proceedings of the International Conference on Computational Science, ICCS 2013. Procedia Computer Science 18.
  Citation Links
• Article
  A. Afanasyeva, S. Ponyaev, and V. Krgiganovskaya. Numerical simulation of synthesis of fullerenes by the arc discharge method. Journal of Physics. Conference Series 461, 012043.
  Abstract Citation Links
• Article
  A. Czaplicka, J. A. Holyst, and P. M. A. Sloot. Noise enhances information transfer in hierarchical networks. Scientific Reports 3, 1223.
  Abstract Citation Links
• Article
  J. Borgdorff, M. Mamonski, B. Bosak, D. Groen, M. Ben Belgacem, K. Kurowski, and A. G. Hoekstra. Multiscale Computing with the Multiscale Modeling Library and Runtime Environment. Procedia Computer Science 18, pp. 1097-1105.
  Abstract Citation Links
• MSc Thesis
  A. M. Abdol. Multi-objective optimization approach to infer Drosophila gene regulatory parameters. Supervised by J. A. Kaandorp and F. R. Jansson.
  Citation
• Article
  H. Tahir, C. Bona-Casas, and A. G. Hoekstra. Modelling the Effect of a Functional Endothelium on the Development of In-Stent Restenosis. PLoS ONE 8(6), e66138.
  Abstract Citation Links
• Article
  A. S. Afanasieva, S. A. Ponyaev, and V. V. Krzhizhanovskaya. Modelling processes in the shock tube experiments with ignition of combustible gas mixtures. Technical Physics Letters .
  Citation
• Proceedings
  H. Tahir, C. Bona-Casas, and A. G. Hoekstra. Modelling in-stent restenosis: morphological differences in the tissue patterns based on the origin of endothelium recovery.
  Citation
• Article
  N. Chindapol, J. A. Kaandorp, C. Cronemberger, T. Mass, and A. Genin. Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics. PLoS Computational Biology 9(1), e1002849.
  Abstract Citation Links
• PhD Thesis
  H. Tahir. Modelling and simulating the dynamics of in-stent restenosis in porcine coronary arteries. Supervised by P. M. A. Sloot and A. G. Hoekstra.
  Abstract Citation
• Article
  N. B. Melnikova, V. V. Krzhizhanovskaya, and P. M. A. Sloot. Modeling earthen dikes using real-time sensor data. Journal of Hydrology 496, pp. 154-165.
  Abstract Citation Links
• Article
  N. B. Melnikova, V. V. Krzhizhanovskaya, and P. M. A. Sloot. Modeling Earthen Dike Stability: Sensitivity Analysis and Automatic Calibration of Diffusivities Based on Live Sensor Data. Journal of Hydrology .
  Citation Links
• Chapter
  N. Javaheri, C. M. Cronemberger, and J. A. Kaandorp. Modeling Biosilicification at Subcellular Scales. In: Biomedical Inorganic Polymers. ISBN 9783642410048. pp. 117-141.
  Abstract Citation Links
• Article
  J. A. Kaandorp. Macroscopic modelling of environmental influence on growth and form of sponges and corals using the accretive growth model. ISRN Biomathematics 2013, p. 159170.
  Abstract Citation Links
• Proceedings
  J. Simm, D. Jordan, A. Topple, I. Mokhov, A. Pyayt, T. Abdoun, V. Bennett, J. Broekhuijsen, and R. Meijer. Interpreting sensor measurements in dikes - experiences from UrbanFlood pilot sites. In: Comprehensive Flood Risk Management: research for policy and practice. ISBN 9780203374511. pp. 81-82.
  Abstract Citation Links
• Book
  V. Alexandrov, M. Lees, V. Krzhizhanovskaya, J. Dongarra, and P. M. A. Sloot. International Conference on Computational Science, ICCS 2013: Barcelona, Spain, June 5- June 7, 2013.
  Citation Links
• Proceedings
  A. P. Kozionov, A. L. Pyayt, and V. T. Kusherbaeva. Intelligent signal processing for dike health monitoring. In: Automation & control: proceedings of the International Conference of Young Scientists, St. Petersburg, Russia, 21-22 November 2013. ISBN 9785742241645. pp. 188-193.
  Citation
• PhD Thesis
  R. Quax. Information processing in complex networks. Supervised by P. M. A. Sloot.
  Abstract Citation
• Article
  R. Quax, D. Kandhai, and P. M. A. Sloot. Information dissipation as an early-warning signal for the Lehman Brothers collapse in financial time series. Scientific Reports 3, 1898.
  Abstract Citation Links
• Article
  R. Quax, D. A. M. C. van de Vijver, D. Frentz, and P. M. A. Sloot. Inferring epidemiological parameters from phylogenetic information for the HIV-1 epidemic among MSM. The European Physical Journal - Special Topics 222(6), pp. 1347-1358.
  Abstract Citation Links
• Proceedings
  H. Tahir, C. Bona-Casas, and A. G. Hoekstra. In-stent restenosis patterns based on the origin of endothelium recovery.
  Citation Links
• MSc Thesis
  J. Hofmann. Heterogeneous Multiscale Simulations of Blood Flow. Supervised by A. G. Hoekstra and E. Lorenz.
  Citation Links
• MSc Thesis
  A. Theiakos. GPU-based hedging of a mortgage portfolio using Monte-Carlo and finite difference methods. Supervised by B. D. Kandhai, J. Tas, and H. van der Lem.
  Citation Links
• Article
  J. Borgdorff, J.-L. Falcone, E. Lorenz, C. Bona-Casas, B. Chopard, and A. G. Hoekstra. Foundations of distributed multiscale computing: formalization, specification, and analysis. Journal of Parallel and Distributed Computing 73(4), pp. 465-483.
  Abstract Citation Links
• MSc Thesis
  S. van Geldermalsen. FlowCL -- Declarative dataflow API for heterogeneous platform computing. Supervised by S. Olabarriaga, A. S. Z. Belloum, and H. Marquering.
  Citation Links
• Chapter
  B. E. Pengel, V. V. Krzhizhanovskaya, N. B. Melnikova, G. S. Shirshov, A. R. Koelewijn, A. L. Pyayt, and I. I. Mokhov. Flood early warning system: sensors and internet. In: Floods: from risk to opportunity. ISBN 9781907161353. pp. 445-453.
  Abstract Citation Links
• Article
  D. Groen, J. Borgdorff, C. Bona-Casas, J. Hetherington, R. W. Nash, S. J. Zasada, I. Saverchenko, M. Mamonski, K. Kurowski, M. O. Bernabeu, A. G. Hoekstra, and P. V. Coveney. Flexible composition and execution of high performance, high fidelity multiscale biomedical simulations. Interface Focus 3(2), 20120087.
  Abstract Citation Links
• Proceedings
  C. Bona-Casas, J. Borgdorff, H. Tahir, and A. G. Hoekstra. First results on a 3D model for in-stent restenosis.
  Citation Links
• MSc Thesis
  C. Chen. Explicit modelling of membrane-bound structures in the cellular Potts model. Supervised by R. M. H. Merks and J. A. Kaandorp.
  Citation
• MSc Thesis
  L. J. Dijkstra. Essays in Computational Science. Supervised by P. M. A. Sloot.
  Citation
• PhD Thesis
  J. T. I. Tanzil. Environmental controls of coral growth: Data driven multi-scale analyses of rates and patterns of growth in massive Porites corals around the Thai-Malay Peninsula. ISBN 9789810783372. Supervised by P. M. A. Sloot and J. A. Kaandorp.
  Abstract Citation
• Article
  V. V. Krzhizhanovskaya, N. B. Melnikova, A. M. Chirkin, S. V. Ivanov, A. V. Boukhanovsky, and P. M. A. Sloot. Distributed Simulation of City Inundation by Coupled Surface and Subsurface Porous Flow for Urban Flood Decision Support System. Procedia Computer Science 18, pp. 1046-1056.
  Abstract Citation Links
• Article
  M. Ben Belgacem, B. Chopard, J. Borgdorff, M. Mamoński, K. Rycerz, and D. Harezlak. Distributed Multiscale Computations using the MAPPER framework. Procedia Computer Science 18, pp. 1106-1115.
  Abstract Citation Links
• Article
  B. E. Nichols, C. A. B. Boucher, J. H. van Dijk, P. E. Thuma, J. L. Nouwen, R. Baltussen, J. van de Wijgert, P. M. A. Sloot, and D. A. M. C. van de Vijver. Cost-effectiveness of Pre-Exposure Prophylaxis (PrEP) in preventing HIV-1 infections in rural Zambia: a modeling study. PLoS ONE 8(3), e59549.
  Abstract Citation Links
• Article
  V. Alexandrov, M. Lees, V. Krzhizhanovskaya, J. Dongarra, and P. M. A. Sloot. Computation at the Frontiers of Science, preface for ICCS 2013. Procedia Computer Science 18, pp. 1-9.
  Citation Links
• PhD Thesis
  N. Zarrabi. Complex networks and agent-based models of HIV epidemic. Supervised by P. M. A. Sloot.
  Abstract Citation
• Article
  N. Zarrabi, M. C. F. Prosperi, R. G. Belleman, S. Di Giambenedetto, M. Fabbiani, A. De Luca, and P. M. A. Sloot. Combining social and genetic networks to study HIV transmission in mixing risk groups. The European Physical Journal - Special Topics 222(6), pp. 1377-1387.
  Abstract Citation Links
• PhD Thesis
  C. V. T. Tamulonis. Cell-based models. Supervised by P. M. A. Sloot and J. A. Kaandorp.
  Citation
• Article
  A. Adamatzky, M. Lees, and P. Sloot. Bio-development of motorway networks in the Netherlands: a slime mould approach. Advances in Complex Systems 16(02n03), 1250034.
  Abstract Citation Links
• Article
  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. Are motorways rational from slime mould's point of view?. International Journal of Parallel, Emergent and Distributed Systems 28(3), pp. 230-248.
  Abstract Citation Links
• Proceedings
  C. Bona-Casas, J. Borgdorff, H. Tahir, and A. G. Hoekstra. An off-lattice 3D model for in-stent restenosis.
  Citation
• Article
  A. L. Pyayt, A. P. Kozionov, I. I. Mokhov, B. Lang, V. V. Krzhizhanovskaya, and P. M. A. Sloot. An Approach for Real-time Levee Health Monitoring Using Signal Processing Methods. Procedia Computer Science 18, pp. 2357-2366.
  Abstract Citation Links
• Article
  P. M. A. Sloot, G. Kampis, and L. Gulyás. Advances in dynamic temporal networks: understanding the temporal dynamics of complex adaptive networks. The European Physical Journal - Special Topics 222(6), pp. 1287-1293.
  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. Journal of Computational Science 4(3), pp. 127-134.
  Abstract Citation Links
• Proceedings
  H. Aydt, Y. Xu, M. Lees, and A. Knoll. A Multi-threaded Execution Model for the Agent-based SEMSim Traffic Simulation. In: AsiaSim 2013. ISBN 9783642450372. pp. 1-12.
  Abstract Citation Links
• MSc Thesis
  J. Tyree. A Linear Boundary for the Heston Model With Parallel ADI Finite Differencing on GPUs. Supervised by B. D. Kandhai.
  Citation Links

2012

• Proceedings
  M. A. Prosnikov and V. V. Krzhizhanovskaya. Обзор основых методов и программ для моделирования наноразмерных систем. In: ХLI Неделя науки СПбГПУ. 6, pp. 128-130.
  Citation
• Proceedings
  V. S. Lebanin and V. V. Krzhizhanovskaya. Модель кинетики реакции двух нейтральных частиц в газе и плазме. In: ХLI Неделя науки СПбГПУ. 6, pp. 146-149.
  Citation
• Proceedings
  S. A. Konakov and V. V. Krzhizhanovskaya. Моделирование механизма образования силаммониевых радикалов в технологии плазмохимического осаждения нитрида кремния азота с малым содержанием. In: ХLI Неделя науки СПбГПУ. 6, pp. 132-135.
  Citation
• Article
  G. Qiu, D. Kandhai, N. F. Johnson, and P. M. A. Sloot. Understanding complex dynamics in derivatives finance: why do options markets smile?. Advances in Complex Systems 15(5), 1250050.
  Abstract Citation Links
• Article
  J. U. Hammel, M. V. Filatov, J. Herzen, F. Beckmann, J. A. Kaandorp, and M. Nickel. The non-hierarchical, non-uniformly branching topology of a leuconoid sponge aquiferous system revealed by 3D reconstruction and morphometrics using corrosion casting and X-ray microtomography. Acta Zoologica 93(2), pp. 160-170.
  Abstract Citation Links
• Article
  D. Botman and J. A. Kaandorp. Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis. BMC Research Notes 5, p. 555.
  Abstract Citation Links
• 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
• 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
• 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
• 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

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