Publications of the CSL group

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2020

• Article
  O. Severiukhina, S. Kesarev, K. Bochenina, A. Boukhanovsky, M. H. Lees, and P. M. A. Sloot. Large-scale forecasting of information spreading. Journal of Big Data 7, 72.
  Abstract Citation Links
• Article
  C. Scherer, R. Scheid, D. Andrienko, and T. Bereau. Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids. Journal of Chemical Theory and Computation 16(5), pp. 3194-3204.
  Abstract Citation Links
• Article
  K. de Vries, A. Nikishova, B. Czaja, G. Závodszky, and A. G. Hoekstra. Inverse Uncertainty Quantification of a cell model using a Gaussian Process metamodel. International Journal for Uncertainty Quantification 10(4), pp. 333-349.
  Abstract Citation Links
• Article
  Yasemin Bozkurt Varolgünes, Tristan Bereau, and Joseph F. Rudzinski. Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders. Machine Learning: Science and Technology 1(1), 015012.
  Abstract Citation Links
• Article
  A. Centi, A. Dutta, S. H. Parekh, and T. Bereau. Inserting Small Molecules across Membrane Mixtures. Biophysical Journal 118(6), pp. 1321-1332.
  Abstract Citation Links
• Article
  P. R. Konduri, H. A. Marquering, E. E. van Bavel, A. Hoekstra, C. B. L. M. Majoie, R. Padmos, and V. Azizi. In-Silico Trials for Treatment of Acute Ischemic Stroke. Frontiers in Neurology 11, 558125.
  Abstract Citation Links
• Article
  O. Metsker, K. Magoev, A. Yakovlev, S. Yanishevskiy, G. Kopanitsa, S. Kovalchuk, and V. V. Krzhizhanovskaya. Identification of risk factors for patients with diabetes: diabetic polyneuropathy case study. BMC Medical Informatics and Decision Making 20, 201.
  Abstract Citation Links
• Article
  B. Csippa, D. Gyürki, G. Závodszky, I. Szikora, and G. Paál. Hydrodynamic Resistance of Intracranial Flow-Diverter Stents. Cardiovascular Engineering and Technology 11(1), pp. 1-13.
  Abstract Citation Links
• Article
  C. Rauer and T. Bereau. Hydration free energies from kernel-based machine learning: Compound-database bias. Journal of Chemical Physics 153(1), 014101.
  Abstract Citation Links
• Proceedings
  Tjula Daelmans, Sophie Hutten, Judith Niks, Emőke Takács, and A. W. Abcouwer. Future Prospects of the Transitioning Energy. In: Proceedings of the 16th European Conference on Management, Leadership and Governance. pp. 57-64.
  Abstract Citation Links
• Article
  C. Liu, J. G. Brandenburg, O. Valsson, K. Kremer, and T. Bereau. Free-energy landscape of polymer-crystal polymorphism. Soft Matter 16(42), pp. 9683-9692.
  Abstract Citation Links
• Article
  J. J. Lever, I. A. van de Leemput, E. Weinans, R. Quax, V. Dakos, E. H. van Nes, J. Bascompte, and M. Scheffer. Foreseeing the future of mutualistic communities beyond collapse. Ecology Letters 23(1), pp. 2-15.
  Abstract Citation Links
• Article
  M. V. Sheraton, G. G. Y. Chiew, V. Melnikov, E. Y. Tan, K. Q. Luo, N. Verma, and P. M. A. Sloot. Emergence of spatio-temporal variations in chemotherapeutic drug efficacy: in-vitro and in-Silico 3D tumour spheroid studies. BMC Cancer 20, 1201.
  Abstract Citation Links
• Proceedings
  L. E. Veen and A. G. Hoekstra. Easing Multiscale Model Design and Coupling with MUSCLE 3. In: Computational Science – ICCS 2020. VI, pp. 425-438.
  Abstract Citation Links
• Proceedings
  B. Nannes, R. Quax, H. Ashikaga, M. Hocini, R. Dubois, O. Bernus, and M. Haïssaguerre. Early signs of critical slowing down in heart surface electrograms of ventricular fibrillation victims. In: Computational Science – ICCS 2020. IV, pp. 334-347.
  Abstract Citation Links
• Proceedings
  A. Presbitero, R. Quax, V. V. Krzhizhanovskaya, and P. M. A. Sloot. Detecting critical transitions in the human innate immune system post-cardiac surgery. In: Computational Science – ICCS 2020. I, pp. 371-384.
  Abstract Citation Links
• Article
  J. W. Barnett, C. R. Bilchak, Y. Wang, B. C. Benicewicz, L. A. Murdock, T. Bereau, and S. K. Kumar. Designing exceptional gas-separation polymer membranes using machine learning. Sciences advances 6(20), eaaz4301.
  Abstract Citation Links
• Article
  C. H. Tan, H.-S. Oh, V. M. Sheraton, E. Mancini, S. C. J. Loo, S. Kjelleberg, P. M. A. Sloot, and S. A. Rice. Convection and the Extracellular Matrix Dictate Inter- and Intra-Biofilm Quorum Sensing Communication in Environmental Systems. Environmental Science and Technology 54(11), p. 6730–6740.
  Abstract Citation Links
• Article
  I. Anagnostou, J. Sanchez Rivero, S. Sourabh, and D. Kandhai. Contagious defaults in a credit portfolio: a Bayesian network approach. Journal of Credit Risk 16(1), pp. 1-26.
  Abstract Citation Links
• Article
  P. J. S. Cardoso, J. M. F. Rodrigues, J. Monteiro, R. Lam, V. V. Krzhizhanovskaya, M. H. Lees, J. Dongarra, and P. M. A. Sloot. Computational Science in the Interconnected World: Selected papers from 2019 International Conference on Computational Science. Journal of Computational Science 47, 101222.
  Citation Links
• Article
  J. F. Rudzinski and T. Bereau. Coarse-grained conformational surface hopping. Journal of Chemical Physics 153(21), 214110.
  Abstract Citation Links
• PhD Thesis
  B. E. Czaja. Cell resolved blood flow modeling with the Lattice Boltzmann method. Supervised by A. G. Hoekstra and G. Závodszky.
  Abstract Citation Links
• Article
  D. W. Wright, R. A. Richardson, W. Edeling, J. Lakhlili, R. C. Sinclair, V. Jancauskas, D. Suleimenova, B. Bosak, M. Kulczewski, T. Piontek, P. Kopta, I. Chirca, H. Arabnejad, O. O. Luk, O. Hoenen, J. Węglarz, D. Crommelin, D. Groen, and P. V. Coveney. Building Confidence in Simulation: Applications of EasyVVUQ. Advanced Theory and Simulations 3(8), 1900246.
  Abstract Citation Links
• Article
  J. Burger, D. C. van der Veen, D. J. Robinaugh, R. Quax, H. Riese, R. A. Schoevers, and S. Epskamp. Bridging the gap between complexity science and clinical practice by formalizing idiographic theories: a computational model of functional analysis. BMC Medicine 18, 99.
  Abstract Citation Links
• Article
  B. J. M. van Rooij, G. Závodszky, A. G. Hoekstra, and D. N. Ku. Biorheology of occlusive thrombi formation under high shear: in vitro growth and shrinkage. Scientific Reports 10, 18604.
  Abstract Citation Links
• Article
  D. Roy, D. Bernal, and M. Lees. An exploratory factor analysis model for slum severity index in Mexico City. Urban Studies 57(4), pp. 789-805.
  Abstract Citation Links
• Article
  Marc Stieffenhofer, Michael Wand, and Tristan Bereau. Adversarial reverse mapping of equilibrated condensed-phase molecular structures. Machine Learning: Science and Technology 1(4), 045014.
  Abstract Citation Links
• Book
  T. Abcouwer, E. Takács, and O.-P. Banga. Adaptive Information Management.
  Abstract Citation
• Article
  P. S. Zun, A. J. Narracott, P. C. Evans, B. J. M. van Rooij, and A. G. Hoekstra. A particle-based model for endothelial cell migration under flow conditions. Biomechanics and Modeling in Mechanobiology 19(2), pp. 681-692.
  Abstract Citation Links
• Article
  G. Závodszky, B. Csippa, G. Paál, and I. Szikora. A novel virtual flow diverter implantation method with realistic deployment mechanics and validated force response. International Journal for Numerical Methods in Biomedical Engineering 36(6), e3340.
  Abstract Citation Links
• Article
  J. R. Helmus, M. H. Lees, and R. van den Hoed. A data driven typology of electric vehicle user types and charging sessions. Transportation Research. Part C, Emerging Technologies 115, 102637.
  Abstract Citation Links
• Proceedings
  B. Czaja, G. Závodszky, and A. Hoekstra. A Heterogeneous Multi-scale Model for Blood Flow. In: Computational Science – ICCS 2020. VI, pp. 403-409.
  Abstract Citation Links
• Article
  S. V. Kovalchuk, V. V. Krzhizhanovskaya, and P. M. A. Sloot. 20 years of computational Science. Journal of Computational Science 46, 101187.
  Citation Links

2019

• Article
  S. Alowayyed, M. Vassaux, B. Czaja, P. V. Coveney, and A. G. Hoekstra. Towards heterogeneous multi-scale computing on large scale parallel supercomputers. Supercomputing Frontiers and Innovations 6(4), pp. 20-43.
  Abstract Citation Links
• Article
  V. Karbovskii, O. Severiukhina, I. Derevitskii, D. Voloshin, A. Presbitero, and M. Lees. The impact of different obstacles on crowd dynamics. Journal of Computational Science 36, 100893.
  Abstract Citation Links
• PhD Thesis
  V. Sheraton Muniraj. The emergence of biofilms. Supervised by P. M. A. Sloot.
  Abstract Citation Links
• Article
  I. Vermeulen, J. R. Helmus, M. Lees, and R. van den Hoed. Simulation of future electric vehicle charging behavior—effects of transition from PHEV to FEV. World Electric Vehicle Journal 10(2), 42.
  Abstract Citation Links
• Article
  V. Sivadasan, E. Lorenz, A. G. Hoekstra, and D. Bonn. Shear thickening of dense suspensions: The role of friction. Physics of Fluids 31(10), 103103.
  Abstract Citation Links
• Article
  A. Nikishova and A. G. Hoekstra. Semi-intrusive uncertainty propagation for multiscale models. Journal of Computational Science 35, pp. 80-90.
  Abstract Citation Links
• Article
  A. Nikishova, L. Veen, P. Zun, and A. G. Hoekstra. Semi-intrusive multiscale metamodelling uncertainty quantification with application to a model of in-stent restenosis. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 2018154.
  Abstract Citation Links
• Article
  S. V. Kovalchuk, V. V. Krzhizhanovskaya, Y. Shi, H. Fua, M. H. Lees, J. Dongarra, and P. M. A. Sloot. Science at the intersection of data, modelling, and computation. Journal of Computational Science 34, pp. 117-119.
  Citation Links
• Article
  I. Anagnostou and D. Kandhai. Risk Factor Evolution for Counterparty Credit Risk under a Hidden Markov Model. Risks 7(2), 66.
  Abstract Citation Links
• Article
  G. Závodszky, B. van Rooij, B. Czaja, V. Azizi, D. de Kanter, and A. G. Hoekstra. Red blood cell and platelet diffusivity and margination in the presence of cross-stream gradients in blood flows. Physics of Fluids 31(3), 031903.
  Abstract Citation Links
• Article
  M. V. Sheraton, V. R. Melnikov, and P. M. A. Sloot. Prediction and quantification of bacterial biofilm detachment using Glazier-Graner–Hogeweg method based model simulations. Journal of Theoretical Biology 482, 109994.
  Abstract Citation Links
• Article
  S. Alowayyed, T. Piontek, J. L. Suter, O. Hoenen, D. Groen, O. Luk, B. Bosak, P. Kopta, K. Kurowski, O. Perks, K. Brabazon, V. Jancauskas, D. Coster, P. V. Coveney, and A. G. Hoekstra. Patterns for High Performance Multiscale Computing. Future Generation Computer Systems 91, pp. 335-346.
  Abstract Citation Links
• Proceedings
  V. Azizi Tarksalooyeh, G. Závodszky, and A. G. Hoekstra. Optimizing Parallel Performance of the Cell Based Blood Flow Simulation Software HemoCell. In: Computational Science – ICCS 2019. 3, pp. 537-547.
  Abstract Citation Links
• Article
  A. G. Hoekstra, S. Portegies Zwart, and P. V. Coveney. Multiscale modelling, simulation and computing: from the desktop to the exascale. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 20180355.
  Abstract Citation Links
• Article
  A. G. Hoekstra, B. Chopard, D. Coster, S. Portegies Zwart, and P. V. Coveney. Multiscale computing for science and engineering in the era of exascale performance. Philosophical Transactions of the Royal Society A - Mathematical, Physical and Engineering Sciences 377(2142), 20180144.
  Abstract Citation Links
• Article
  P. Berg, S. Voß, G. Janiga, S. Saalfeld, A. W. Bergersen, K. Valen-Sendstad, J. Bruening, L. Goubergrits, A. Spuler, T. L. Chiu, A. C. O. Tsang, G. Copelli, B. Csippa, G. Paál, G. Závodszky, F. J. Detmer, B. J. Chung, J. R. Cebral, S. Fujimura, H. Takao, C. Karmonik, S. Elias, N. M. Cancelliere, M. Najafi, D. A. Steinman, V. M. Pereira, S. Piskin, E. A. Finol, M. Pravdivtseva, P. Velvaluri, H. Rajabzadeh-Oghaz, N. Paliwal, H. Meng, S. Seshadhri, S. Venguru, M. Shojima, S. Sindeev, S. Frolov, Y. Qian, Y.-A. Wu, K. D. Carlson, D. F. Kallmes, D. Dragomir-Daescu, and O. Beuing. Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH)—phase II: rupture risk assessment. International Journal of Computer Assisted Radiology and Surgery 14(10), p. 1795–1804.
  Abstract Citation Links
• Article
  W. R. J. Vermeulen, D. Roy, and R. Quax. Modelling the Influence of Regional Identity on Human Migration. Urban Science 3(3), 78.
  Abstract Citation Links
• Article
  V. Prana, P. Tieri, M. C. Palumbo, E. Mancini, and F. Castiglione. Modeling the effect of high calorie diet on the interplay between adipose tissue, inflammation and diabetes. Computational and Mathematical Methods in Medicine 2019, 7525834.
  Abstract Citation Links
• Proceedings
  S. Shakeri, V. Maccatrozzo, L. Veen, R. Bakhshi, L. Gommans, C. de Laat, and P. Grosso. Modeling and matching digital data marketplace policies. In: IEEE 15th International Conference on eScience. pp. 570-577.
  Abstract Citation Links
• Article
  Z. Huang, E. Lum, G. Jimenez, M. Semwal, P. Sloot, and J. Car. Medication management support in diabetes: a systematic assessment of diabetes self-management apps. BMC Medicine 17, 127.
  Abstract Citation Links
• Article
  E. Caroselli, F. Gizzi, F. Prada, C. Marchini, V. Airi, J. Kaandorp, G. Falini, Z. Dubinsky, and S. Goffredo. Low and variable pH decreases recruitment efficiency in populations of a temperate coral naturally present at CO2 vent. Limnology and Oceanography 64(3), pp. 1059-1069.
  Abstract Citation Links
• Article
  P. S. Zun, A. J. Narracott, C. Chiastra, J. Gunn, and A. G. Hoekstra. Location-Specific Comparison Between a 3D In-Stent Restenosis Model and Micro-CT and Histology Data from Porcine In Vivo Experiments. Cardiovascular Engineering and Technology 10(4), p. 568–582.
  Abstract Citation Links
• Proceedings
  D. Groen, R. A. Richardson, D. W. Wright, V. Jancauskas, R. Sinclair, P. Karlshoefer, M. Vassaux, H. Arabnejad, T. Piontek, P. Kopta, B. Bosak, J. Lakhlili, O. Hoenen, D. Suleimenova, W. Edeling, D. Crommelin, A. Nikishova, and P. V. Coveney. Introducing VECMAtk - Verification, Validation and Uncertainty Quantification for Multiscale and HPC Simulations. In: Computational Science – ICCS 2019. IV, pp. 479-492.
  Abstract Citation Links
• Article
  J. Runge, S. Bathiany, E. Bollt, G. Camps-Valls, D. Coumou, E. Deyle, C. Glymour, M. Kretschmer, M. D. Mahecha, J. Muñoz-Marí, E. H. van Nes, J. Peters, R. Quax, M. Reichstein, M. Scheffer, B. Schölkopf, P. Spirtes, G. Sugihara, J. Sun, K. Zhang, and J. Zscheischler. Inferring causation from time series in Earth system sciences. Nature Communications 10, 2553.
  Abstract Citation Links
• Article
  E. Ranguelova, B. Weel, D. Roy, M. Kuffer, K. Pfeffer, and M. Lees. Image Based Classification of Slums, Built-Up and Non-Built-Up Areas in Kalyan and Bangalore, India. European Journal of Remote Sensing 52(S1), pp. 40-61.
  Abstract Citation Links
• Article
  B. J. M. van Rooij, G. Závodszky, V. W. Azizi Tarksalooyeh, and A. G. Hoekstra. Identifying the start of a platelet aggregate by the shear rate and the cell-depleted layer. Journal of the Royal Society Interface 16(159), 20190148.
  Abstract Citation Links
• Article
  A. Presbitero, E. Mancini, F. Castiglione, V. V. Krzhizhanovskaya, and R. Quax. Game of neutrophils: modeling the balance between apoptosis and necrosis. BMC Bioinformatics 20(Supplement 6), 475.
  Abstract Citation Links
• Article
  E. Weinans, J. J. Lever, S. Bathiany, R. Quax, J. Bascompte, E. H. van Nes, M. Scheffer, and I. A. van de Leemput. Finding the direction of lowest resilience in multivariate complex systems. Journal of the Royal Society Interface 16(159), 20190629.
  Abstract Citation Links
• Article
  S. Georgievska, P. Rutten, J. Amoraal, E. Ranguelova, R. Bakhshi, B. L. de Vries, M. Lees, and S. Klous. Detecting high indoor crowd density with Wi-Fi localization: a statistical mechanics approach. Journal of Big Data 6, 31.
  Abstract Citation Links
• Article
  J. Wang, M. Kuffer, D. Roy, and K. Pfeffer. Deprivation pockets through the lens of convolutional neural networks. Remote Sensing of the Environment 234, 111448.
  Abstract Citation Links
• Article
  M. G. M. Olde Rikkert, P. P. M. van Zuijlen, M. de Kleuver, A. van Reekum, A. G. Hoekstra, and P. M. A. Sloot. Complexiteit van ziekten. Nederlands Tijdschrift voor Geneeskunde 163(35), D3970.
  Abstract Citation Links
• Chapter
  G. Moysiadis, I. Anagnostou, and D. Kandhai. Calibrating the Mean-Reversion Parameter in the Hull-White Model Using Neural Networks. In: ECML PKDD 2018 Workshops. pp. 23-36.
  Abstract Citation Links
• Article
  P. Dutta, L. Ma, Y. Ali, P. M. A. Sloot, and J. Zheng. Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus. BMC Systems Biology 13(Supplement 2), 36.
  Abstract Citation Links
• Article
  Z. Huang, E. Tan, E. Lum, P. Sloot, B. O. Boehm, and J. Car. A Smartphone App to Improve Medication Adherence in Patients With Type 2 Diabetes in Asia. JMIR mHealth and uHealth 7(9), e14914.
  Abstract Citation Links
• PhD Thesis
  P. Zun. 3D modelling of in-stent restenosis. Supervised by A. G. Hoekstra, A. V. Boukhanovsky, and A. Svitenkov.
  Abstract Citation Links

2018

• Proceedings
  M. Glombek, J. R. Helmus, M. Lees, R. van den Hoed, and R. Quax. Vulnerability Of Charging Infrastructure, A Novel Approach For Improving Charging Station Deployment. In: Proceedings of 7th Transport Research Arena TRA 2018.
  Abstract Citation Links
• Article
  A. G. Hoekstra, E. T. van Bavel, M. Siebes, F. Gijsen, and L. Geris. Virtual physiological human 2016: translating the virtual physiological human to the clinic. Interface Focus 8(1), 20170067.
  Citation Links
• Article
  A. V. Boukhanovsky, V. V. Krzhizhanovskaya, and M. Bubak. Urgent computing for decision support in critical situations. Future Generation Computer Systems 79(1), pp. 111-113.
  Abstract Citation Links
• Proceedings
  J. S. Y. Tan, G. Závodszky, and P. M. A. Sloot. Understanding Malaria Induced Red Blood Cell Deformation Using Data-Driven Lattice Boltzmann Simulations. In: Computational Science – ICCS 2018. pp. 392-403.
  Abstract Citation Links
• Article
  A. Nikishova, L. Veen, P. Zun, and A. G. Hoekstra. Uncertainty Quantification of a Multiscale Model for In-Stent Restenosis. Cardiovascular Engineering and Technology 9(4), pp. 761-774.
  Abstract Citation Links
• PhD Thesis
  A. M. Abdol. Toward reverse engineering spatiotemporal gene regulatory networks of Nematostella vectensis. Supervised by P. M. A. Sloot and J. A. Kaandorp.
  Abstract Citation Links
• Article
  S. V. Kovalchuk, V. V. Krzhizhanovskaya, P. Koumoutsakos, E. Chatzi, M. H. Lees, J. Dongarra, and P. M. A. Sloot. The art of computational science: Bridging gaps – forming alloys. Journal of Computational Science 26, pp. 190-192.
  Citation Links
• Article
  A. G. Hoekstra, F. van de Vosse, and O. Röhrle. The Virtual Physiological Human Conference 2016. Journal of Computational Science 24, pp. 65-67.
  Citation Links
• Article
  V. Melnikov, V. V. Krzhizhanovskaya, M. H. Lees, and P. M. A. Sloot. System dynamics of human body thermal regulation in outdoor environments. Building and Environment 143, pp. 760-769.
  Abstract Citation Links
• Article
  D. Roy, B. Palavalli, N. Menon, R. King, K. Pfeffer, M. Lees, and P. M. A. Sloot. Survey-based socio-economic data from slums in Bangalore, India. Scientific Data 5, 170200.
  Abstract Citation Links
• Article
  A. Presbitero, E. Mancini, R. Brands, V. V. Krzhizhanovskaya, and P. M. A. Sloot. Supplemented alkaline phosphatase supports the immune response in patients undergoing cardiac surgery: Clinical and computational evidence. Frontiers in Immunology 9, 2342.
  Abstract Citation Links
• Article
  D. Roy, M. H. Lees, K. Pfeffer, and P. M. A. Sloot. Spatial segregation, inequality, and opportunity bias in the slums of Bengaluru. Cities : The International Journal of Urban Policy and Planning 74, pp. 269-276.
  Abstract Citation Links
• Article
  C. Reeb, J. Kaandorp, F. Jansson, N. Puillandre, J.-Y. Dubuisson, R. Cornette, F. Jabbour, Y. Coudert, J. Patiño, J.-F. Flot, and A. Vanderpoorten. Quantification of complex modular architecture in plants. New Phytologist 218(2), pp. 859-872.
  Abstract Citation Links
• PhD Thesis
  S. A. Alowayyed. Patterns for multiscale computing. Supervised by P. M. A. Sloot and A. G. Hoekstra.
  Abstract Citation Links
• Proceedings
  M. V. Sheraton and P. M. A. Sloot. Parallel performance analysis of bacterial biofilm simulation models. In: Computational Science – ICCS 2018. I, pp. 496-505.
  Abstract Citation Links
• Article
  M. de Haan, G. Zavodszky, V. Azizi, and A. G. Hoekstra. Numerical investigation of the effects of red blood cell cytoplasmic viscosity contrasts on single cell and bulk transport behaviour. Applied Sciences 8(9), 1616.
  Abstract Citation Links
• Article
  B. Chopard, J.-L. Falcone, P. Kunzli, L. Veen, and A. G. Hoekstra. Multiscale Modeling: recent progress and open questions. Multiscale and Multidisciplinary Modeling, Experiments and Design 1(1), p. 57–68.
  Abstract Citation Links
• Article
  D. Slavkov, N. Carrillo-Zapata, N. Carranza, X. Diego, F. Jansson, J. Kaandorp, S. Hauert, and J. Sharpe. Morphogenesis in Robot Swarms. Science Robotics 3(25), eaau9178.
  Abstract Citation Links
• Article
  A. V. Presbitero, E. Mancini, and V. V. Krzhizhanovskaya. Modelling Neutrophils' Response to Various Levels of Insults. Procedia Computer Science 136, pp. 390-397.
  Abstract Citation Links
• Article
  M. V. Sheraton, J. K. H. Yam, H. S. Oh, E. Mancini, L. Yang, S. A. Rice, and P. M. A. Sloot. Mesoscopic Energy Minimization Drives Pseudomonas aeruginosa Biofilm Morphologies and Consequent Stratification of Antibiotic Activity Based on Cell Metabolism. Antimicrobial Agents and Chemotherapy 62(4), e02544-17.
  Abstract Citation Links
• Article
  S. Alowayyed, G. Závodszky, V. Azizi, and A. G. Hoekstra. Load balancing of parallel cell-based blood flow simulations. Journal of Computational Science 24, pp. 1-7.
  Abstract Citation Links
• Article
  S. Sourabh, M. Hofer, and D. Kandhai. Liquidity risk in derivatives valuation: an improved credit proxy method. Quantitative Finance 18(3), pp. 467-481.
  Abstract Citation Links
• Report
  J. Sandberg, R. Belleman, A. Visser, T. Abcouwer, and M. Lees. IvI Education vision.
  Abstract Citation
• Article
  R. Quax, G. Chliamovitch, A. Dupuis, J.-L. Falcone, B. Chopard, A. G. Hoekstra, and P. M. A. Sloot. Information processing features can detect behavioral regimes of dynamical systems. Complexity 2018, 6047846.
  Abstract Citation Links
• Article
  V. W. Azizi Tarksalooyeh, G. Závodszky, B. J. M. van Rooij, and A. G. Hoekstra. Inflow and outflow boundary conditions for 2D suspension simulations with the immersed boundary lattice Boltzmann method. Computers & fluids 172, p. 312–317.
  Abstract Citation Links
• Article
  I. Anagnostou, S. Sourabh, and D. Kandhai. Incorporating Contagion in Portfolio Credit Risk Models Using Network Theory. Complexity 2018, 6076173.
  Abstract Citation Links
• Article
  A. M. Abdol, A. Bedard, I. Lánský, and J. A. Kaandorp. High-throughput method for extracting and visualizing the spatial gene expressions from in situ hybridization images: A case study of the early development of the sea anemone Nematostella vectensis. Gene expression patterns : GEP 27, pp. 36-45.
  Abstract Citation Links
• Article
  M. Boersma, S. Sourabh, L. Hoogduin, and D. Kandhai. Financial statement networks: an application of network theory in audit. The Journal of Network Theory in Finance 4(4), pp. 59-85.
  Abstract Citation Links
• Proceedings
  A. Presbitero, E. Mancini, F. Castiglione, V. V. Krzhizhanovskaya, and R. Quax. Evolutionary Game Theory Can Explain the Choice Between Apoptotic and Necrotic Pathways in Neutrophils. In: Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine. pp. 1401-1405.
  Abstract Citation Links
• Article
  Y. J. Liew, D. Zoccola, Y. Li, E. Tambutté, A. A. Venn, C. T. Michell, G. Cui, E. S. Deutekom, J. A. Kaandorp, C. R. Voolstra, S. Forêt, D. Allemand, S. Tambutté, and M. Aranda. Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Sciences advances 4(6), eaar8028.
  Abstract Citation Links
• Article
  L. Li, A. J. Fijneman, J. A. Kaandorp, J. Aizenberg, and W. L. Noorduin. Directed nucleation and growth by balancing local supersaturation and substrate/nucleus lattice mismatch. Proceedings of the National Academy of Sciences of the United States of America 115(14), pp. 3575-3580.
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  X. Fu, A. Presbitero, S. V. Kovalchuk, and V. V. Krzhizhanovskaya. Coupling Game Theory and Discrete-Event Simulation for Model-Based Ambulance Dispatching. Procedia Computer Science 136, pp. 398-407.
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