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2023

• Article
  H. F. Willard, E. S. Deutekom, D. Allemand, S. Tambutté, and J. A. Kaandorp. Testing hypotheses on the calcification in scleractinian corals using a spatio-temporal model that shows a high degree of robustness. Journal of Theoretical Biology 561(21), 111382.
  Abstract Citation Links
• Article
  R. A. Manzuk, A. C. Maloof, J. A. Kaandorp, and M. Webster. Branching archaeocyaths as ecosystem engineers during the Cambrian radiation. Geobiology 21(1), pp. 66-85.
  Abstract Citation Links

2022

• Article
  Q. Palazzo, M. Stagioni, S. Raaijmakers, R. G. Belleman, F. Prada, J. U. Hammel, S. Fermani, J. Kaandorp, S. Goffredo, and G. Falini. Multiscale analysis on otolith structural features reveals differences in ontogenesis and sex in Merluccius merluccius in the western Adriatic Sea. Royal Society Open Science 9(5), 211943.
  Abstract Citation Links
• Article
  D. Wangpraseurt, Y. Sun, S. You, S.-T. Chua, S. K. Noel, H. F. Willard, D. B. Berry, A. M. Clifford, S. Plummer, Y. Xiang, H. H. Hwang, J. Kaandorp, J. M. Diaz, T. C. La Jeunesse, M. Pernice, S. Vignolini, M. Tresguerres, and S. Chen. Bioprinted Living Coral Microenvironments Mimicking Coral‐Algal Symbiosis. Advanced Functional Materials 32(35), 2202273.
  Abstract Citation Links
• Article
  C. Ramírez-Portilla, I. M. Bieger, R. G. Belleman, T. Wilke, J.-F. Flot, A. H. Baird, S. Harii, F. Sinniger, and J. A. Kaandorp. Quantitative three-dimensional morphological analysis supports species discrimination in complex-shaped and taxonomically challenging corals. Frontiers in Marine Science 9, 955582.
  Abstract Citation Links

2019

• 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

2018

• 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
• 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.
  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. Science Advances 4(6), eaar8028.
  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. 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

2017

• Article
  A. M. Abdol, D. Cicin-Sain, J. A. Kaandorp, and A. Crombach. Scatter Search Applied to the Inference of a Development Gene Network. Computation 5(2), 22.
  Abstract Citation Links
• Article
  A. M. Abdol, E. Röttinger, F. Jansson, and J. A. Kaandorp. A novel technique to combine and analyse spatial and temporal expression datasets: A case study with the sea anemone Nematostella vectensis to identify potential gene interactions. Developmental Biology 428(1), pp. 204-214.
  Abstract Citation Links
• Article
  R. H. Ong, A. J. C. King, J. A. Kaandorp, B. J. Mullins, and M. J. Caley. The effect of allometric scaling in coral thermal microenvironments. PLoS ONE 12(10), e0184214.
  Abstract Citation Links
• Article
  P. Konglerd, C. Reeb, F. Jansson, and J. A. Kaandorp. Quantitative morphological analysis of 2D images of complex-shaped branching biological growth forms: the example of branching thalli of liverworts. BMC Research Notes 10(1), 103.
  Abstract Citation Links

2016

• Chapter
  E. S. Deutekom, P. Konglerd, P. Ramos-Silva, and J. A. Kaandorp. From Molecules to Morphologies, a Multiscale Modeling Approach to Unravel the Complex System of Coral Calcification. In: The Cnidaria, Past, Present and Future. ISBN 9783319313054. pp. 223-236.
  Abstract Citation Links
• Article
  J. T. I. Tanzil, J. N. Lee, B. E. Brown, R. Quax, J. A. Kaandorp, J. M. Lough, and P. A. Todd. Luminescence and density banding patterns in massive Porites corals around the Thai-Malay Peninsula, Southeast Asia. Limnology and Oceanography 61(6), pp. 2003-2026.
  Abstract Citation Links

2014

• Article
  P. Ramos-Silva, J. Kaandorp, F. Herbst, L. Plasseraud, G. Alcaraz, C. Stern, M. Corneillat, N. Guichard, C. Durlet, G. Luquet, and F. Marin. The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization. PLoS ONE 9(6), e97454.
  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
  N. Javaheri, R Dries, and J. Kaandorp. Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization. PLoS Computational Biology 10(6), e1003687.
  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

2013

• 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
• 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
  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
• Article
  P. Ramos-Silva, F. Marin, J. Kaandorp, and B. Marie. Biomineralization toolkit: the importance of sample cleaning prior to the characterization of biomineral proteomes. Proceedings of the National Academy of Sciences of the United States of America 110(24), pp. E2144-E2146.
  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
  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
• 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

2012

• 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
  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
• 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
• 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
• 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

2011

• 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
  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
  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
• 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
• 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
  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
• 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

2010

• 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
  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
• 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

2009

• Article
  J. Cui, J. A. Kaandorp, P. M. A. Sloot, C. M. Lloyd, and M. V. Filatov. Calcium homeostasis and signaling in yeast cells and cardiac myocytes. FEMS Yeast Research 9(8), pp. 1137-1147.
  Abstract Citation Links
• Article
  Y. Fomekong-Nanfack, M. Postma, and J. A. Kaandorp. Inferring Drosophila gap gene regulatory network: Pattern analysis of simulated gene expression profiles and stability analysis. BMC Research Notes 2, p. 256.
  Abstract Citation Links
• Article
  M. Ashyraliyev, Y. Fomekong-Nanfack, J. A. Kaandorp, and J. G. Blom. Systems biology: parameter estimation for biochemical models. The FEBS Journal 276(4), pp. 886-902.
  Abstract Citation Links
• Article
  Y. Fomekong-Nanfack, M. Postma, and J. A. Kaandorp. Inferring Drosophila gap gene regulatory network: A parameter sensitivity and perturbation analysis. BMC Systems Biology 3, p. 94.
  Abstract Citation Links
• Article
  J. Cui, J. A. Kaandorp, O. O. Ositelu, V. Beaudry, A. Knight, Y. F. Nanfack, and K. W. Cunningham. Simulating calcium influx and free calcium concentrations in yeast. Cell Calcium 45(2), pp. 123-132.
  Abstract Citation Links

2008

• Other: misc
  J. A. Kaandorp. Book review: P. Pelce, New visions on growth and form: fingering growth, dendrites, and flames. Mathematical Biosciences in press.
  Citation
• Other: misc
  J. A. Kaandorp. Exploring Theoretical Morphospaces, Book review: The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces. George R. McGhee. BioScience 58, pp. 271-273.
  Citation
• Article
  X. Wang, A. Boreiko, U. Schloßmacher, D. Brandt, H. C. Schröder, J. Li, J. A. Kaandorp, H. Götz, H. Duschner, and W. E. G. Müller. Axial growth of hexactinellid spicules: Formation of cone-like structural units in the giant basal spicules of the hexactinellid Monorhaphis. Journal of Structural Biology 164(3), pp. 270-280.
  Abstract Citation Links
• Article
  J. A. Kaandorp, J. G. Blom, J. Verhoef, M. Filatov, M. Postma, and W. E. G. Müller. Modelling genetic regulation of growth and form in a branching sponge. Proceedings of the Royal Society B-Biological Sciences 275(1651), pp. 2569-2575.
  Abstract Citation Links
• Proceedings
  J. Cui and J. A. Kaandorp. Simulating complex calcium-calcineurin signaling network. In: Computational Science – ICCS 2008. ISBN 9783540693895. III, pp. 110-119.
  Abstract Citation Links
• Article
  J. Cui, J. A. Kaandorp, and C. M. Lloyd. Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli. BMC Systems Biology 2, 89.
  Abstract Citation Links
• Article
  M. Wiens, S. I. Belikov, O. V. Kaluzhnaya, T. Adell, H. C. Schröder, S. Perovic-Ottstadt, J. A. Kaandorp, and W. E. G. Müller. Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis. Micron 39(4), pp. 447-460.
  Abstract Citation Links
• Article
  J. A. Kaandorp. Exploring theoretical morphospaces [Review of: G.R. McGhee (2006) The geometry of evolution: adaptive landscapes and theoretical morphospaces]. BioScience 58(3), pp. 271-272.
  Citation Links

2007

• Article
  K. Kruszynski, J. A. Kaandorp, and R. van Liere. A computational method for quantifying morphological variation in scleractinian corals. Coral reefs 26, pp. 831-840.
  Citation Links
• Article
  J. Vidal Rodríguez and J. A. Kaandorp. Inferring the distribution of Inter-Reaction Intervals for Diffusion-Limited Reactions on Lattices. International Journal of Modern Physics C 18, pp. 749-757.
  Citation Links
• Article
  W. E. G. Müller, A. Boreiko, U. Schloemacher, X. Wang, M. Nawaz Tahir, W. Tremel, D. Brandt, J. A. Kaandorp, and H. C. Schroeder. Fractal-related assembly of the axial filament in the demosponge Suberites domuncula: relevance to biomineralization and the formation of biogenic silica,. Biomaterials 28, pp. 4501-4511.
  Citation Links
• Article
  M. Dobrzyński, J. Vidal Rodríguez, J. A. Kaandorp, and J. G. Blom. Computational methods for diffusion-influenced biochemical reactions. Bioinformatics 23, pp. 1969-1977.
  Citation Links
• Article
  Y. Fomekong Nanfack, J. A. Kaandorp, and J. G. Blom. Efficient parameter estimation for spatio-temporal models of pattern formation: Case study of Drosophila melanogaster. Bioinformatics 23, pp. 3356-3363.
  Citation Links
• Article
  J. A. Kaandorp. [Review of: P. Pelcé (2004) New visions on growth and form: fingering growth, dendrites, and flames]. Mathematical Biosciences 210(2), pp. 700-702.
  Citation Links

2006

• Article
  R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, P. M. A. Sloot, and P. Hogeweg. Problem-Solving Environments for Biological Morphogenesis. IEEE Computational Science and Engineering 8, pp. 61-72.
  Citation Links
• Article
  J. Vidal Rodríguez, J. A. Kaandorp, M. Dobrzyński, and J. G. Blom. Spatial Stochastic Modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli. Bioinformatics 22, pp. 1895-1901.
  Citation Links
• Article
  J. Cui and J. A. Kaandorp. Mathematical modeling of calcium homeostasis in yeast cells. Cell Calcium 39, pp. 337-348.
  Citation Links
• Proceedings
  K. Kruszynski, R. van Liere, and J. A. Kaandorp. An Interactive Visualization System for Quantifying Coral Structures. In: Eurographics/ IEEE-VGTC Symposium on Visualization. pp. 1-8.
  Citation Links
• Article
  J. A. Kaandorp. Groei en vorm van koralen & de invloed van atmosferische CO2 en stijgende zeetemperaturen. Ecologie & Ontwikkeling 71, pp. 13-15.
  Citation Links
• Article
  K. E. Müller, O. V. Kaluzhnaya, S. I. Belikov, M. Rothenberger, H. C. Schröder, A. Reiber, J. A. Kaandorp, B. Manz, D. Mietchen, and F. Volke. Magnetic resonance imaging of the siliceous skeleton of the demosponge Lubomirskia baicalensis. Journal of Structural Biology 153, pp. 31-41.
  Citation Links

2005

• Other: misc
  J. A. Kaandorp. 'De witte dood': about coral bleaching and simulation models.
  Citation
• Article
  P. M. A. Sloot, J. A. Kaandorp, and A. G. Hoekstra. Towards Virtual Physiological Human: Multilevel Modelling and Simulation of the Human Anatomy and Phsyiology.
  Citation Links
• Article
  O. V. Kaluzhnaya, S. I. Belikov, H. C. Schröder, S. Zapf, A. Borejko, J. A. Kaandorp, A. Krasko, I. M. Müller, and W. E. G. Müller. Dynamics of skeletal formation in the Lake Baikal sponge Lubomirskia baicalensis. Part I biological and biochemical studies. Naturwissenschaften 92, pp. 128-133.
  Citation Links
• Report
  P. M. A. Sloot, J. A. Kaandorp, A. G. Hoekstra, N. Ayache, J-P. Boissel, S. Brunak, G. Clapworthy, J Fingberg, G. Lonsdale, A. F. Frangi, G. Deco, P. Hunter, P. L. Nielsen, M. Halstead, R. Hose, I. Magnin, F. Martin-Sanchez, S. van Sint Jan, and M. Viceconti. Towards Virtual Physiological Human: multilevel modelling and simulation of the human anatomy and phsyiology.
  Citation Links
• Proceedings
  K. Kruszynski, R. van Liere, and J. A. Kaandorp. Quantifying performance of 3D skeletonization algorithms. In: IASTED International Conference on Visualization, Imaging, and Image Processing (VIIP '05).
  Citation Links
• Article
  J. A. Kaandorp, P. M. A. Sloot, R. M. H. Merks, R. P. M. Bak, M. J. A. Vermeij, and C. Maier. Morphogenesis of the branching reef coral Madracis mirabilis. Proceedings of the Royal Society B-Biological Sciences 272, pp. 127-133.
  Abstract Citation Links

2004

• Proceedings
  J. Cui and J. A. Kaandorp. Mathematical modelling of calcium homeostasis in yeast cells. In: Proceedings of the 12th International Conference on Intelligent Systems for Molecular Biology and 3rd European Conference on Computational Biology (ISMB/ECCB).
  Citation Links
• Chapter
  J. A. Kaandorp and R. A. Garcia Leiva. Morphological analysis of two- and three-dimensional images of branching sponges and corals. In: Morphometrics - Applications in Biology and Paleontology. ISBN 3540214291, 9783540214298.
  Citation Links
• Article
  R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. Polyp oriented modelling of coral growth. Journal of Theoretical Biology 228(4), pp. 559-576.
  Abstract Citation Links

2003

• Proceedings
  R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. Problem Solving Environment for Modelling Stony Coral Morphogenesis. In: Computational Science - ICCS 2003. ISBN 3540401946, 9783540401940. 2657, pp. 639-648.
  Citation Links
• Article
  J. A. Kaandorp, E. A. Koopman, P. M. A. Sloot, R. P. M. Bak, M. J. A. Vermeij, and L. E. H. Lampmann. Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassaing and Michelotti). Philosophical Transactions of the Royal Society B - Biological Sciences 358(1437), pp. 1551-1557.
  Citation Links
• Proceedings
  J. A. Kaandorp. Modelling growth and form of stony corals and the influence of hydrodynamics on suspension feeding. In: Proceedings 9th International Coral Reef Symposium. 1, pp. 541-547.
  Citation Links
• Proceedings
  R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. Branching and compactification in a model of coral growth: a critical reinvestigation of the effect of hydrodynamics. In: Mathematical modelling & Computing in Biology and Medicine; 5th ESMTB Conference 2002. pp. 539-544.
  Citation Links
• Proceedings
  T. Krul, J. A. Kaandorp, and J. G. Blom. Modelling Developmental Regulatory Networks. In: Computational Science- ICCS 2003, Proceedings Part I. ISBN 3540401946, 9783540401940. 2660, pp. 688-697.
  Citation Links
• Article
  R. Merks, A. Hoekstra, J. Kaandorp, and P. Sloot. Models of coral growth: spontaneous branching, compactification and the Laplacian growth assumption. Journal of Theoretical Biology 224(2), pp. 153-166.
  Abstract Citation Links
• Article
  R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. Diffusion-limited Aggregation in Laminar Flows. International Journal of Modern Physics C 14(9), pp. 1171-1182.
  Abstract Citation Links

2002

• Proceedings
  R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. Branching and compactification in a model of coral growth: a critical reinvestigation of the effect of hydrodynamics. In: ECMTB2002: 5th Conference of the European Society of the Mathematical and Theoretical Biology, book of abstracts.
  Citation Links
• Proceedings
  R. M. H. Merks, A. G. Hoekstra, J. A. Kaandorp, and P. M. A. Sloot. Spontaneous branching in a polyp oriented model of stony coral growth. In: Computational Science- ICCS 2002, Proceedings Part I. 2329, pp. 88-96.
  Citation Links
• Article
  H. Afsarmanesh, R. G. Belleman, A. S. Z. Belloum, A. Benabdelkader, J. F. J. van den Brand, G. B. Eijkel, A. Frenkel, C. Garita, D. L. Groep, R. M. A. Heeren, Z. W. Hendrikse, L. O. Hertzberger, J. A. Kaandorp, E. C. Kaletas, V. Korkhov, C. T. A. M. de Laat, P. M. A. Sloot, D. Vasunin, A. Visser, and H. H. Yakali. VLAM-G: A Grid-based virtual laboratory. Scientific Programming 10(2), pp. 173-181.
  Citation Links

2001

• Proceedings
  J. A. Kaandorp. Simulation and visualization of processes at irregular and complex-shaped interfaces. In: Proceedings of the 7th annual conference of the Advanced School for Computing and Imaging (abstract). ISBN 9080308668, 9789080308664. p. 15.
  Citation Links
• Chapter
  P. M. A. Sloot, J. A. Kaandorp, A. G. Hoekstra, and B. J. Overeinder. Distributed Cellular Automata: Large Scale Simulation of Natural Phenomena. In: Solutions to Parallel and Distributed Computing Problems: Lessons from Biological Sciences. pp. 1-46.
  Citation Links
• Article
  J. A. Kaandorp and P. M. A. Sloot. Morphological Models of Radiate Accretive Growth and the Influence of Hydrodynamics. Journal of Theoretical Biology 209(3), pp. 257-274.
  Citation Links
• Book
  J. A. Kaandorp and J. E. Kübler. The algorithmic beauty of seaweeds, sponges and corals.
  Citation Links
• Article
  J. A. Kaandorp and S. Gueron. Special issue on particle based modelling in biology. Future Generation Computer Systems .
  Citation Links

2000

• Other: misc
  H. Jones and J. A. Kaandorp. Modelling of growing natural forms. Tutorial T2, Eurographics 2000 T2, pp. 1-32.
  Citation
• Chapter
  J. A. Kaandorp and P. M. A. Sloot. Growth and Form of Sponges and Corals in a Moving Fluid. In: Pattern Formation in Biology, Vision and Dynamics. ISBN 978-981-02-3792-9. pp. 24-41.
  Citation
• Chapter
  P. M. A. Sloot, J. A. Kaandorp, A. G. Hoekstra, and B. J. Overeinder. Distributed Cellular Automata: Large Scale Simulation of Natural Phenomena. In: Bio-inspired Computation.
  Citation Links

1999

• Proceedings
  R. G. Belleman, J. A. Kaandorp, D. Dijkman, and P. M. A. Sloot. GEOPROVE: Geometric Probes for Virtual Environments. In: High-Performance Computing and Networking (HPCN Europe '99), Amsterdam, The Netherlands. ISBN 978-3-540-65821-4. Lecture Notes in Computer Science pp. 817-827.
  Citation
• Other: misc
  J. A. Kaandorp. Thematic issue on Virtual Reality in Industry and Research. Future Generation Computer Systems 14, pp. 467-536.
  Citation
• Proceedings
  P. M. A. Sloot, J. A. Kaandorp, A. G. Hoekstra, and B. J. Overeinder. Distributed Simulation with Cellular Automata: Architecture and Applications. In: SOFSEM'99 Theory and Practice of Informatics, Proceedings of 26th Seminar on Current Trends, in Theory and Practice of Informatics, Milovy, Czech Republic, November 27 - December 4. ISBN 978-3-540-66694-3. Lecture Notes on Computer Science pp. 203-249.
  Citation Links
• Chapter
  J. A. Kaandorp and P. M. A. Sloot. Growth and form of sponges and corals in a moving fluid. In: Pattern Formation in biology, vision and dynamics. pp. 24-41.
  Citation Links
• Article
  P. M. A. Sloot, J. A. Kaandorp, A. G. Hoekstra, and B. J. Overeinder. Distributed simulation with cellular automata: Architecture and applications. Lecture Notes in Computer Science 1725, pp. 203-249.
  Citation Links
• Proceedings
  R. M. H. Merks, J. A. Kaandorp, and P. M. A. Sloot. The interplay of hydrodynamics and genetic regulation in the morphogenesis of sponges and stony corals: pilot studies. In: Theory and Mathematics in Biology and Medicine: Abstracts. p. 345.
  Citation Links
• Article
  R. G. Belleman, J. A. Kaandorp, P. M. A. Sloot, and D. Dijkman. Geoprove: Geometric probes for virtual environments. Lecture Notes in Computer Science 1593, pp. 817-827.
  Citation Links
• Article
  J. A. Kaandorp. Morphological analysis of growth forms of branching marine sessile organisms along environmental gradients. Marine Biology 134, pp. 295-306.
  Citation Links
• Book
  M. Boasson, J. A. Kaandorp, J. F. M. Tonino, and M. G. Vosselman. Proceedings of the fifth annual conference of the Advanced School for Computing and Imaging ASCI.
  Citation Links
• Proceedings
  R. G. Belleman, J. A. Kaandorp, D. Dijkman, and P. M. A. Sloot. Geoprove: Geometric probes for virtual environments. In: Proceedings of the fifth annual conference of the Advanced School for Computing and Imaging ASCI, June 15-17, 1999. June 1999, pp. 38-43.
  Citation Links

1998

• Other: misc
  J. A. Kaandorp. Special Issue on EURO-VR Mini-conference '97: Virtual reality in industry and research. Future Generation Computer Systems 14(3-4), pp. 143-300.
  Citation
• Proceedings
  R. G. Belleman, J. A. Kaandorp, and P. M. A. Sloot. Interactive environments for the exploration of large data sets. In: ASCI'98: proceedings of the fourth annual conference of the Advanced School for Computing and Imaging, Lommel, Belgium, June 9-11 1998. ISBN 9080308633, 9789080308633. pp. 264-268.
  Citation Links
• Article
  J. A. Kaandorp. Guest Editorial EURO-VR Mini-conference '97: Virtual reality in industry and research. Future Generation Computer Systems 14, pp. 143-145.
  Citation Links
• Article
  J. A. Kaandorp. Guest editorial EURO-VR Mini-conference '97: Virtual reality in industry ansd research. Future Generation Computer Systems 275-276, pp. 281-286.
  Citation Links
• Article
  R. G. Belleman, J. A. Kaandorp, and P. M. A. Sloot. A virtual environment for the exploration of diffusion and flow phenomena in complex geometries. Future Generation Computer Systems 14(3/4), pp. 209-214.
  Abstract Citation Links

1997

• Chapter
  J. A. Kaandorp and P. M. A. Sloot. A mesoscopic model for simulating the combined effect of hydrodynamics and diffusion on nutrient driven growth processes. In: Proceedings of the international conference Multi-scale Phenomena and their Simulation conference. pp. 250-254.
  Citation Links
• Article
  J. A. Kaandorp and P. M. A. Sloot. Parallel simulation of accretive growth in 3-dimensions. Biosystems 44(3), pp. 181-192.
  Citation Links

1996

• Other: unpublished
  J. A. Kaandorp. From July 1996 until March 1997 (monthly), cover picture and abstract. Mathematical Seminar .
  Citation
• Chapter
  A. Schoneveld, J. F. de Ronde, P. M. A. Sloot, and J. A. Kaandorp. A Parallel Cellular Genetic Algorithm Used in Finite Element Simulation. In: Parallel Problem Solving from Nature IV. pp. 533-542.
  Citation Links
• Chapter
  P. M. A. Sloot and J. A. Kaandorp. Particle modelling environment for dynamic complex system simulation. In: Biocomplexity and the essence of the living state. pp. 83-85.
  Citation Links
• Chapter
  P. M. A. Sloot, D. Frenkel, J. A. Kaandorp, and R. van Driel. Modelling and simulation of reactivity, diffusion, and flow in biological systems using the lattice Boltzmann method. In: Biocomplexity and the essence of the living state. pp. 80-82.
  Citation Links
• Article
  J. A. Kaandorp, C. P. Lowe, D. Frenkel, and P. M. A. Sloot. The effect of nutrient diffusion and flow on coral morphology. Physical Review Letters 77(11), pp. 2328-2331.
  Citation Links
• Article
  H. E. McEvoy and J. A. Kaandorp. On modelling environmentally-sensitive growth forms and cellular automata using multiset transformation. Fractals 4(4), pp. 509-520.
  Citation Links
• Chapter
  J. A. Kaandorp and P. M. A. Sloot. Modelling and simulation of accretive growth and form on a parallel platform. In: ASCI '96, Proceedings of the second annual conference of the Advanced School for Computing and Imaging. pp. 54-59.
  Citation Links
• Article
  J. A. Kaandorp. Cover picture and abstract (in Japanese). Mathematical Seminar .
  Citation Links
• Chapter
  J. A. Kaandorp. Simulation of growth and form of sponges and corals and the influence of the physical environment. In: Modeling complex data for creating information: real and virtual objects. pp. 199-208.
  Citation Links
• Chapter
  J. A. Kaandorp. Modelling and simulation of the effect of diffusion and flow on growth processes. In: Proceedings 1996 CERN School of computing. pp. 239-246.
  Citation Links
• Chapter
  J. A. Kaandorp and P. M. A. Sloot. Modelling growth and form of marine sessile suspension feeders. In: Advances in Computational Life Sciences Vol. 1. pp. 129-132.
  Citation Links
• Proceedings
  J. A. Kaandorp and P. M. A. Sloot. Modelling diffusion and flow limited morphogenesis of marine sessile orginisms. In: 3rd European conference of mathematics applied to biology and medicine.
  Citation Links
• Article
  J. A. Kaandorp. De invloed van diffusie en stroming op groei en vorm. Afleiding 1(6), pp. 2-5.
  Citation Links

1995

• Other: unpublished
  J. A. Kaandorp, C. P. Lowe, D. Frenkel, P. M. A. Sloot, and N. C. Rozemeijer. Flow and diffusion Limited growth of aggregates.
  Citation
• Article
  J. A. Kaandorp and P. M. A. Sloot. Parallel Solvers for Simulating Morphogenesis. PowerXplorer User Report, 1st edition pp. 77-84.
  Citation
• Article
  J. A. Kaandorp. Analysis and synthesis of radiate accretive growth in three dimensions. Journal of Theoretical Biology 175, pp. 39-55.
  Citation Links
• Chapter
  A. Schoneveld, J. A. Kaandorp, and P. M. A. Sloot. Parallel Dynamical Complex Systems. In: PowerXplorer User Report, 1st edition. pp. 152-156.
  Citation Links
• Chapter
  J. A. Kaandorp and P. M. A. Sloot. A parallel hybrid solver for diffusion limited growth. In: Parallel Programming and Applications Proceedings of the Workshop on Parallel Programming and Computation (ZEUS '95) and the 4th Nordic Transputer Conference (NTUG '95). pp. 254-258.
  Citation Links
• Report
  J. A. Kaandorp and P. M. A. Sloot. Parallel solvers for simulating morphogenesis.
  Citation Links
• Report
  A. Schoneveld, J. A. Kaandorp, and P. M. A. Sloot. Parallel Dynamic Complex Systems.
  Citation Links
• Report
  P. M. A. Sloot, J. A. Kaandorp, and A. Schoneveld. Dynamic Complex Systems (DCS): A New Approach to Parallel Computing in Computational Physics.
  Citation Links

1994

• Other: unpublished
  J. A. Kaandorp. Diffusion-limited growth of sponges.
  Citation
• Chapter
  J. A. Kaandorp. Growth models of sponges using geometric modelling techniques. In: Sponges in time and space. pp. 235-240.
  Citation Links
• Chapter
  J. A. Kaandorp. Diffusion limited radiate accretive growth. In: Proceedings of the 6th joint EPS-APS International Conference on Physics Computing. pp. 281-284.
  Citation Links
• Book
  J. A. Kaandorp. Fractal modelling: growth and form in biology.
  Citation Links
• Chapter
  J. A. Kaandorp. Simulation of environmentally induced growth forms in marine sessile organisms. In: Fractals in natural sciences. pp. 96-100.
  Citation Links
• Article
  J. A. Kaandorp. A formal description of radiate accretive growth. Journal of Theoretical Biology 166, pp. 149-161.
  Citation Links

1993

• Proceedings
  J. A. Kaandorp. 2D and 3D modelling of marine sessile organisms. In: Applications of fractals and chaos. pp. 41-61.
  Citation Links
• Proceedings
  J. A. Kaandorp. Simulating radiate accretive growth using iterative geometric constructions. In: Growth patterns in physical sciences and biology, NATO ASI Series B: Physics Vol. 304. pp. 331-340.
  Citation Links
• Proceedings
  J. A. Kaandorp. Fractal modelling of growth forms of the sponge em Haliclona oculata/. In: Mathematics applied to biology and medicine. pp. 104-106.
  Citation Links
• Article
  J. A. Kaandorp. Simulation of environmentally induced growth forms in marine sessile organisms. Fractals 1, pp. 375-379.
  Citation Links

1992

• Other: unpublished
  J. A. Kaandorp. Sponges in Space.
  Citation
• PhD Thesis
  J. A. Kaandorp. Modelling growth forms of biological objects using fractals. Supervised by F. C. A. Groen, J. H. Stock, E. H. Dooijes, and H. A. Lauwerier.
  Citation Links
• Article
  J. A. Kaandorp and M. J. de Kluijver. Verification of fractal growth models of the sponge em Haliclona oculata/ (Porifera; class Demospongiae) with transplantation experiments. Marine Biology 113, pp. 133-143.
  Citation Links

1991

• Proceedings
  J. A. Kaandorp. Modelling growth forms of sponges with fractal techniques. In: Fractals and Chaos. pp. 71-88.
  Citation Links
• Article
  J. A. Kaandorp. Modelling growth forms of the sponge em Haliclona oculata/ (Porifera; Demospongiae) using fractal techniques. Marine Biology 110, pp. 203-215.
  Citation Links

1990

• Article
  J. A. Kaandorp. Fractal growth models of sponges (Porifera). Netherlands Journal of Zoology 199, p. 140.
  Citation Links

1988

• Proceedings
  H. A. Lauwerier and J. A. Kaandorp. Fractals (mathematics, programming and applications). In: Advances in computer graphics III. pp. 177-205.
  Citation Links

1987

• Proceedings
  J. A. Kaandorp. Interactive generation of fractal objects. In: Proceedings of the European Computer Graphics Conference. pp. 181-196.
  Citation Links

1986

• Article
  J. A. Kaandorp. Rocky substrate communities of the infralittoral fringe of the Boulonnais coast, NW France: a quantitative survey. Marine Biology 92, pp. 255-265.
  Citation Links