For best experience please turn on javascript and use a modern browser!
You are using a browser that is no longer supported by Microsoft. Please upgrade your browser. The site may not present itself correctly if you continue browsing.

Dr. J.A. (Jaap) Kaandorp

Faculty of Science
Informatics Institute

Visiting address
  • Science Park 904
  • Room number: C3.147
Postal address
  • Postbus 94323
    1090 GH Amsterdam
  • Publications


    • Caroselli, E., Gizzi, F., Prada, F., Marchini, C., Airi, V., Kaandorp, J., ... Goffredo, S. (2019). Low and variable pH decreases recruitment efficiency in populations of a temperate coral naturally present at CO2 vent. Limnology and Oceanography, 64(3), 1059-1069. [details]


    • Abdol, A. M., Bedard, A., Lánský, I., & Kaandorp, J. A. (2018). 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, 36-45. [details]
    • Li, L., Fijneman, A. J., Kaandorp, J. A., Aizenberg, J., & Noorduin, W. L. (2018). 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), 3575-3580. [details]
    • Liew, Y. J., Zoccola, D., Li, Y., Tambutté, E., Venn, A. A., Michell, C. T., ... Aranda, M. (2018). Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Science Advances, 4(6), [eaar8028]. [details]
    • Reeb, C., Kaandorp, J., Jansson, F., Puillandre, N., Dubuisson, J-Y., Cornette, R., ... Vanderpoorten, A. (2018). Quantification of complex modular architecture in plants. New Phytologist, 218(2), 859-872. [details]
    • Slavkov, D., Carrillo-Zapata, N., Carranza, N., Diego, X., Jansson, F., Kaandorp, J., ... Sharpe, J. (2018). Morphogenesis in Robot Swarms. Science Robotics, 3(25), [eaau9178]. [details]



    • Deutekom, E. S., Konglerd, P., Ramos-Silva, P., & Kaandorp, J. A. (2016). From Molecules to Morphologies, a Multiscale Modeling Approach to Unravel the Complex System of Coral Calcification. In S. Goffredo, & Z. Dubinsky (Eds.), The Cnidaria, Past, Present and Future: The world of Medusa and her sisters (pp. 223-236). Cham: Springer. [details]
    • Tanzil, J. T. I., Lee, J. N., Brown, B. E., Quax, R., Kaandorp, J. A., Lough, J. M., & Todd, P. A. (2016). Luminescence and density banding patterns in massive Porites corals around the Thai-Malay Peninsula, Southeast Asia. Limnology and Oceanography, 61(6), 2003-2026. [details]




    • Carey, L. B., van Dijk, D., Sloot, P. M. A., Kaandorp, J. A., & Segal, E. (2013). Promoter sequence determines the relationship between expression level and noise. PLoS Biology, 11(4), [e1001528]. [details]
    • Chindapol, N., Kaandorp, J. A., Cronemberger, C., Mass, T., & Genin, A. (2013). Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics. PLoS Computational Biology, 9(1), [e1002849]. [details]
    • Filatov, M. V., Frade, P. R., Bak, R. P. M., Vermeij, M. J. A., & Kaandorp, J. A. (2013). Comparison between colony morphology and molecular phylogeny in the Caribbean scleractinian coral genus Madracis. PLoS ONE, 8(8), e71287. [details]
    • Javaheri, N., Cronemberger, C. M., & Kaandorp, J. A. (2013). Modeling Biosilicification at Subcellular Scales. In W. E. G. Müller, X. Wang, & H. C. Schröder (Eds.), Biomedical Inorganic Polymers: Bioactivity and Applications of Natural and Synthetic Polymeric Inorganic Molecules (pp. 117-141). (Progress in molecular and subcellular biology; Vol. 54). Heidelberg: Springer. [details]
    • Kaandorp, J. A. (2013). Macroscopic modelling of environmental influence on growth and form of sponges and corals using the accretive growth model. ISRN Biomathematics, 2013, 159170. [details]
    • Ramos-Silva, P., Kaandorp, J., Huisman, L., Marie, B., Zanella-Cléon, I., Guichard, N., ... Marin, F. (2013). The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling. Molecular Biology and evolution, 30(9), 2099-2112. [details]
    • Tanzil, J. T. I., Brown, B. E., Dunne, R. P., Lee, J. N., Kaandorp, J. A., & Todd, P. A. (2013). Regional decline in growth rates of massive Porites corals in Southeast Asia. Global Change Biology, 19(10), 3011-3023. [details]


    • Botman, D., & Kaandorp, J. A. (2012). Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis. BMC Research Notes, 5, 555. [details]
    • Hammel, J. U., Filatov, M. V., Herzen, J., Beckmann, F., Kaandorp, J. A., & Nickel, M. (2012). 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), 160-170. [details]
    • Kaandorp, J. A., Botman, D., Tamulonis, C., & Dries, R. (2012). Multi-scale modeling of gene regulation of morphogenesis. In S. B. Cooper, A. Dawar, & B. Löwe (Eds.), How the World Computes: Turing Centenary Conference and Eighth Conference on Computability in Europe, CiE 2012, Cambridge, UK, June 18-23, 2012 : proceedings (pp. 355-362). (Lecture Notes in Computer Science; Vol. 7318). Heidelberg: Springer. [details]
    • Kim, Y., Sinclair, R., Chindapol, N., Kaandorp, J. A., & De Schutter, E. (2012). Geometric theory predicts bifurcations in minimal wiring cost trees in biology are flat. PLoS Computational Biology, 8(4), e1002474. [details]
    • Ramos-Silva, P., Benhamada, S., Le Roy, N., Marie, B., Guichard, N., Zannella-Cléon, I., ... Marin, F. (2012). Novel molluskan biomineralization proteins retrieved from proteomics: a case study with Upsalin. ChemBioChem, 13(7), 1067-1078. [details]
    • Wang, X., Schröder, H. C., Wang, K., Kaandorp, J. A., & Müller, W. E. G. (2012). Genetic, biological and structural hierarchies during sponge spicule formation: From soft sol-gels to solid 3D silica composite structures. Soft Matter, 8(37), 9501-9518. [details]


    • Kaandorp, J. A., Filatov, M., & Chindapol, N. (2011). Simulating and quantifying the environmental influence on coral colony growth and form. In Z. Dubinsky, & N. Stambler (Eds.), Coral reefs: An ecosystem in transition (pp. 177-185). Dordrecht: Springer. [details]
    • Tamulonis, C., Postma, M., & Kaandorp, J. (2011). Modeling filamentous cyanobacteria reveals the advantages of long and fast trichomes for optimizing light exposure. PLoS ONE, 6(7). [details]
    • Tamulonis, C., Postma, M., Marlow, H. Q., Magie, C. R., de Jong, J., & Kaandorp, J. (2011). A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering. Developmental Biology, 351(1), 217-228. [details]


    • Cui, J., Kaandorp, J. A., Sloot, P. M. A., & Thiagarajan, P. S. (2010). Simulating Calcineurin-Centered Calcium Signaling Network in Cardiac Myocytes. In J. E. García, & V. R. Wright (Eds.), Congestive heart failure: symptoms, causes and treatment (pp. 111-127). (Cardiology research and clinical developments). New York: Nova Publishers. [details]
    • Filatov, M. V., Kaandorp, J. A., Postma, M., van Liere, R., Kruszyński, K. J., Vermeij, M. J. A., Streekstra, G. J., & Bak, R. P. M. (2010). A comparison between coral colonies of the genus Madracis and simulated forms. Proceedings of the Royal Society B-Biological Sciences, 277(1700), 3555-3561. [details]
    • Frade, P. R., Reyes-Nivia, M. C., Faria, J., Kaandorp, J. A., Luttikhuizen, P. C., & Bak, R. P. M. (2010). Semi-permeable species boundaries in the coral genus Madracis: Introgression in a brooding coral system. Molecular Phylogenetics and Evolution, 57(3), 1072-1090. [details]



    • Cui, J., & Kaandorp, J. A. (2008). Simulating complex calcium-calcineurin signaling network. In M. Bubak, G. D. van Albada, J. Dongarra, & P. M. A. Sloot (Eds.), Computational Science – ICCS 2008: 8th International Conference, Kraków, Poland, June 23-25, 2008 : proceedings (Vol. III, pp. 110-119). (Lecture Notes in Computer Science; Vol. 5103). Berlin: Springer. [details]
    • Cui, J., Kaandorp, J. A., & Lloyd, C. M. (2008). Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli. BMC Systems Biology, 2, 89. [details]
    • Kaandorp, J. A., Blom, J. G., Verhoef, J., Filatov, M., Postma, M., & Müller, W. E. G. (2008). Modelling genetic regulation of growth and form in a branching sponge. Proceedings of the Royal Society B-Biological Sciences, 275(1651), 2569-2575. [details]
    • Wang, X., Boreiko, A., Schloßmacher, U., Brandt, D., Schröder, H. C., Li, J., ... Müller, W. E. G. (2008). 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), 270-280. [details]
    • Wiens, M., Belikov, S. I., Kaluzhnaya, O. V., Adell, T., Schröder, H. C., Perovic-Ottstadt, S., ... Müller, W. E. G. (2008). Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis. Micron, 39(4), 447-460. [details]


    • Ramos-Silva, P., Marin, F., Kaandorp, J., & Marie, B. (2013). 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), E2144-E2146. [details]


    • Kaandorp, J. A., Cronemberger, C., & Huisman, L. (2011). A spatial model of calcification in scleractinian corals. In V. Matranga (Ed.), Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application: Biomintec International Workshop, 2011 Palermo : abstracts (pp. 14). Palermo: IBIM-CNR. [details]
    • Ramos-Silva, P., Combet, C., Marin, F., & Kaandorp, J. A. (2011). Finding patterns and differences on biomineralization-related proteins from Metazoans. In V. Matranga (Ed.), Molecular iomineralization in marine organisms: Nanobiotechnology and biomedical application: Biomintec International Workshop, 2011 Palermo : abstracts (pp. 21). Palermo: IBIM-CNR. [details]


    • Kaandorp, J. A., Meesters, E., Osinga, R., Verreth, J., & Wijgerde, T. (2010). Euro ISRS symposium 2010: reefs in a changing environment: book of abstracts. Wageningen, the Netherlands: Grafisch Service Center, Wageningen, the Netherlands. [details]


    • Kaandorp, J. A. (2008). Exploring theoretical morphospaces [Review of: G.R. McGhee (2006) The geometry of evolution: adaptive landscapes and theoretical morphospaces]. BioScience, 58(3), 271-272. [details]


    • Botman, D., & Kaandorp, J. A. (2011). An integrated approach to infer the gene network in early development of the cnidarian Nematostella vectensis.. Abstract from ISNB 2011: The 8th International Symposium on Networks in Bioinformatics, .
    • Botman, D., Kaandorp, J. A., & Sloot, P. (2011). An integrated approach to infer the gene network in early development of the cnidarian Nematostella venctensis. 101. Poster session presented at International Workshop: Searching for Eve, .


    • Botman, D., & Kaandorp, J. A. (2010). An integrated approach to infer and model the gene network in early development of the cnidarian Nematostella vectensis. 62. Abstract from Euro ISRS symposium 2010, .
    This list of publications is extracted from the UvA-Current Research Information System. Questions? Ask the library or the Pure staff of your faculty / institute. Log in to Pure to edit your publications. Log in to Personal Page Publication Selection tool to manage the visibility of your publications on this list.
  • Ancillary activities
    • No ancillary activities