dhr. dr. J.A. (Jaap) Kaandorp

  • Faculteit der Natuurwetenschappen, Wiskunde en Informatica
  • Bezoekadres
    Science Park A
    Science Park 904  Amsterdam
    Kamernummer: C3.147
  • Postadres:
    Postbus  94323
    1090 GH  Amsterdam
  • J.A.Kaandorp@uva.nl
    T: 0205257539


  • 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. (pp. 223-236). Springer. [details]
  • Tanzil, J. T. I., Lee, J., Brown, B., 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]


  • Javaheri, N., Dries, R., Burson, A., Stal, L. J., Sloot, P. M. A., & Kaandorp, J. A. (2015). Temperature affects the silicate morphology in a diatom. Scientific Reports, 5, [11652]. DOI: 10.1038/srep11652 [details / files]


  • Botman, D., Röttinger, E., Martindale, M. Q., de Jong, J., & Kaandorp, J. A. (2014). A computational approach towards a gene regulatory network for the developing Nematostella vectensis gut. PLoS One, 9(7), [e103341]. DOI: 10.1371/journal.pone.0103341 [details / files]
  • Javaheri, N., Dries, R., & Kaandorp, J. (2014). 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]. DOI: 10.1371/journal.pcbi.1003687 [details] [PDF]
  • Ramos-Silva, P., Kaandorp, J., Herbst, F., Plasseraud, L., Alcaraz, G., Stern, C., ... Marin, F. (2014). The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization. PLoS One, 9(6), [e97454]. DOI: 10.1371/journal.pone.0097454 [details] [PDF]
  • Tamulonis, C., & Kaandorp, J. (2014). A model of filamentous cyanobacteria leading to reticulate pattern formation. Life Sciences, 4(3), 433-456. DOI: 10.3390/life4030433 [details / files]


  • 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]. DOI: 10.1371/journal.pcbi.1002849 [details] [PDF]
  • 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. DOI: 10.1371/journal.pone.0071287 [details / files]
  • Javaheri, N., Cronemberger, C. M., & Kaandorp, J. A. (2013). Modeling Biosilicification at Subcellular Scales In: Biomedical inorganic polymers - Bioactivity and applications of natural and synthetic polymeric inorganic molecules. 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; No. 54). Heidelberg: Springer. DOI: 10.1007/978-3-642-41004-8_5 [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. DOI: 10.1155/2013/159170 [details] [PDF]
  • Ramos-Silva, P., Marin, F., Kaandorp, J. A., & 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, E2144. DOI: 10.1073/pnas.1303657110 [details]
  • Ramos-Silva, P., Kaandorp, J. A., 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 cooption and domain shuffling. Molecular Biology and evolution, 30(9), 2099-2112. DOI: 10.1093/molbev/mst109 [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]. DOI: 10.1371/journal.pbio.1001528 [details] [PDF]
  • Tanzil, J. T., 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, 3011-3023. DOI: 10.1111/gcb.12279 [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. DOI: 10.1186/1756-0500-5-555 [details] [PDF]
  • Kaandorp, J. A., Botman, D., Tamulonis, C., & Dries, R. (2012). Multi-scale modeling of gene regulation of morphogenesis. Lecture Notes in Computer Science, 7318, 355-362. DOI: 10.1007/978-3-642-30870-3_36 [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. DOI: 10.1002/cbic.201100708 [details] [PDF]
  • 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. DOI: 10.1111/j.1463-6395.2010.00492.x [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. DOI: 10.1371/journal.pcbi.1002474 [details] [PDF]
  • 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. DOI: 10.1039/c2sm25889g [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. DOI: 10.1007/978-94-007-0114-4_11 [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. DOI: 10.1016/j.ydbio.2010.10.017 [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). DOI: 10.1371/journal.pone.0022084 [details] [PDF]


  • 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., ... 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. DOI: 10.1098/rspb.2010.0957 [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. DOI: 10.1016/j.ympev.2010.09.010 [details]


  • Ashyraliyev, M., Fomekong-Nanfack, Y., Kaandorp, J. A., & Blom, J. G. (2009). Systems biology: parameter estimation for biochemical models. The FEBS Journal, 276(4), 886-902. DOI: 10.1111/j.1742-4658.2008.06844.x [details]
  • Cui, J., Kaandorp, J. A., Ositelu, O. O., Beaudry, V., Knight, A., Nanfack, Y. F., & Cunningham, K. W. (2009). Simulating calcium influx and free calcium concentrations in yeast. Cell Calcium, 45(2), 123-132. DOI: 10.1016/j.ceca.2008.07.005 [details]
  • Cui, J., Kaandorp, J. A., Sloot, P. M. A., Lloyd, C. M., & Filatov, M. V. (2009). Calcium homeostasis and signaling in yeast cells and cardiac myocytes. FEMS Yeast Research, 9(8), 1137-1147. DOI: 10.1111/j.1567-1364.2009.00552.x [details]
  • Fomekong-Nanfack, Y., Postma, M., & Kaandorp, J. A. (2009). Inferring Drosophila gap gene regulatory network: A parameter sensitivity and perturbation analysis. BMC Systems Biology, 3, 94. DOI: 10.1186/1752-0509-3-94 [details] [PDF]
  • Fomekong-Nanfack, Y., Postma, M., & Kaandorp, J. A. (2009). Inferring Drosophila gap gene regulatory network: Pattern analysis of simulated gene expression profiles and stability analysis. BMC Research Notes, 2, 256. DOI: 10.1186/1756-0500-2-256 [details] [PDF]


  • Cui, J., & Kaandorp, J. A. (2008). Simulating complex calcium-calcineurin signaling network. Lecture Notes in Computer Science, 110-119. DOI: 10.1007/978-3-540-69389-5_14 [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. DOI: 10.1186/1752-0509-2-89 [details] [PDF]
  • 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. DOI: 10.1098/rspb.2008.0746 [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. DOI: 10.1016/j.jsb.2008.08.005 [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. DOI: 10.1016/j.micron.2007.02.003 [details]


  • Botman, D., Kaandorp, J. A., & Sloot, P. (2011). An integrated approach to infer the gene network in early development of the cnidarian Nematostella venctensis. In T. C. G. Bosch, & T. W. Holstein (Eds.), Searching for Eve: Basal metazoans and the evolution of multicellular complexity. (pp. 101-101). Tutzing, Germany. [details]
  • Kaandorp, J. A., Cronemberger, C., & Huisman, L. (2011). A spatial model of calcification in scleractinian corals. In V. Matranga (Ed.), Molecular Biomineralization in marine organisms: Nanobiotechnology and biomedical application. (pp. 14). Palermo, Italy: IBIM institute. [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 Biomineralization in marine organisms: Nanobiotechnology and biomedical application. (pp. 21-21). Palermo, Italy: IBIM institute. [details]


  • Botman, D., & Kaandorp, J. A. (2010). An integrated approach to infer and model the gene network in early development of the cnidarian Nematostella vectensis. In J. A. Kaandorp, E. Meesters, R. Osinga, J. A. J. Verreth, & T. H. M. Wijgerde (Eds.), Euro ISRS symposium 2010: Reefs in a changing environment. (pp. 62). Wageningen. [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. DOI: 10.1641/BS80315 [details] [PDF]


  • 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, . [details]
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