Dr. J.A. (Jaap) Kaandorp
Faculteit der Natuurwetenschappen, Wiskunde en Informatica
Informatics Institute
Bezoekadres
- Science Park 904
- Kamernummer: C3.147
Postadres
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Postbus 94323
1090 GH Amsterdam
Contactgegevens
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Publicaties
2023
Manzuk, R. A., Maloof, A. C., Kaandorp, J. A., & Webster, M. (2023). Branching archaeocyaths as ecosystem engineers during the Cambrian radiation. Geobiology, 21(1), 66-85. https://doi.org/10.1111/gbi.12521 [details]- Willard, H. F., Deutekom, E. S., Allemand, D., Tambutté, S., & Kaandorp, J. A. (2023). 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), Article 111382. Advance online publication. https://doi.org/10.1016/j.jtbi.2022.111382 [details]
2022
- Palazzo, Q., Stagioni, M., Raaijmakers, S., Belleman, R. G., Prada, F., Hammel, J. U., Fermani, S., Kaandorp, J., Goffredo, S., & Falini, G. (2022). 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), Article 211943. https://doi.org/10.1098/rsos.211943 [details]
- Ramírez-Portilla, C., Bieger, I. M., Belleman, R. G., Wilke, T., Flot, J-F., Baird, A. H., Harii, S., Sinniger, F., & Kaandorp, J. A. (2022). Quantitative three-dimensional morphological analysis supports species discrimination in complex-shaped and taxonomically challenging corals. Frontiers in Marine Science, 9, Article 955582. https://doi.org/10.3389/fmars.2022.955582 [details]
- Wangpraseurt, D., Sun, Y., You, S., Chua, S-T., Noel, S. K., Willard, H. F., Berry, D. B., Clifford, A. M., Plummer, S., Xiang, Y., Hwang, H. H., Kaandorp, J., Diaz, J. M., La Jeunesse, T. C., Pernice, M., Vignolini, S., Tresguerres, M., & Chen, S. (2022). Bioprinted Living Coral Microenvironments Mimicking Coral‐Algal Symbiosis. Advanced Functional Materials, 32(35), Article 2202273. https://doi.org/10.1002/adfm.202202273 [details]
2019
- Caroselli, E., Gizzi, F., Prada, F., Marchini, C., Airi, V., Kaandorp, J., Falini, G., Dubinsky, Z., & 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. Advance online publication. https://doi.org/10.1002/lno.11097 [details]
2018
- 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. Advance online publication. https://doi.org/10.1016/j.gep.2017.10.005 [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. https://doi.org/10.1073/pnas.1712911115 [details]
- Liew, Y. J., Zoccola, D., Li, Y., Tambutté, E., Venn, A. A., Michell, C. T., Cui, G., Deutekom, E. S., Kaandorp, J. A., Voolstra, C. R., Forêt, S., Allemand, D., Tambutté, S., & Aranda, M. (2018). Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral. Science Advances, 4(6), Article eaar8028. https://doi.org/10.1126/sciadv.aar8028 [details]
- Reeb, C., Kaandorp, J., Jansson, F., Puillandre, N., Dubuisson, J-Y., Cornette, R., Jabbour, F., Coudert, Y., Patiño, J., Flot, J-F., & Vanderpoorten, A. (2018). Quantification of complex modular architecture in plants. New Phytologist, 218(2), 859-872. Advance online publication. https://doi.org/10.1111/nph.15045 [details]
- Slavkov, D., Carrillo-Zapata, N., Carranza, N., Diego, X., Jansson, F., Kaandorp, J., Hauert, S., & Sharpe, J. (2018). Morphogenesis in Robot Swarms. Science Robotics, 3(25), Article eaau9178. https://doi.org/10.1126/scirobotics.aau9178 [details]
2017
- Abdol, A. M., Cicin-Sain, D., Kaandorp, J. A., & Crombach, A. (2017). Scatter Search Applied to the Inference of a Development Gene Network. Computation, 5(2), Article 22. https://doi.org/10.3390/computation5020022 [details]
- Abdol, A. M., Röttinger, E., Jansson, F., & Kaandorp, J. A. (2017). 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), 204-214. Advance online publication. https://doi.org/10.1016/j.ydbio.2017.06.004 [details]
- Konglerd, P., Reeb, C., Jansson, F., & Kaandorp, J. A. (2017). 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), Article 103. https://doi.org/10.1186/s13104-017-2424-0 [details]
- Ong, R. H., King, A. J. C., Kaandorp, J. A., Mullins, B. J., & Caley, M. J. (2017). The effect of allometric scaling in coral thermal microenvironments. PLoS ONE, 12(10), Article e0184214. https://doi.org/10.1371/journal.pone.0184214 [details]
2016
- 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). Springer. https://doi.org/10.1007/978-3-319-31305-4_14 [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. Advance online publication. https://doi.org/10.1002/lno.10350 [details]
2015
- 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, Article 11652. https://doi.org/10.1038/srep11652 [details]
2014
- 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), Article e103341. Advance online publication. https://doi.org/10.1371/journal.pone.0103341 [details]
- 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), Article e1003687. https://doi.org/10.1371/journal.pcbi.1003687 [details]
- Ramos-Silva, P., Kaandorp, J., Herbst, F., Plasseraud, L., Alcaraz, G., Stern, C., Corneillat, M., Guichard, N., Durlet, C., Luquet, G., & Marin, F. (2014). The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization. PLoS ONE, 9(6), Article e97454. https://doi.org/10.1371/journal.pone.0097454 [details]
- Tamulonis, C., & Kaandorp, J. (2014). A model of filamentous cyanobacteria leading to reticulate pattern formation. Life (Basel), 4(3), 433-456. https://doi.org/10.3390/life4030433 [details]
2013
- 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), Article e1001528. https://doi.org/10.1371/journal.pbio.1001528 [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), Article e1002849. https://doi.org/10.1371/journal.pcbi.1002849 [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. https://doi.org/10.1371/journal.pone.0071287 [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). Springer. https://doi.org/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. https://doi.org/10.1155/2013/159170 [details]
- Ramos-Silva, P., Kaandorp, J., Huisman, L., Marie, B., Zanella-Cléon, I., Guichard, N., Miller, D. J., & 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. Advance online publication. https://doi.org/10.1093/molbev/mst109 [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. https://doi.org/10.1111/gcb.12279 [details]
2012
- 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. Advance online publication. https://doi.org/10.1186/1756-0500-5-555 [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. Advance online publication. https://doi.org/10.1111/j.1463-6395.2010.00492.x [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). Springer. https://doi.org/10.1007/978-3-642-30870-3_36 [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. https://doi.org/10.1371/journal.pcbi.1002474 [details]
- Ramos-Silva, P., Benhamada, S., Le Roy, N., Marie, B., Guichard, N., Zannella-Cléon, I., Plasseraud, L., Corneillat, M., Alcaraz, G., Kaandorp, J., & Marin, F. (2012). Novel molluskan biomineralization proteins retrieved from proteomics: a case study with Upsalin. ChemBioChem, 13(7), 1067-1078. Advance online publication. https://doi.org/10.1002/cbic.201100708 [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. https://doi.org/10.1039/c2sm25889g [details]
2011
- 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). Springer. https://doi.org/10.1007/978-94-007-0114-4_11 [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). https://doi.org/10.1371/journal.pone.0022084 [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. https://doi.org/10.1016/j.ydbio.2010.10.017 [details]
2010
- 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). Nova Publishers. https://www.novapublishers.com/catalog/product_info.php?products_id=11091 [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. https://doi.org/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. https://doi.org/10.1016/j.ympev.2010.09.010 [details]
2009
- 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. https://doi.org/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. https://doi.org/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. https://doi.org/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. https://doi.org/10.1186/1752-0509-3-94 [details]
- 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. https://doi.org/10.1186/1756-0500-2-256 [details]
2008
- 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). Springer. https://doi.org/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, Article 89. https://doi.org/10.1186/1752-0509-2-89 [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. https://doi.org/10.1098/rspb.2008.0746 [details]
- Wang, X., Boreiko, A., Schloßmacher, U., Brandt, D., Schröder, H. C., Li, J., Kaandorp, J. A., Götz, H., Duschner, H., & 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. https://doi.org/10.1016/j.jsb.2008.08.005 [details]
- Wiens, M., Belikov, S. I., Kaluzhnaya, O. V., Adell, T., Schröder, H. C., Perovic-Ottstadt, S., Kaandorp, J. A., & Müller, W. E. G. (2008). Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis. Micron, 39(4), 447-460. https://doi.org/10.1016/j.micron.2007.02.003 [details]
2013
- 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. https://doi.org/10.1073/pnas.1303657110 [details]
2011
- 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). IBIM-CNR. https://biomintec.ibim.cnr.it/images/stories/book_abstracts.pdf [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). IBIM-CNR. http://biomintec.ibim.cnr.it/images/stories/book_abstracts.pdf [details]
2010
- 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]
2008
- 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. https://doi.org/10.1641/BS80315 [details]
2011
- 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. http://isnb.amc.uva.nl/isnb2011/abstracts1.html#Daniel%20Botman
- 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. http://www.hydra-meeting.de/docs/programm2011.pdf
2010
- 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. https://togather.eu/view-abstractbook?collection_id=76
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. -
Nevenwerkzaamheden
- Geen nevenwerkzaamheden
Manzuk, R. A., Maloof, A. C., Kaandorp, J. A., & Webster, M. (2023). Branching archaeocyaths as ecosystem engineers during the Cambrian radiation. Geobiology, 21(1), 66-85.