Computational Biology

Section Computational Science

Refereed publications first author

[ 1 ] J.A. Kaandorp. Rocky substrate communities of the infralittoral fringe of the Boulonnais coast, NW france: a quantitative survey. Mar. Biol., 92:255--265, 1986.

[ 2 ] J.A. Kaandorp. Interactive generation of fractal objects. In G.~Marechal, editor, Proceedings of the European Computer Graphics Conference, pages 181--196, Amsterdam, New York, 1987. North-Holland.

[ 3 ] J.A. Kaandorp. Modelling growth forms of sponges with fractal techniques. In A.J. Crilly, R.A. Earnshaw, and H.~Jones, editors, Fractals and chaos, pages 71--88, New York, Berlin, 1991. Springer-Verlag.

[ 4 ] J.A. Kaandorp. Modelling growth forms of the sponge Haliclona oculata (Porifera; Demospongiae) using fractal techniques. Mar. Biol., 110:203--215, 1991.

[ 5 ] J.A. Kaandorp. Modelling growth forms of biological objects using fractals. PhD thesis, University of Amsterdam, 1992.

[ 6 ] J.A. Kaandorp and M.J. de Kluijver. Verification of fractal growth models of the sponge Haliclona oculata (Porifera; class Demospongiae) with transplantation experiments. Mar. Biol., 113:133--143, 1992.

[ 7 ] J.A. Kaandorp. 2D and 3D modelling of marine sessile organisms. In A.J. Crilly, R.A. Earnshaw, and H.~Jones, editors, Applications of fractals and chaos, pages 41--61, New York, Berlin, 1993. Springer-Verlag.

[ 8 ] J.A. Kaandorp. Fractal modelling of growth forms of the sponge Haliclona oculata. In J. Demongeot and V. Capasso, editors, Mathematics applied to biology and medicine, pages 104--106, Winnipeg, Canada, 1993. Wuerz

[ 9 ] J.A. Kaandorp. Simulating radiate accretive growth using iterative geometric constructions. In E. Louis, L.M. Sander, P. Meakin, and J.M. Garcia.Ruiz, editors, Growth patterns in physical sciences and biology, pages 331--340, New York, 1993. Plenum Press.

[ 10 ] J.A. Kaandorp. Simulation of environmentally induced growth forms in marine sessile organisms. Fractals, 1(3):375--379, 1993.

[ 11 ] J.A. Kaandorp. Diffusion-limited growth of sponges. In M. Hammel and P. Prusinkiewicz, editors, Visual models of morphogenesis: a guided tour, section 6, 1994. URL:http://www.cpsc.ucalgary.ca/projects/bmv/index.html.

[ 12 ] J.A. Kaandorp. Diffusion limited radiate accretive growth. In R.~Gruber and M.~Tomassini, editors, Physics Computing '94, pages pp 281--284, Geneva, 1994. European Physical Society.

[ 13 ] J.A. Kaandorp. A formal description of radiate accretive growth. J. Theor. Biol., 166:149--161, 1994.

[ 14 ] J.A. Kaandorp. Fractal modelling: growth and form in biology. Springer-Verlag, Berlin, New York, 1994.

[ 15 ] J.A. Kaandorp. Growth models of sponges using geometric modelling techniques. In R.W.M. van Soest, Th.M.G. van Kempen, and J.C. Braekman, editors, Sponges in time and space, pages 235--240, Rotterdam, 1994. Balkema.

[ 16 ] J.A. Kaandorp. Simulation of environmentally induced growth forms in marine sessile organisms. In T. Vicsek, M. Shlesinger, and M. Matsushita, editors, Fractals in natural sciences, pages 96--100, Singapore, 1994. World Scientific.

[ 17 ] J.A. Kaandorp. Analysis and synthesis of radiate accretive growth in three dimensions. J. Theor. Biol., 175:39--55, 1995.

[ 18 ] J.A. Kaandorp and P.M.A. Sloot. A parallel hybrid solver for diffusion limited growth. In P. Fritzon and L.Finmo, editors, Parallel Programming and Applications Proceedings of the Workshop on Parallel Programming and Computation (ZEUS '95) and the 4th Nordic Transputer Conference (NTUG '95), pages 254--258, Amsterdam, 1995. IOS Press, the Netherlands.

[ 19 ] J.A. Kaandorp. Simulation of growth and form of sponges and corals and the influence of the physical environment. In J. Dubois and N. Gershon, editors, Modeling complex data for creating information: real and virtual objects, pages 199-208, Berlin, 1996, Springer-Verlag.

[ 20 ] J.A. Kaandorp, C.Lowe, D.Frenkel, and P.M.A. Sloot. The effect of nutrient diffusion and flow on coral morphology. Phys. Rev. Lett., 77(11):2328--2331, 1996.

[ 21 ] J.A. Kaandorp and P.M.A. Sloot. Modelling growth and form of marine sessile suspension feeders. In: Advances in Computational Life Sciences Vol. I M. T. Michalewicz (ed.) pp 129-132, CSIRO Publishing, Collingwood, Australia, 1996

[ 22 ] J.A. Kaandorp and P.M.A. Sloot. Parallel simulation of accretive growth in 3-dimensions. BioSystems 44(3):181-192, 1997.

[ 23 ] 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, E.J.H. Kerckhoffs, P.M.A. Sloot, J.F.M. Tonino and A.M. Vossepoel (eds.), pp 54-59, Advanced School for Computing and Imaging (ASCI), Delft, 1996

[ 24 ] J.A. Kaandorp. Modelling and simulation of the effect of diffusion and flow on growth processes, In: Proceedings 1996 CERN School of Computing, C.E. Vandon (ed.), pp. 239-246, CERN European Organization for Nuclear Research, Geneva, 1996.

[ 25 ] J.A. Kaandorp and P.M.A. Sloot. A mesoscopic Model for simulating and their Simulation conference, F. Karsch, B. Monien and H. Satz (eds), pp 250-254, World Scientific, Singapore, 1997.

[ 26 ] J.A. Kaandorp, Guest editorial EURO-VR Mini-conference '97: Virtual reality in industry and research, Future Generation Computer Systems 14(3-4) (1998).

[ 27 ] J.A. Kaandorp and P.M.A. Sloot. Growth and form of sponges and corals in a moving fluid. In Pattern formation in biology, vison and dynamics A. Carbone, M. Gromov and P.Pruzinkiewicz (eds.), pp. 24--41 World Scientific Publishing Company, Singapore, 2000.

[ 28 ] J.A. Kaandorp. Morphological analysis of growth forms of branching marine sessile organisms along environmental gradients Mar. Biol 134:295-306 (1999)

[ 29 ] J.A. Kaandorp, (Guest editor) Thematic issue on Virtual Reality in Industry and Research Future Generation Computer Systems 15: 467-536 (1999)

[ 30 ] J.A. Kaandorp and J.E. Kuebler, The algorithmic beauty of seaweeds, sponges and corals, Springer-Verlag, Heidelberg, New York, 2001

[ 31 ] J A Kaandorp, P M A Sloot, Morphological models of radiate accretive growth and the influence of hydrodynamics, J. Theor. Biol., 209:257-274, 2001

[ 32 ] J.A. Kaandorp and S. Gueron, special issue Future Generation Computer Systems on particle based modelling in biology, 17: (7) V-VI MAY 2001

[ 33 ] J.A. Kaandorp. Modelling growth and form of stony corals and the influence of hydrodynamics on suspension feeding, 541-547, Vol. I Proceedings 9th International Coral Reef Symposium Bali, Indonesia, 2003.

[ 34 ] 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). Phil. Trans. R. Soc. Lond. B 358 (1437): 1551 - 1557, 2003.

[ 35 ] J.A. Kaandorp and R.A. Garcia Leiva Morphological analysis of two- and three-dimensional images of branching sponges and corals In: Morphometrics and their applications in Paleontology and Biology, A.M.T. Elewa (Ed.), Springer-Verlag, pp 83-94, 2004.

[ 36 ] 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, Proc. Roy. Soc. B. 272:127-133, 2005

[ 37 ] J.A. Kaandorp, R.P.M. Bak, M.J.A. Vermeij Modelling of nutrient gradients in three-dimensional images - and simulated morphologies of a branching coral. Proceedings 10th International Coral Reef Symposium Okinawa, Japan

[ 38 ] J.A. Kaandorp, Modelling the skeletal architecture in a sponge with radiate accretive growth In: Biosilica in Evolution, Morphogenesis and Nanobiotechnology: Case Study Lake Baikal W.E.G. M\FCller and M.A.Grachev (eds.), Springer-Verlag, 2009

[ 39 ] J.A. Kaandorp, Book review: P. Pelce, New visions on growth and form: fingering growth, dendrites, and flames, Mathematical Biosciences 210:700-702, 2007

[ 40 ] J.A. Kaandorp, Exploring Theoretical Morphospaces, Book review: The Geometry of Evolution: Adaptive Landscapes and Theoretical Morphospaces. George R. McGhee., BioScience 58:271-273, 2008

[ 41 ] J.A. Kaandorp, J.G. Blom, J. Verhoef, M. Filatov, M. Postma and W.E.G. M\FCller, Modelling genetic regulation of growth and form in a branching sponge Proc. Roy. Soc. B. 275:2569-2577, 2008

[ 41 ] J.A. Kaandorp, Modelling growth and form of sponges, In: From insect nest to human architectures, Proc. of the International Workshop on Engineering Princples of Innovation in swarm-made Architectures, G. Theraulaz, R. Sole and P. Kuntz (eds) September, 2009, Venice, Italy

[ 42 ] J.A. Kaandorp, M. Filatov and N. Chindapol, Simulating and quantifying the environmental influence on coral growth and form. In Coral Reefs: An Ecosystem in Transition (Eds. Z. Dubinsky & N. Stambler). Part 3, 177-185, 2011, DOI: 10.1007/978-94-007-0114-4_11

[ 43 ] J.A. Kaandorp, D. Botman, C. Tamulonis and R. Dries (2012). Multi-scale modeling of gene regulation of morphogenesis. In. S.B. Cooper, A. Dawar and B. Lowe (Eds.), How the world computes, Turing Centenary Conference and 8th Conference on Computability in Europe, Cambridge, UK (pp. 355-362)

[ 44 ] J. A. Kaandorp, Macroscopic Modelling of Environmental Influence on Growth and Form of Sponges and Corals Using the Accretive Growth Model, ISRN Biomathematics, vol. 2013, Article ID 159170, 14 pages, 2013. doi:10.1155/2013/159170.

Refereed publications co-authored

[ 45 ] H.A. Lauwerier and J.A. Kaandorp. Fractals (mathematics, programming and applications). In M.M. de~Ruiter, editor, Advances in computer graphics III, pages 177--205, Berlin, New York, 1988. Springer-Verlag.

[ 46 ] H. McEvoy and J.A. Kaandorp. On modelling environmentally-sensitive growth forms and cellular automata using multiset transformation. Fractals, 4(4):509-520, 1996.

[ 47 ] 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 - PPSN IV, H.M. Voigt, W. Ebeling, I. Rechenberg and H.P. Schwefel (eds.), pp 533-542, Springer-Verlag, Berlin, 1996.

[ 48 ] C.P. Lowe and J.A. Kaandorp, Simulating the effect of fluid flow on aggregation, Proceedings Sixth International Conference on Discrete Models for Fluid Mechanics, Boston University, Boston, USA, 1996

[ 49 ] 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, R. van grondelle, S. van der Kolk, O.J.G. Somsen, H.V. Westerhoff and J.E. Wijker, pp 80-82, Free University, Amsterdam, 1996.

[ 50 ] 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, R. van grondelle, S. van der Kolk, O.J.G. Somsen, H.V. Westerhoff and J.E. Wijker, pp 83-85, Free University, Amsterdam, 1996.

[ 51 ] P.M.A. Sloot, A. Schoneveld, J. F. de Ronde and J. A. Kaandorp Large scale simulations of complex systems Part I: conceptual framework SFI Working Paper: 97-07-070, 1997.

[ 52 ] 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): 209-214, 1998.

[ 53 ] 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, B.M. ter Haar, D.H.J. Epema, J.F.M Tonino and A.A. Wolters (eds.), pp 264-268.

[ 54 ] 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, A. Zomaya (ed.), Wiley (in press).

[ 55 ] R.G. Belleman, J.A. Kaandorp, D. Dijkman and P.M.A. Sloot, Geoprove: Geometric probes for virtual environments In: ASCI '99, Proceedings of the fifth annual conference of the Advanced School for Computing and Imaging, M. Boasson, J.A. Kaandorp, J.F.M. Tonino and M.G. Vosselman (eds.), pp 38-43, Advanced School for Computing and Imaging (ASCI), 1999.

[ 56 ] R.G.Belleman, J.A. Kaandorp and D. Dijkman and P.M.A. Sloot GEOPROVE: Geometric Probes for Virtual Environments, In: High Performance Computing and Networking HPCN'99, P.M.A. Sloot, M. Bubak, A.G. Hoekstra, and L.O. Hertzberger (eds.) Springer-verlag, Amsterdam, pp 817-827, 1999

[ 57 ] 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 (1999) SOFSEM'99, 26th Conference on Current Trends in Theory and Practice of Informatocs, Milovy, Czech Republic. November 27 - December 4. J. Pavelka, G. Tel and M. Bartosek (eds.), Springer Berlin, Heidelberg.

[ 58 ] 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, ASCI, ASCI, Delft, June 1999.

[ 59 ] 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 Proceedings of the 2002 International Conference on Computational Science ICCS2002, (in press) in series Lecture Notes in Computer Science, 2002.

[ 60 ] 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):173-181, 2002

[ 61 ] R.M.H. Merks; A.G. Hoekstra and P.M.A. Sloot: Validation of the Lowe-Frenkel tracer dispersion method in the lattice Boltzmann method, in R.L. Lagendijk; J.W.J. Heijnsdijk; A.D. Pimentel and M.H.F. Wilkinson, editors, Proceedings of the 7th annual conference of the Advanced School for Computing and Imaging, pp. 137-141. ASCI, May 2001. ISBN 90-803086-6-8.

[ 62 ] 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 P.M.A. Sloot; C.J.K. Tan; J.J. Dongarra and A.G. Hoekstra, editors, Computational Science - ICCS 2002, Proceedings Part I, in series Lecture Notes in Computer Science, vol. 2329, pp. 88-96. Springer Verlag, April 2002.

[ 63 ] R.M.H. Merks; A.G. Hoekstra; J.A. Kaandorp and P.M.A. Sloot: Models of coral growth: Spontaneous branching, compactification and the Laplacian growth assumption, Journal of Theoretical Biology, 224: 153--166, 2003.

[ 64 ] 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: 1171-1182, 2003.

[ 65 ] R.M.H. Merks, A.G. Hoekstra, J.A. Kaandorp, and P.M.A. Sloot (2003). Branching and compactification in a model of coral growth: a critical reinvestigation of the effect of hydrodynamics. in: V. Capasso (ed.) "Mathematical modelling & Computing in Biology and Medicine; 5th ESMTB Conference 2002.", pp. 539-544. MIRIAM (Milan Research Centre for Industrial and Applied Mathematics), 2003.

[ 66 ] R.M.H. Merks, A.G. Hoekstra, J.A. Kaandorp, and P.M.A. Sloot (2003) A problem solving environment for modelling stony coral morphogenesis. In: P.M.A. Sloot, D. Abramson, A.V. Bogdanov, J.J. Dongarra, A.Y. Zomaya, and Y.E. Gorbachev, editors, Computational Science - ICCS 2003, volume 2657 of Lecture Notes in Computer Science, pages 639-648, Melbourne, Australia and St. Petersburg, Russia, 2003.

[ 67 ] T. Krul, J.A. Kaandorp and J.G. Blom. Modelling Developmental Regulatory Networks. In: Proceedings of Computational Science - ICCS 2003, International Conference Saint Petersburg Russian Federation, Melbourne Australia, June 2-4, 2003. Eds: P.M.A. Sloot, D. Abramson, A. Bogdanov, J.J Dongarra, A. Zomaya, and Y. Gorbachev. upringer-Verlag, Berlin pp 688-697 (2003).

[ 68 ] 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 228:559-576, 2004

[ 69 ] O.V. Kaluzhnaya, S.I. Belikov, H.C. Schroeder, S. Zapf, A. Borejko, J.A. Kaandorp, A. Krasko, I.M. Mueller and W.E.G. Mueller. Dynamics of skeletal formation in the Lake Baikal sponge Lubomirskia baicalensis. Part I biological and biochemical studies, Naturwissenschaften, 92: 128-133 (2005).

[ 70 ] O.V. Kaluzhnaya, S.I. Belikov, H.C. Schroeder, S. Zapf, A. Borejko, J.A. Kaandorp, A. Krasko, I.M. Mueller and W.E.G. Mueller. Dynamics of skeletal formation in the Lake Baikal sponge Lubomirskia baicalensis. Part II Molecular biological studies, Naturwissenschaften, 92:134-138.

[ 71 ] R.M.H. Merks, A.G. Hoekstra; J.A. Kaandorp, P.M.A. Sloot and P. Hogeweg, Problem-Solving Environments for Biological Morphogenesis, Comput. Sci. Eng. 8(1): 61-72, 2006

[ 72 ] K. Kruszynski, R. van Liere and J.A. Kaandorp, Quantifying Differences in Skeletonization Algorithms: a Case Study IASTED, Visualization, Imaging, & Image Processing (VIIP 2005) , September 2005.

[ 73 ] K. Kruszynski, R. van Liere and J.A. Kaandorp, An Interactive Visualization System for Quantifying Coral Structures Eurographics / IEEE-VGTC Symposium on Visualization 2006, T. Ertl, K.Joy and B. Santos (eds.), 2006, pp 1-8.

[ 74 ] J. Cui, J.A. Kaandorp Mathematical Modelling of Calcium Homeostasis in Yeast Cells Cell Calcium 39:337-348, 2006

[ 75 ] W.E.G. Mueller, O.V. Kaluzhnaya, S.I. Belikov, M. Rothenberger, H.C. Schroeder, A. Reiber, J.A. Kaandorp, B. Manz, D. Mietchen and F. Volke J. Magnetic resonance imaging of the siliceous skeleton of the demosponge Lubomirskia baicalensis, Journal of Structural Biology, 153:31-41, 2006

[ 76 ] J. Vidal Rodriquez, J.A. Kaandorp, M. Dobrzynski and J.G. Blom. Spatial Stochastic Modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli, Bioinformatics, 22:1895-1901, 2006

[ 77 ] J. Vidal Rodriquez and J.A. Kaandorp, Inferring the distribution of inter-reaction intervals for diffusion-limited reactions on lattices Int. J. Mod. Phys. C 18: 749-758, 2007.

[ 78 ] M. Dobrzynski, J. Vidal Rodriquez, J.A. Kaandorp and J.G. Blom Computational methods for diffusion-limited biochemical reactions Bioinformatics 23:15:1969--1977, 2007.

[ 79 ] M. Wiens, S.I. Belikov, O.V. Kaluzhnayaa, T. Adella, H.C. Schr\F6dera, S. Perovic-Ottstadt, J.A. Kaandorp and W.E.G. M\FCller, Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis Micron, 39:447-460, 2008.

[ 80 ] K. Kruszynski, J.A. Kaandorp and R. van Liere A computational method for quantifying morphological variation in scleractinian corals, Coral Reefs 26:831-840, 2007.

[ 81 ] W.E.G. Mueller, 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 28:4501-4511, 2007

[ 82 ] 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 23:3356-3363, 2007

[ 83 ] J. Cui, J.A. Kaandorp , O. O. Ositelu, V. Beaudry, A. Knight, Y. Fomekong Nanfack, K. W. Cunningham, Simulating Calcium Influx and Free Calcium Concentrations in Yeast, Cel Calcium 45: 123-132, (2009)

[ 84 ] J. Cui and J.A. Kaandorp, Simulating complex calcium-calcineurin signaling network, in M.T. Bubak; G.D. van Albada; J.J. Dongarra and P.M.A. Sloot, editors, Computational Science - ICCS 2008: 8th International Conference, Krakow, Poland, Proceedings, Part II, in series Lecture Notes in Computer Science, vol. 5103, pp. 110-119. Springer, Berlin, Heidelberg, June 2008.

[ 85 ] X. Wang, D. Brandt, H. C. Schroeder, J. Li, A. Boreiko, U. Schlossmacher, J.A. Kaandorp, H. Gotz, H. Duschner, and W.E.G. Mueller Axial growth of hexactinellid spicules: formation of cone-like structural units in the giant basal spicules of the hexactinellid Monorhaphis, Journal of Structural Biology 164:270-280, 2008

[ 86 ] 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, 2008

[ 87 ] M. Ashyraliyev, Y. Fomekong Nanfack, J.A. Kaandorp, J.G. Blom Systems biology: Parameter estimation for biochemical models, FEBS journal 276:886-902, 2009

[ 88 ] J.Cui, J.A. Kaandorp, P.M.A. Sloot, P. Thiagarajan, C. Lloyd, M. Filatov Calcium homeostasis and signalling in yeast cells and cardiac myocytes FEMS Yeast Research 9(8):1137-1147. 2009

[ 89 ] Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis BMC Systems Biology, 3:94, 2009

[ 90 ] Y. Fomekong Nanfack, M. Postma J.A. Kaandorp, Inferring Drosophila} gap gene regulatory network: pattern analysis of gene expression profiles and stability analysis, BMC Research Notes, 2:256, 2009

[ 91 ] J. Cui; J.A. Kaandorp; P.M.A. Sloot and P.S. Thiagarajan: Simulating Calcineurin-Centered Calcium Signaling Network in Cardiac Myocytes, in J.E. Garc\EDa and V.R. Wright, editors, Congestive Heart Failure: Symptoms, Causes and Treatment, 2010. Nova Publishers, 2010. ISBN 978-1-60876-677-2.

[ 92 ] M.V. Filatov, J.A. Kaandorp, M. Postma, R. van Liere, K.J. Kruszynski, M.J.A. Vermeij, G.J. Streekstra and R.P.M.Bak, A comparison between coral colonies from the Madracis genus and simulated forms, Proc. R. Soc. B 277:3555-3561, 2010

[ 93 ] P.R. Frade, M.C. Reyes-Nivia, J. Faria, J.A. Kaandorp, P.C. Luttikhuizen R.P.M. Bak, Semi-permeable species boundaries in the coral genus Madracis: the role of introgression in a brooding coral system, Molecular Phylogenetics and Evolution 57:1072-1090, 2010

[ 94 ] C. Tamulonis, M. Postma, H. Marlow, C. Magie, J. de Jong, and J.A. Kaandorp, Morphometrics & Modeling of Nematostella vectensis Gastrulation, Developmental Biology, 351: 217-228, 2011

[ 95 ] J. Hammel, M.V. Filatov, J. Herzen, F. Beckmann, J.A. Kaandorp, 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, 93:160-170, 2012

[ 96 ] C. Tamulonis, M. Postma, J.A. Kaandorp, Gliding Filamentous Cyanobacteria Reveals the Advantages of Longer, Faster and Photophobic Trichomes, PlosOne 6: e22084, 2011

[ 97 ] W. E.G. M\FCller, M. Binder, J. von Lintig, Yue-Wei Guo, Xiaohong Wang, J. A. Kaandorp, M. Wiens, H. C. Schr\F6der Interaction of the retinoic acid signaling pathway with spicule formation in the marine sponge Suberites domuncula through activation of bone morphogenetic protein- Biochim Biophys Acta. 2011 1810:1178-94

[ 98 ] P. Ramos-Silva, S. Benhamada, N. Le Roy, B. Marie, N. Guichard, I. Zanella-Cl\E9on, L. Plasseraud, M. Corneillat, G. Alcaraz, J. Kaandorp and F. Marin. Orphan proteins in molluscan shell biomineralization: a case study with Upsalin ChemBioChem, 2012, 13:1\BF13 DOI: 10.1002/cbic.201100708

[ 99 ] Y. Kim., R. Sinclair, N. Chindapol, J. A. Kaandorp, E. De Schutter, Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat, Plos Computational Biology 8: e1002474, 2012 DOI:10.1371/journal.pcbi.1002474

[ 100 ] X. Wang, H. C. Schr\F6der, K. Wang, J. A. Kaandorp and W. E. G. M\FCller, Genetic, biological and structural hierarchies during sponge spicule formation: From soft sol-gels to solid 3D silica composite structures, Soft Matter, DOI:10.1039/C2SM25889G , 2012

[ 101 ] 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, . BMC Research Notes 5:555, 2012 DOI:

[ 102 ] 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, e1002849, 2013 DOI:10.1371/journal.pcbi.1002849

[ 103 ] 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 Biol. 11, e1001528, 2013 DOI: DOI:10.1371/journal.pbio.1001528

[ 104 ] P. Ramos-Silva, F. Marin, J.A. Kaandorp, and B. Marie, \AB Biomineralization toolkit \BB: the importance of sample cleaning prior to the characterization of biomineral proteomes, PNAS ., 3<96>5. doi:10.1073/pnas.1303657110, 2013

[ 105 ] P. Ramos-Silva J.A, Kaandorp, L. Huisman, B. Marie, I. Zanella-Cl\E9on4, N. Guichard, D.J. Miller and F. Marin, The skeletal proteome of the coral Acropora millepora: the evolution of calcification by cooption and domain shuffling, Molecular Biology and Evolution, online available http//mbe.oxfordjournals.org/content/early/2013/06/12/molbev.mst109.full.pdf 2013

[ 106 ] N. Javaheri, C. Cronemberger, J.A. Kaandorp, Modeling Biosilicification at Subcellular Scales In: Biomedical inorganic polymers - Bioactivity and applications of natural and synthetic polymeric inorganic molecules in the series "Progress in Molecular and Subcellular Biology" (Eds. H.C. Schroeder and W.E.G. Mueller) (Springer Press)

[ 107 ] J. Tanzil, Jani; B. Brown, R. Dunne, L. Jen Nie; J.A. Kaandorp, and P. Todd, Regional decline in growth rates of massive Porites corals in Southeast Asia, Global Change Biology, online available http://onlinelibrary.wiley.com/doi/10.1111/gcb.12279/abstract, 2013

[ 108 ] M. V. Filatov, P. R. Frade, , R. P.M. Bak, M. J.A. Vermeij, and J. A. Kaandorp, Comparison between colony morphology and molecular phylogeny in the Caribbean scleractinian coral genus Madracis, Plos One Plos One 8, e71287, 2013 DOI:10.1371/journal.pone.0071287

[ 109 ] N. Javaheri, R. Dries, J.A. Kaandorp Understanding the Sub-Cellular Dynamics of Silicon Transportation and Synthesis in Diatoms Using Population-Level Data and Computational Optimization, Plos Computational Biology,. 06/2014; 10(6):e1003687. DOI: 10.1371/journal.pcbi.1003687

[ 110 ] Ramos-Silva, P., Kaandorp, J., Marin, F., et al. The skeleton of the staghorn coral Acropora millepora: a molecular and structural characterization, Plos One, 01/2014; 9(6):e97454. DOI: 10.1371/journal.pone.0097454

[ 111 ] D. Botman, E. Rottinger, M. Q. Martindale, J. de Jong and J. A. Kaandorp, Computational Approach towards a Gene Regulatory Network for the Developing Nematostella vectensis Gut., Plos One, 9: e103341, 2014

[ 112 ] C. Tamulonis and J.A. Kaandorp A model of filamentous cyanobacteria leading to reticulate pattern formation, Life 09/2014; 4:433-456. DOI: 10.3390/life4030433

[ 113 ] P. Fantazzini, S. Mengoli, L. Pasquini, V. Bortolotti, L. Brizi1, M. Mariani, M. Di Giosia, S. Fermani, B. Capaccioni, E. Caroselli, F. Prada, F. Zaccanti, O. Levy, Z. Dubinsky, J. A. Kaandorp, P. Konglerd, J. U. Hammel, Y. Dauphin, J. Cuif, J. C. Weaver, K. E. Fabricius, W. Wagermaier, P. Fratzl, G. Falini and S. Goffredo, Gains and losses of coral skeletal porosity changes with ocean acidification acclimation, Nature Communications, DOI: 10.1038/ncomms8785, 2015

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

[ 115 ] F. Jansson, M. Hartley, M. Hinsch, I. Slavkov,N. Carranza, T. S. G. Olsson, R.M. Dries, J. H. Grönqvist, A. F. M. Marée, J. Sharpe, J. A. Kaandorp, V. A. Grieneisen, Kilombo: a Kilobot simulator to enable effective research in swarm robotics, arXiv preprint arXiv:1511.04285, 2015

[ 116 ] D. Botman; F. Jansson; E. Röttinger; M. Q. Martindale; J. de Jong; J.A. Kaandorp Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development BMC Systems Biology 9::63, 2015

[ 117 ] J. Tanzil , J.N. Lee , B.E. Brown, R. Quax, J.A. Kaandorp , J.M. Lough , P.A. Todd. Luminescence and density banding patterns in massive Porites corals around the Thai-Malay Peninsula, Southeast Asia, Limnology & Oceanography, doi: 10.1002/lno.1035, 2016

[ 118 ] 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, Chapter: 14, Springer-Verlag, Eds: S. Goffredo, Z. Dubinsky, pp.223-236, 2016

[ 119 ] 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 Res Notes DOI 10.1186/s13104-017-2424-0, 2017

Reports

[ 109 ] J.A. Kaandorp. Interactive generation of fractal objects. Technical report R 8706, Centre for Mathematics and Computer Science, Department of Computer Science, Amsterdam, 1987.

[ 110 ] H.A. Lauwerier and J.A. Kaandorp. Fractals (mathematics, programming and applications). Technical report R 8762, Centre for Mathematics and Computer Science, Department of Computer Science, Amsterdam, 1987.

[ 111 ] A. Schoneveld, J.A. Kaandorp, and P.M.A. Sloot. Parallel dynamic complex systems. PowerXplorer User Report, Heinrich-Heine-Universitat Dusseldorf, Parsytec Computer GmbH, 1995.

[ 112 ] J.A. Kaandorp. Modelling and simulation of morphogenesis. Technical report, University of Amsterdam, 1996. Mastercourses Wiskunde, Dynamische Modellen, 19 april 1996.

[ 113 ] J.A. Kaandorp and P.M.A. Sloot. Parallel solvers for simulating morphogenesis. PowerXplorer User report, Heinrich-Heine-Universitat Dusseldorf, Parsytec Computer GmbH, 1995.

[ 114 ] P.M.A. Sloot, J.A. Kaandorp, and A.~Schoneveld. Dynamical Complex Systems (DCS): A new approach to parallel computing in computational physics. Technical report, University of Amsterdam, 1995. Technical Report FWI TR: CS-95-08.

Other Publications

[ 115 ] J.A. Kaandorp. Sponges in space. video made at the University of Calgary, Canada, 1992.

[ 116 ] J.A. Kaandorp, C. Lowe, D. Frenkel, P.M.A. Sloot, and N. C. Rozemeijer. Flow and diffusion limited growth of aggregates. video made at the University of Amsterdam, 1995.

[ 117 ] J.A. Kaandorp, R. Belleman, and P.M.A. Sloot Growth and form in a moving fluid. Video made at the University of Amsterdam, January 1998.

[ 118 ] J.A. Kaandorp, R. Belleman, F. Lakeman, and P.M.A. Sloot The impact of hydrodynamics on growth and form. Video made at the University of Amsterdam, August 1998.

[ 119 ] J.A. Kaandorp. From July 1996 until March 1997 (monthly), cover picture and abstract in Mathematical Seminar (in Japanese).

[ 120 ] J.A. Kaandorp. De invloed van diffusie en stroming op groei en vorm, Afleiding 6:2-5, 1996 (in Dutch)

[ 121 ] H. Jones and J.A.Kaandorp Modelling of growing natural forms", Tutorial T2, Eurographics 2000, Interlaken, Switzerland.

[ 122 ] J.A. Kaandorp. Modelleren en simuleren van groei en vorm van sponzen en koralen. In: De dubbele uitdaging: biologisch inzicht en wiskundig gereedschap, Eds H. Heesterbeek, O. Diekmann and H.Metz (to appear in 2005?, in Dutch)

[ 123 ] J.A. Kaandorp. Groei en vorm van koralen & de invloed van atmosferische CO2 en stijgende zeetemperaturen, Ecologie & Ontwikkeling, 71:13-15, 2006 (in Dutch)

[ 124 ] Euro ISRS symposium 2010: reefs in a changing envrionment, J.A. Kaandorp, E. Meesters, R. Osinga, J. Verreth and T. Wijgerde Grafisch Service Center, Wageningen, the Netherlands, 2010 ISBN 978-90-8585-897-3

Publications Submitted

[ 128 ] Ramos-Silva, P., Kaandorp, J., Marin, F., et al. The skeleton of the staghorn coral Acropora millepora: a molecular and structural characterization

Books

blank image
J.A. Kaandorp and J.E. Kuebler, The algorithmic beauty of seaweeds, sponges and corals, Springer-Verlag, Heidelberg, New York, 2001
blank image
J.A. Kaandorp. Fractal modelling: growth and form in biology. Springer-Verlag, Berlin, New York, 1994.