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Items: 44

1.

Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral.

Liew YJ, Zoccola D, Li Y, Tambutté E, Venn AA, Michell CT, Cui G, Deutekom ES, Kaandorp JA, Voolstra CR, Forêt S, Allemand D, Tambutté S, Aranda M.

Sci Adv. 2018 Jun 6;4(6):eaar8028. doi: 10.1126/sciadv.aar8028. eCollection 2018 Jun.

2.

Directed nucleation and growth by balancing local supersaturation and substrate/nucleus lattice mismatch.

Li L, Fijneman AJ, Kaandorp JA, Aizenberg J, Noorduin WL.

Proc Natl Acad Sci U S A. 2018 Apr 3;115(14):3575-3580. doi: 10.1073/pnas.1712911115. Epub 2018 Mar 19.

PMID:
29555753
3.

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.

Abdol AM, Bedard A, Lánský I, Kaandorp JA.

Gene Expr Patterns. 2018 Jan;27:36-45. doi: 10.1016/j.gep.2017.10.005. Epub 2017 Nov 6.

PMID:
29122675
4.

The effect of allometric scaling in coral thermal microenvironments.

Ong RH, King AJC, Kaandorp JA, Mullins BJ, Caley MJ.

PLoS One. 2017 Oct 12;12(10):e0184214. doi: 10.1371/journal.pone.0184214. eCollection 2017.

5.

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.

Abdol AM, Röttinger E, Jansson F, Kaandorp JA.

Dev Biol. 2017 Aug 1;428(1):204-214. doi: 10.1016/j.ydbio.2017.06.004. Epub 2017 Jun 8.

PMID:
28602952
6.

Quantitative morphological analysis of 2D images of complex-shaped branching biological growth forms: the example of branching thalli of liverworts.

Konglerd P, Reeb C, Jansson F, Kaandorp JA.

BMC Res Notes. 2017 Feb 20;10(1):103. doi: 10.1186/s13104-017-2424-0.

7.

Analysis of a spatial gene expression database for sea anemone Nematostella vectensis during early development.

Botman D, Jansson F, Röttinger E, Martindale MQ, de Jong J, Kaandorp JA.

BMC Syst Biol. 2015 Sep 24;9:63. doi: 10.1186/s12918-015-0209-4.

8.

Gains and losses of coral skeletal porosity changes with ocean acidification acclimation.

Fantazzini P, Mengoli S, Pasquini L, Bortolotti V, Brizi L, Mariani M, Di Giosia M, Fermani S, Capaccioni B, Caroselli E, Prada F, Zaccanti F, Levy O, Dubinsky Z, Kaandorp JA, Konglerd P, Hammel JU, Dauphin Y, Cuif JP, Weaver JC, Fabricius KE, Wagermaier W, Fratzl P, Falini G, Goffredo S.

Nat Commun. 2015 Jul 17;6:7785. doi: 10.1038/ncomms8785.

9.

Temperature affects the silicate morphology in a diatom.

Javaheri N, Dries R, Burson A, Stal LJ, Sloot PM, Kaandorp JA.

Sci Rep. 2015 Jun 26;5:11652. doi: 10.1038/srep11652.

10.

A computational approach towards a gene regulatory network for the developing Nematostella vectensis gut.

Botman D, Röttinger E, Martindale MQ, de Jong J, Kaandorp JA.

PLoS One. 2014 Jul 30;9(7):e103341. doi: 10.1371/journal.pone.0103341. eCollection 2014.

11.

Modeling biosilicification at subcellular scales.

Javaheri N, Cronemberger CM, Kaandorp JA.

Prog Mol Subcell Biol. 2013;54:117-41. doi: 10.1007/978-3-642-41004-8_5. Review.

PMID:
24420712
12.

Comparison between colony morphology and molecular phylogeny in the Caribbean scleractinian coral genus Madracis.

Filatov MV, Frade PR, Bak RP, Vermeij MJ, Kaandorp JA.

PLoS One. 2013 Aug 14;8(8):e71287. doi: 10.1371/journal.pone.0071287. eCollection 2013.

13.

Regional decline in growth rates of massive Porites corals in Southeast Asia.

Tanzil JT, Brown BE, Dunne RP, Lee JN, Kaandorp JA, Todd PA.

Glob Chang Biol. 2013 Oct;19(10):3011-23. doi: 10.1111/gcb.12279. Epub 2013 Jul 29.

PMID:
23744603
14.

Promoter sequence determines the relationship between expression level and noise.

Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E.

PLoS Biol. 2013;11(4):e1001528. doi: 10.1371/journal.pbio.1001528. Epub 2013 Apr 2.

15.

Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics.

Chindapol N, Kaandorp JA, Cronemberger C, Mass T, Genin A.

PLoS Comput Biol. 2013;9(1):e1002849. doi: 10.1371/journal.pcbi.1002849. Epub 2013 Jan 10.

16.
17.

Geometric theory predicts bifurcations in minimal wiring cost trees in biology are flat.

Kim Y, Sinclair R, Chindapol N, Kaandorp JA, De Schutter E.

PLoS Comput Biol. 2012;8(4):e1002474. doi: 10.1371/journal.pcbi.1002474. Epub 2012 Apr 12.

18.

Interaction of the retinoic acid signaling pathway with spicule formation in the marine sponge Suberites domuncula through activation of bone morphogenetic protein-1.

Müller WE, Binder M, von Lintig J, Guo YW, Wang X, Kaandorp JA, Wiens M, Schröder HC.

Biochim Biophys Acta. 2011 Dec;1810(12):1178-94. doi: 10.1016/j.bbagen.2011.09.006. Epub 2011 Sep 16.

PMID:
21952113
19.

Semi-permeable species boundaries in the coral genus Madracis: introgression in a brooding coral system.

Frade PR, Reyes-Nivia MC, Faria J, Kaandorp JA, Luttikhuizen PC, Bak RP.

Mol Phylogenet Evol. 2010 Dec;57(3):1072-90. doi: 10.1016/j.ympev.2010.09.010. Epub 2010 Sep 21.

PMID:
20863897
20.

A comparison between coral colonies of the genus Madracis and simulated forms.

Filatov MV, Kaandorp JA, Postma M, van Liere R, Kruszyński KJ, Vermeij MJ, Streekstra GJ, Bak RP.

Proc Biol Sci. 2010 Dec 7;277(1700):3555-61. doi: 10.1098/rspb.2010.0957. Epub 2010 Jun 23.

21.

Inferring Drosophila gap gene regulatory network: pattern analysis of simulated gene expression profiles and stability analysis.

Fomekong-Nanfack Y, Postma M, Kaandorp JA.

BMC Res Notes. 2009 Dec 16;2:256. doi: 10.1186/1756-0500-2-256.

22.

Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis.

Fomekong-Nanfack Y, Postma M, Kaandorp JA.

BMC Syst Biol. 2009 Sep 21;3:94. doi: 10.1186/1752-0509-3-94.

23.

Calcium homeostasis and signaling in yeast cells and cardiac myocytes.

Cui J, Kaandorp JA, Sloot PM, Lloyd CM, Filatov MV.

FEMS Yeast Res. 2009 Dec;9(8):1137-47. doi: 10.1111/j.1567-1364.2009.00552.x. Epub 2009 Jul 16. Review.

24.

Systems biology: parameter estimation for biochemical models.

Ashyraliyev M, Fomekong-Nanfack Y, Kaandorp JA, Blom JG.

FEBS J. 2009 Feb;276(4):886-902. doi: 10.1111/j.1742-4658.2008.06844.x. Review.

25.

Modelling the skeletal architecture in a sponge with radiate accretive growth.

Kaandorp JA.

Prog Mol Subcell Biol. 2009;47:237-47. doi: 10.1007/978-3-540-88552-8_10.

PMID:
19198780
26.

Simulating in vitro transcriptional response of zinc homeostasis system in Escherichia coli.

Cui J, Kaandorp JA, Lloyd CM.

BMC Syst Biol. 2008 Oct 24;2:89. doi: 10.1186/1752-0509-2-89.

27.

Axial growth of hexactinellid spicules: formation of cone-like structural units in the giant basal spicules of the hexactinellid Monorhaphis.

Wang X, Boreiko A, Schlossmacher U, Brandt D, Schröder HC, Li J, Kaandorp JA, Götz H, Duschner H, Müller WE.

J Struct Biol. 2008 Dec;164(3):270-80. doi: 10.1016/j.jsb.2008.08.005. Epub 2008 Sep 6.

PMID:
18805491
28.

Simulating calcium influx and free calcium concentrations in yeast.

Cui J, Kaandorp JA, Ositelu OO, Beaudry V, Knight A, Nanfack YF, Cunningham KW.

Cell Calcium. 2009 Feb;45(2):123-32. doi: 10.1016/j.ceca.2008.07.005. Epub 2008 Sep 10.

29.

Modelling genetic regulation of growth and form in a branching sponge.

Kaandorp JA, Blom JG, Verhoef J, Filatov M, Postma M, Müller WE.

Proc Biol Sci. 2008 Nov 22;275(1651):2569-75. doi: 10.1098/rspb.2008.0746.

30.

Efficient parameter estimation for spatio-temporal models of pattern formation: case study of Drosophila melanogaster.

Fomekong-Nanfack Y, Kaandorp JA, Blom J.

Bioinformatics. 2007 Dec 15;23(24):3356-63. Epub 2007 Sep 24.

PMID:
17893088
31.

Fractal-related assembly of the axial filament in the demosponge Suberites domuncula: relevance to biomineralization and the formation of biogenic silica.

Müller WE, Boreiko A, Schlossmacher U, Wang X, Tahir MN, Tremel W, Brandt D, Kaandorp JA, Schröder HC.

Biomaterials. 2007 Oct;28(30):4501-11. Epub 2007 Jul 12.

PMID:
17628661
32.

Computational methods for diffusion-influenced biochemical reactions.

Dobrzynski M, Rodríguez JV, Kaandorp JA, Blom JG.

Bioinformatics. 2007 Aug 1;23(15):1969-77. Epub 2007 May 30.

PMID:
17537752
33.

Regional and modular expression of morphogenetic factors in the demosponge Lubomirskia baicalensis.

Wiens M, Belikov SI, Kaluzhnaya OV, Adell T, Schröder HC, Perovic-Ottstadt S, Kaandorp JA, Müller WE.

Micron. 2008 Jun;39(4):447-60. Epub 2007 Feb 22.

PMID:
17383885
34.

Spatial stochastic modelling of the phosphoenolpyruvate-dependent phosphotransferase (PTS) pathway in Escherichia coli.

Rodríguez JV, Kaandorp JA, Dobrzyński M, Blom JG.

Bioinformatics. 2006 Aug 1;22(15):1895-901. Epub 2006 May 26.

PMID:
16731694
35.

Mathematical modeling of calcium homeostasis in yeast cells.

Cui J, Kaandorp JA.

Cell Calcium. 2006 Apr;39(4):337-48. Epub 2006 Jan 30.

PMID:
16445978
36.

Magnetic resonance imaging of the siliceous skeleton of the demosponge Lubomirskia baicalensis.

Müller WE, Kaluzhnaya OV, Belikov SI, Rothenberger M, Schröder HC, Reiber A, Kaandorp JA, Manz B, Mietchen D, Volke F.

J Struct Biol. 2006 Jan;153(1):31-41. Epub 2005 Nov 30.

PMID:
16364658
37.

Morphogenesis of the branching reef coral Madracis mirabilis.

Kaandorp JA, Sloot PM, Merks RM, Bak RP, Vermeij MJ, Maier C.

Proc Biol Sci. 2005 Jan 22;272(1559):127-33.

38.

Dynamics of skeleton formation in the Lake Baikal sponge Lubomirskia baicalensis. Part I. Biological and biochemical studies.

Kaluzhnaya OV, Belikov SI, Schröder HC, Rothenberger M, Zapf S, Kaandorp JA, Borejko A, Müller IM, Müller WE.

Naturwissenschaften. 2005 Mar;92(3):128-33. Epub 2005 Jan 18.

PMID:
15655662
39.

Polyp oriented modelling of coral growth.

Merks RM, Hoekstra AG, Kaandorp JA, Sloot PM.

J Theor Biol. 2004 Jun 21;228(4):559-76.

PMID:
15178203
40.

Simulation and analysis of flow patterns around the scleractinian coral Madracis mirabilis (Duchassaing and Michelotti).

Kaandorp JA, Koopman EA, Sloot PM, Bak RP, Vermeij MJ, Lampmann LE.

Philos Trans R Soc Lond B Biol Sci. 2003 Sep 29;358(1437):1551-7.

41.

Morphological models of radiate accretive growth and the influence of hydrodynamics.

Kaandorp JA, Sloot PM.

J Theor Biol. 2001 Apr 7;209(3):257-74.

PMID:
11312588
42.

Parallel simulation of accretive growth and form in three dimensions.

Kaandorp JA, Sloot PM.

Biosystems. 1997;44(3):181-92.

PMID:
9460559
43.

Effect of Nutrient Diffusion and Flow on Coral Morphology.

Kaandorp JA, Lowe CP, Frenkel D, Sloot PM.

Phys Rev Lett. 1996 Sep 9;77(11):2328-2331. No abstract available.

PMID:
10061916
44.

Analysis and synthesis of radiate accretive growth in three dimensions

Kaandorp JA.

J Theor Biol. 1995 Jul 7;175(1):39-55.

PMID:
9441814

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