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List of works by Jaap A. Kaandorp

A cell-based boundary model of gastrulation by unipolar ingression in the hydrozoan cnidarian Clytia hemisphaerica

scientific article published on 02 January 2020

A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering ⬇️

scientific article published on October 23, 2010

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

scientific article published on 23 June 2010

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

scientific article

A model of filamentous cyanobacteria leading to reticulate pattern formation

scientific article

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.

scientific article

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

scientific article published on 24 September 2015

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

scientific article

Biomineralization toolkit: the importance of sample cleaning prior to the characterization of biomineral proteomes.

scientific article published on 3 May 2013

Calcium homeostasis and signaling in yeast cells and cardiac myocytes

scientific article published on 16 July 2009

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

scientific article

Computational methods for diffusion-influenced biochemical reactions

scientific article published on 30 May 2007

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

article

Effect of Nutrient Diffusion and Flow on Coral Morphology

scientific article published in Physical Review Letters

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

scientific article published on 24 September 2007

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

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

scientific article published on 6 June 2018

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

scientific article published on 12 July 2007

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article published on 16 September 2011

Macroscopic Modelling of Environmental Influence on Growth and Form of Sponges and Corals Using the Accretive Growth Model

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

scientific article

Mathematical modeling of calcium homeostasis in yeast cells

scientific article published on 30 January 2006

Modeling Filamentous Cyanobacteria Reveals the Advantages of Long and Fast Trichomes for Optimizing Light Exposure ⬇️

scientific article published on July 18, 2011

Modeling biosilicification at subcellular scales

scientific article published on January 2013

Modelling genetic regulation of growth and form in a branching sponge

scientific article published in November 2008

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

scientific article

Modelling the skeletal architecture in a sponge with radiate accretive growth

scientific article published in January 2009

Models of coral growth: spontaneous branching, compactification and the Laplacian growth assumption.

scientific article

Morphogenesis of the branching reef coral Madracis mirabilis.

scientific article

Novel molluskan biomineralization proteins retrieved from proteomics: a case study with Upsalin

scientific article published on 4 April 2012

Polyp oriented modelling of coral growth

scientific article published on 01 June 2004

Promoter sequence determines the relationship between expression level and noise

scientific article

Quantification of complex modular architecture in plants

scientific article published on 22 February 2018

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

scientific article

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

scientific article published on 22 February 2007

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

scientific article

Simulating calcium influx and free calcium concentrations in yeast

scientific article

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

scientific article

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

scientific article

Spatial gene expression quantification: a tool for analysis of in situ hybridizations in sea anemone Nematostella vectensis

scientific article

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

scientific article published on 26 May 2006

Systems biology: parameter estimation for biochemical models

scientific article published on February 2009

The effect of allometric scaling in coral thermal microenvironments.

scientific article published on 12 October 2017

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

scientific article published in 2011

The skeletal proteome of the coral Acropora millepora: the evolution of calcification by co-option and domain shuffling

scientific article published on 12 June 2013

The skeleton of the staghorn coral Acropora millepora: molecular and structural characterization

scientific article (publication date: 2014)

Understanding the sub-cellular dynamics of silicon transportation and synthesis in diatoms using population-level data and computational optimization

scientific article (publication date: June 2014)

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