Computational Biology

Section Computational Science

Computational Biology Group

The groups research interests are: morphogenesis, marine sessile organisms, evolutionary processes, modelling and simulation of developmental regulatory networks and metabolic pathways, modelling and simulation of growth and form, biomechanics. The group is part of the Section Computational Science of the Faculty of Science of the University of Amsterdam. We do research at a range of different levels of organisation (genome-gene regulatory networks-cells-tissue-organism). We work on modelling and analysis of gene regulation in cnidarians (corals and Nematostella vectensis), sponges, yeast and Drosophila. We do research on biomineralisation in corals and sponges (experimental and modelling work). We are working on growth and form of corals and the influence of light and hydrodynamics on the morphological plasticity and calcification in corals. This work is a combination of modelling work, a genetic comparison between different growth forms, phylogenetics, morphometrics of three-dimensional growth forms obtained from CT scans and field work.

Image Summary of the Research:

Simulation of a diffusion limited aggregation process, ``nutrient'' concentration is displayed in blue (light colours indicate a depletion of nutrients)

Simulation of a sponge with an accretive growth process (for example Haliclona oculata)

surface rendering of a CT scan of the coral Madracis mirabilis

Simulated flow density pattern around a 3D image of Madracis mirabilis

Morphological analysis of complex-shaped branching morphologies of the scleractinian coral Madracis mirabilis

Simulated growth of a scleractinian coral

Madracis mirabilis reef in Curacao (photograph Mark Vermeij)

Volume rendering of a CT scan of the coral Madracis mirabilis

Simulated growth and body plan of a branching sponge. The simulated regulatory network produces light blue spots indicating relatively high concentrations of Iroquois marking the future positions of the exhalant pores in the sponge

The sponge Haliclona oculat (Oosterschelde, the Netherlands, Photograph by Mario de Kluijver)

Cell-based modelling of gastrulation in the sea anemone Nematostella vectensis

Morpho space of simulated coral growth forms

Flat bifurcations in coral (green) and a neuron (red) (picture by R. Sinclair)