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Systems Biology

The focus of the Research Priority Area Systems Biology is on Host-Microbiome Interactions divided over various sub-themes. It is a collaboration of research groups in SILS and IBED.

Systems biology has become an intrinsic part of contemporary life-science research. It is based on the notion that to better understand the complexity of biological systems, these should be considered as a whole. Hence, the different intricate components of any living system ought to be studied and contextualized with a combination of experimental and theoretical approaches. This type of research, given its multidisciplinary nature, needs to be executed in collaborative efforts, integrating many ´╗┐scientific disciplines, such as biology, mathematics, physics, biochemistry, bioinformatics, computer science and so on. The main focus is to acquire a (quantitative) understanding of how biological systems change over time and respond to changing conditions.

The subthemes of Systems Biology are:

  • Systems biology in plant sciences: there is a growing insight that the interplay between environment (e.g. soil) and plants depend to a large extent on the microbiome of the roots.
    Research groups: Plant Hormone Biology (Harro Bouwmeester)
  • Gut-microbiome-host interactions: this is highly relevant for nutritional interventions and disease development. Many research activities are ongoing in this field and the Amsterdam Microbiome Initiative (AMI) is a focal point of these research activities.
    Research groups: Molecular Biology and Microbial Food Safety (Stanley Brul); Biosystems Data Analysis (Age Smilde)
  • Systems biology in ecology: In ecology there is a growing interest in host-microbe interactions, such as for sponges (Jasper de Goeij), corals (Petra Visser), seagrasses (Gerard Muyzer), algae (Gerard Muyzer/Susanne Wilken), insects (Astrid Groot), as well as in the role of microbes in biogeochemical cycles in terrestrial and aquatic environments, such as freshwater lakes (Gerard Muyzer/Jef Huisman).

Next to an overlap by focussing on host-microbiome interactions in different organisms or environments, all subthemes make use of generic modelling and data analysis. This encompass methods to combine top-down and bottom-up systems biology methods such as:

  • Combining genome-scale models with measured data of different omics types
  • Combining mechanistic models with measured data of different omics types
  • Applying causal modelling to omics data
  • Imposing prior biological and biochemical knowledge on methods fusing omics data

For more information from the research groups themselves, check their website: systemsbiology.amsterdam.