Contact Details

work +44 (0)1224 272520
The University of Aberdeen Fraser Noble Building
Room 163
Old Aberdeen
Aberdeen AB24 3UE
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Since November 2013 I work part-time for the University of Aberdeen. My main affiliation is now the Heinrich-Heine University Düsseldorf, Germany. Please follow our activities on the group's homepage.


Oliver Ebenhoeh studied Mathematics and Physics at the University of Heidelberg (Germany), and did his PhD in Theoretical Biophysics at the Humboldt University, Berlin (Germany), where he continued to work as a postdoctoral researcher until 2006. He established his research group 'Systems Biology and Mathematical Modelling' at the Max-Planck-Institute of Molecular Plant Physiology in Potsdam (Germany) in 2007. He moved to the University of Aberdeen in 2009 where he was appointed Reader in Systems Biology as a joint position of the Institute for Complex Systems and Mathematical Biology and the Institute of Medical Sciences. Since 2010 he is coordinator of the Theroetical Systems Biology research programme. Since October 2012 he is the coordinator of the Marie-Curie Initial Training Network 'AccliPhot', which is supported by €4 Mio by the European Commission and comprises 12 partners from 6 countries.


Research Interests

Oliver Ebenhoeh's research group is focussed on understanding molecular interaction networks using theoretical approaches. An overall goal of his research is to link physical sciences to biology to derive a theoretical understanding of living systems. 

Plant Systems Biology

A strong research focus lies on the development of mathematical models of photosynthesis and plant metabolism. This research is now supported by the European Commission through the Marie-Curie Initial Training Network AccliPhot.

  • How do plants adapt to rapidly changing light intensities while maximally exploiting the available light? 
  • How is the photosynthetic electron transport chain regulated by metabolic demand? 
  • How is starch partitioning controlled? 
  • How is metabolism connected with the circadian clock in plants? 
  • What mechanisms are responsible for creating the highly ordered, macroscopic starch granules?
  • How is the catalysis on the granule surface regulated?

Polymer biochemistry

Enzymes acting on polymers are difficult to describe in mathematical models because of the complexity of all possible polymeric structures. We are developing new concepts in which we describe biochemical systems involving polymers in the language of statistical thermodynamics. This powerful links between the fields of biochemistry and physics enables completely new kinds of analysis. We aim to gather understanding how complex structures can emerge from relatively simple enzymatic action patterns.

Large-scale network analysis

His group has developed a novel concept, the method of network expansion, to study large-scale metabolic networks. By this, structural to functional properties of such networks could be systematically related. Moreover, from identifying characteristic features that cannot be expected to have appeared by chance, important clues about the evolutionary history of such networks could be obtained.

Specific small-scale systems

His group also applies traditional, differential equation based, modelling techniques to study metabolic, signalling and regulatory systems to understand their underlying design principles. Systems under investigation include starch metabolism in plants and photosynthesis, circadian clocks in plants and green algae, transport and metabolic processes taking place in plant roots and the surrounding soil. 

Symbiosis and Parasitism

A key observation is that almost no organism lives in complete isolation. In fact, only a small number of microbes are easily cultivatable. A strategic goal of our research activities is to understand the principles that lead to a stability of complex communities. To this end, we study specific parasites and compare their metabolism and genomes to free living relatives. By this, we hope to gain insight into the evolutionary origins of parasitism. To study symbiosis, we focus on the interaction of plants with their rhizosphere. Many plants undergo symbiosis with mycorrhizal fungi, from which both interaction partners benefit.

Research Grants

Investigator on BBSRC sLoLa BB/L002957/1 "Algal oils by design: a new biotech platform for high-value lipids". 05/2014-04/2018. Coordinator: S. Purton, University College London. £2,363,928

Investigator on BBSRC sLoLa BB/K003356/1 "A platform for rapid and precise DNA module rearrangements in Synthetic Biology". 04/2013-03/2018. Coordinator: M. Stark, University of Glasgow. £3,265,356

Environmental Acclimation of Photosynthesis (AccliPhot). FP7 Marie-Curie Initial Training Network. 10/2012-09/2016. Coordinator: O. Ebenhöh. €4,000,000.

LINKING THE CLOCK TO METABOLISM - TIMET (EUROPEAN COMMISSION). 03/2010-02/2015. Coordinator: A. Millar, University of Edinburgh. €5,844,329


A genetic dissection of traits required for sustainable water use in rice using Genome Wide Association Studies (GWAS). BBSRC. 01/2012-12/2015
A. Price, A. Meharg, O. Ebenhöh, D. Salt, G. Norton. £931,130
A systems approach to optimise photosynthetic production of molecular hydrogen. Royal Society International Exchanges. 03/2012-02/2014. O. Ebenhöh & J.-D. Rochaix (Université de Genève). £12,000



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Contributions to Journals


  • Christopher, A., Hameister, H., Corrigall, H., Ebenhoeh, O., Muller, B. & Ullner, E. (2016). 'Modelling Robust Feedback Control Mechanisms That Ensure Reliable Coordination of Histone Gene Expression with DNA Replication'. PLoS ONE, vol 11, no. 10, e0165848.
    [Online] DOI: 10.1371/journal.pone.0165848
    [Online] AURA: journal.pone.0165848.PDF
  • Pokhilko, A., Zhao, J., Ebenhöh, O., Smith, MCM., Stark, WM. & Colloms, SD. (2016). 'The mechanism of ϕC31 integrase directionality: experimental analysis and computational modelling'. Nucleic Acids Research, vol 44, no. 15, pp. 7360-7372.
    [Online] DOI: 10.1093/nar/gkw616
    [Online] AURA: Nucl._Acids_Res._2016_Pokhilko_7360_72.pdf
  • Matuszyńska, A. & Ebenhöh, O. (2015). 'A reductionist approach to model photosynthetic self-regulation in eukaryotes in response to light'. Biochemical Society Transactions, vol 43, no. 6, pp. 1133-1139.
    [Online] DOI: 10.1042/BST20150136
    [Online] AURA: 033894.full.pdf
  • Adlakha, N., Pfau, T., Ebenhöh, O. & Yazdani, SS. (2015). 'Insight into metabolic pathways of the potential biofuel producer, Paenibacillus polymyxa ICGEB2008'. Biotechnology for biofuels, vol 8, 159.
    [Online] DOI: 10.1186/s13068-015-0338-4
    [Online] AURA: s13068_015_0338_4.pdf
  • Pokhilko, A., Bou-Torrent, J., Pulido, P., Rodríguez-Concepción, M. & Ebenhöh, O. (2015). 'Mathematical modelling of the diurnal regulation of the MEP pathway in Arabidopsis'. New Phytologist, vol 206, no. 3, pp. 1075-1085.
    [Online] DOI: 10.1111/nph.13258
  • Pokhilko, A. & Ebenhöh, O. (2015). 'Mathematical modelling of diurnal regulation of carbohydrate allocation by osmo-related processes in plants'. Journal of the Royal Society Interface, vol 12, no. 104, 20141357.
    [Online] DOI: 10.1098/rsif.2014.1357
    [Online] AURA: 20141357.full.pdf
  • Ebenhoeh, O., Fucile, G., Finazzi, G., Rochaix, J-D & Goldschmidt-Clermont, M. (2014). 'Short-term acclimation of the photosynthetic electron transfer chain to changing light: a mathematical model'. Philosophical Transactions of the Royal Society B: Biological Sciences, vol 369, no. 1640, 20130223.
    [Online] DOI: 10.1098/rstb.2013.0223
  • Pokhilko, A., Flis, A., Sulpice, R., Stitt, M. & Ebenhoeh, O. (2014). 'Adjustment of carbon fluxes to light conditions regulates the daily turnover of starch in plants: a computational model'. Molecular BioSystems, vol 10, no. 3, pp. 613-627.
    [Online] DOI: 10.1039/c3mb70459a
    [Online] AURA: c3mb70459a.pdf
  • Christian, N., Skupin, A., Morante, S., Jansen, K., Rossi, G. & Ebenhoeh, O. (2014). 'Mesoscopic behavior from microscopic Markov dynamics and its application to calcium release channels'. Journal of Theoretical Biology, vol 343, pp. 102-112.
    [Online] DOI: 10.1016/j.jtbi.2013.11.010
    [Online] AURA: 1309.5829v2.pdf
  • Seaton, DD., Ebenhoeh, O., Millar, AJ. & Pokhilko, A. (2014). 'Regulatory principles and experimental approaches to the circadian control of starch turnover'. Journal of the Royal Society Interface, vol 11, no. 91, 20130979.
    [Online] DOI: 10.1098/rsif.2013.0979
    [Online] AURA: Regulatory_principles_andexperimental_approaches.pdf
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