Dr OLIVER EBENHOEH

Dr OLIVER EBENHOEH The University of Aberdeen School of Medical Sciences Reader work +44 (0)1224 272520 pref Meston Building, Room 341 Meston Walk Old Aberdeen Aberdeen AB24 3UE

Reader in Systems Biology

Personal Details

Telephone: +44 (0)1224 272520
Email: ebenhoeh@abdn.ac.uk
Address: Meston Building, Room 341
Meston Walk
Old Aberdeen
Aberdeen AB24 3UE
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Biography

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.


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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. 

  • 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.


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Research Grants

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

DO NOVEL ACIDOPHILIC ARCHAEAL AMMONIA OXIDISERS SOLVE THE PARADOX OF NITRIFICATION IN ACID SOILS? (NERC). 10/2011-03/2015. Nicol, G. W., Prosser, J. I. & Ebenhöh, O. £430,811

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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Publications

Contributions to Journals

Articles

  • Heiland, I., Bodenstein, C., Hinze, T., Voytsekh, O., Ebenhöh, O., Mittag, M. & Schuster, S. (in press). 'Modelling temperature entrainment of circadian clocks using a reconstructed model from Chlamydomonas reinhardtii'. Journal of Biological Physics, vol in press.
  • Basler, G., Ebenhöh, O., Selbig, J. & Nikoloski, Z. (2011). 'Mass-balanced randomization of metabolic networks'. Bioinformatics, vol 27, no. 10, pp. 1397-1403.
    [Online] DOI: 10.1093/bioinformatics/btr145
  • Ebenhöh, O., Houwaart, T., Lokstein, H., Schlede, S. & Tirok, K. (2011). 'A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence'. Bio Systems, vol 103, no. 2, pp. 196-204.
    [Online] DOI: 10.1016/j.biosystems.2010.10.011
    [Online] AURA: paper.pdf
  • Kartal, O., Mahlow, S., Skupin, A. & Ebenhöh, O. (2011). 'Carbohydrate-active enzymes exemplify entropic principles in metabolism'. Molecular Systems Biology, vol 7.
    [Online] DOI: 10.1038/msb.2011.76
  • Pfau, T., Christian, N. & Ebenhöh, O. (2011). 'Systems approaches to modelling pathways and networks'. Briefings in Functional Genomics, vol 10, no. 5, pp. 266-279.
    [Online] DOI: 10.1093/bfgp/elr022
  • Basler, G., Grimbs, S., Ebenhöh, O., Selbig, J. & Nikoloski, Z. (in press). 'Evolutionary significance of metabolic network properties'. Journal of the Royal Society Interface.
    [Online] DOI: 10.1098/rsif.2011.0652
  • Mutwil, M., Usadel, B., Schütte, M., Loraine, A., Ebenhoeh, O. & Persson, S. (2010). 'Assembly of an Interactive Correlation Network for the Arabidopsis Genome Using a Novel Heuristic Clustering Algorithm'. Plant Physiology, vol 152, no. 1, pp. 29-43.
    [Online] DOI: 10.1104/pp.109.145318
  • Witzel, F., Goetze, J. & Ebenhoeh, O. (2010). 'Slow deactivation of ribulose 1,5-bisphosphate carboxylase/oxygenase elucidated by mathematical models'. FEBS Journal, vol 277, pp. 931-950.
    [Online] DOI: 10.1111/j.1742-4658.2009.07541.x
    [Online] AURA: paper.pdf
    [Online] AURA: supplement.pdf
  • Brackley, CA., Ebenhoeh, O., Grebogi, C., Kurths, J., Moura, AD., Romano, MC. & Thiel, M. (2010). 'Introduction to Focus Issue: Dynamics in Systems Biology'. Chaos, vol 20, no. 4.
    [Online] DOI: 10.1063/1.3530126
  • Schütte, M., Skupin, A., Segrè, D. & Ebenhoeh, O. (2010). 'Modeling the complex dynamics of enzyme-pathway coevolution'. Chaos, vol 20, no. 4.
    [Online] DOI: 10.1063/1.3530440
    [Online] AURA: schuette_etal.pdf
  • Christian, N., May, P., Kempa, S., Handorf, T. & Ebenhoeh, O. (2009). 'An integrative approach towards completing genome-scale metabolic networks'. Molecular BioSystems, vol 5, no. 12, pp. 1889-1903.
    [Online] DOI: 10.1039/B915913b
  • Ebenhoeh, O. & Handorf, T. (2009). 'Functional Classification Of Genome-Scale Metabolic Networks'. EURASIP Journal on Bioinformatics & Systems Biology.
    [Online] DOI: 10.1155/2009/570456
  • Kartal, Ö & Ebenhoeh, O. (2009). 'Ground State Robustness as an Evolutionary Design Principle in Signaling Networks'. PLoS one, vol 4, no. 12, pp. e8001.
    [Online] DOI: 10.1371/journal.pone.0008001
  • Schuette, M., Klitgord, N., Segre, D. & Ebenhoeh, O. (2009). 'Co-evolution of metabolism and protein sequences'. Genome Informatics, vol 22, pp. 156-166.
  • Tamura, T., Christian, N., Takemoto, K., Ebenhoeh, O. & Akutsu, T. (2009). 'Analysis and Prediction of Nutritional Requirements Using Structural Properties of Metabolic Networks and Support Vector Machines'. Genome Informatics, vol 22, pp. 176-190.
    [Online] DOI: 10.1142/9781848165786_0015
  • Basler, G., Nikoloski, Z., Ebenhoeh, O. & Handorf, T. (2008). 'Biosynthetic potentials from species-specific metabolic networks'. Genome Informatics, vol 20, pp. 135-148.
    [Online] DOI: 10.1142/9781848163003_0012
  • Handorf, T., Christian, N., Ebenhoeh, O. & Kahn, D. (2008). 'An environmental perspective on metabolism'. Journal of Theoretical Biology, vol 252, no. 3, pp. 530-537.
    [Online] DOI: 10.1016/j.jtbi.2007.10.036
  • Matthaeus, F., Salazar, C. & Ebenhoeh, O. (2008). 'Biosynthetic potentials of metabolites and their hierarchical organization'. PLoS Computational Biology, vol 4, no. 4, pp. e1000049.
    [Online] DOI: 10.1371/journal.pcbi.1000049
  • May, P., Wienkoop, S., Kempa, S., Usadel, B., Christian, N., Rupprecht, J., Weiss, J., Recuenco-Munoz, L., Ebenhoeh, O., Weckwerth, W. & Walther, D. (2008). 'Metabolomics- and Proteomics-Assisted Genome Annotation and Analysis of the Draft Metabolic Network of Chlamydomonas reinhardtii'. Genetics, vol 179, no. 1, pp. 157-166.
    [Online] DOI: 10.1534/genetics.108.088336
  • Christian, N., Handorf, T. & Ebenhoeh, O. (2007). 'Metabolic synergy: Increasing biosynthetic capabilities by network cooperation'. Genome Informatics, vol 18, pp. 321-330.
  • Handorf, T. & Ebenhoeh, O. (2007). 'MetaPath Online: A web server implementation of the network expansion algorithm'. Nucleic Acids Research, vol 35, no. supp. 2, pp. W613-W618.
    [Online] DOI: 10.1093/nar/gkm287
  • Bruck, J., Ebenhoeh, O. & Heinrich, R. (2006). 'Patterns of interactions of reaction pairs in metabolic networks'. Genome Informatics, vol 17, no. 1, pp. 208-218.
  • Ebenhoeh, O., Handorf, T. & Kahn, D. (2006). 'Evolutionary changes of metabolic networks and their biosynthetic capacities'. IEE Proceedings. Systems Biology, vol 153, no. 5, pp. 354-358.
  • Binder, B., Ebenhoeh, O., Hashimoto, K. & Heinrich, R. (2006). 'Expansion of signal transduction networks'. IEE Proceedings. Systems Biology, vol 153, no. 5, pp. 364-368.
    [Online] DOI: 10.1049/ip-syb:20060030
  • Ebenhoeh, O. & Liebermeister, W. (2006). 'Structural analysis of expressed metabolic subnetworks'. Genome Informatics, vol 17, no. 1, pp. 163-172.
  • Handorf, T., Ebenhoeh, O., Kahn, D. & Heinrich, R. (2006). 'Hierarchy of metabolic compounds based on their synthesising capacity'. IEE Proceedings. Systems Biology, vol 153, no. 5, pp. 359-363.
  • Matthäus, F., Salazar, C. & Ebenhoeh, O. (2006). 'Large-scale analysis of metabolic networks: clustering metabolites by their synthesizing capacities'. InterJournal, pp. 1674.
  • Ringemann, C., Ebenhoeh, O., Heinrich, R. & Ginsburg, H. (2006). 'Can biochemical properties serve as selective pressure for gene selection during inter-species and endosymbiotic lateral gene transfer?'. IEE Proceedings. Systems Biology, vol 153, no. 4, pp. 212-222.
  • Salazar, C., Schuetze, J. & Ebenhoeh, O. (2006). 'Bioinformatics meets systems biology'. Genome Biology, vol 7, no. 1, pp. 303.
    [Online] DOI: 10.1186/gb-2006-7-1-303
  • Ebenhöh, O., Handorf, T. & Heinrich, R. (2005). 'A cross species comparison of metabolic network functions'. Genome Informatics, vol 16, no. 1, pp. 203-213.
  • Handorf, T., Ebenhöh, O. & Heinrich, R. (2005). 'Expanding metabolic networks: scopes of compounds, robustness, and evolution'. Journal of Molecular Evolution, vol 61, no. 4, pp. 498-512.
    [Online] DOI: 10.1007/s00239-005-0027-1
  • Ebenhoeh, O., Handorf, T. & Heinrich, R. (2004). 'Structural analysis of expanding metabolic networks'. Genome Informatics, vol 15, no. 1, pp. 35-45.
  • Ebenhoeh, O. & Heinrich, R. (2003). 'Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness'. Bulletin of Mathematical Biology, vol 65, no. 2, pp. 323-357.
    [Online] DOI: 10.1016/S0092-8240(03)00002-8
  • Ebenhoeh, O. & Heinrich, R. (2001). 'Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems'. Bulletin of Mathematical Biology, vol 63, no. 1, pp. 21-55.
    [Online] DOI: 10.1006/bulm.2000.0197

Chapters in Books, Reports and Conference Proceedings

Chapters

  • May, P., Christian, N., Ebenhoeh, O., Werkwerth, W. & Walther, D. (2011). 'Integration of proteomic and metabolomic profiling as well as metabolic modeling for the functional analysis of metabolic networks'. in CH Wu & C Chen (eds), Bioinformatics for Comparative Proteomics vol. 694, Methods in Molecular Biology, no. 3, vol. 694, Humana Press, Totowa, NJ, USA, pp. 341-363.
    [Online] DOI: 10.1007/978-1-60761-977-2_21
  • Kempa, S., Walther, D., Ebenhoeh, O. & Weckwerth, W. (2009). 'Metabolic Engineering'. in JM Walker & R Rapley (eds), Molecular Biology and Biotechnology 5th edn, Royal Society of Chemistry (Great Britain), Cambridge, United KIngdom, pp. 196-219.
  • Nikoloski, Z., Grimbs, S., Selbig, J. & Ebenhoeh, O. (2008). 'Hardness and Approximability of the Inverse Scope Problem'. in KA Crandall & J Lagergren (eds), Algorithms in Bioinformatics: Proceedings of the 8th International Workshop, WABI 2008 vol. 5251, Lecture Notes in Computer Science/Lecture Notes in Bioinformatics, no. 5251, Springer Science+Business Media, Berlin, Germany, pp. 99-112, 8th International Workshop, WABI 2008, Karlsruhe, Germany, 15/09/08.
    [Online] DOI: 10.1007/978-3-540-87361-7
  • Numata, J., Ebenhoeh, O. & Knapp, EW. (2008). 'Measuring correlations in metabolomic networks with mutual information'. in E Knapp (ed.), Genome Informatics 2008: Proceedings of the 8th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2008) vol. 20, Genome Informatics Series, vol. 20, Imperial College Press, London, United Kingdom, pp. 112-122, 8th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2008), Zeuten Lake, Berlin, Germany, 9/06/08.
    [Online] DOI: 10.1142/9781848163003_0010

Conference Proceedings

  • Kruse, K. & Ebenhoeh, O. (2008). 'Comparing Flux Balance Analysis to Network Expansion: Producibility,Sustainability and the Scope of Compounds'. in E Knapp, G Benson & H Holzhutter (eds), Genome Informatics 2008: Proceedings of the 8th International Workshop on Bioinformatics and Systems Biology vol. 20, Genome Informatics Series (GIS), vol. 20, Imperial College Press, London, United Kingdom, pp. 91-101, 8th International Workshop on Bioinformatics and Systems Biology (IBSB 2008), Berlin, Germany, 9/06/07.

Contributions to Conferences

Papers

  • Kartal, Ö & Ebenhoeh, O. (2008). 'The Glucan, Water Dikinase - A Kinetic Model to Understand the Initial Step in Starch Mobilization in Plant Leaves'. pp. 245--248.

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