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Professor Orkun Soyer

Professor

Email: O.Soyer@warwick.ac.uk

Phone: 024 765 72968

Office: M131.1

Twitter: @osslab:ns in a new windowLink opens in a new windowother social media handlesLink opens in a new window

See more info on group page


Research Clusters

Quantitative, Systems & Engineering Biology (Co-Lead)

Microbiology & Infectious disease

Environment & Ecology

Cells & Development


Other GRPs/Centres etc

Warwick Integrative Synthetic Biology (WISB) Centre

Bio-electrical Engineering Innovation Hub


Vacancies and Opportunities

For PhD and postdoctoral opportunities, and interest in potential collaborations, please contact me at the above email address.


Research/Teaching Interests

The current focus of my research is to develop a predictive and quantitative understanding of cellular metabolism and metabolic interactions among cells. In the latter domain, we study metabolic interactions in well-defined microbial communities. Our ongoing research is funded by NSF/BBSRC and by an investigator award from the Gordon and Betty Moore FoundationLink opens in a new window

You can find more details of my research on our group websiteLink opens in a new window. In brief, we combine experiments with mathematical modelling to study microbial communities and cellular metabolism. We use time-lapse microscopy and metabolic measurements to study cell metabolism over time and under different conditions. We aim to use the resulting data to support or test mathematical models. These models tend to be developed at an abstract level, using differential equations and systems theory.

On the teaching front, I have co-designed and am delivering two modules relating to understanding cellular systems and engineering microbial communities. Both modules are thought at Y3 level. Recently, I have been also involved in an open book projectLink opens in a new window on cellular metabolism and physiology.

Research: Technical Summary

Our current research efforts focus on the following main areas:

1. Emergence and evolution of metabolic excretions (funded by NSF/BBSRC) (in collaboration with Wenying Shou). We develop abstract models of cellular metabolism and aim to test these with experimental data. Our modelling work focuses on understanding the role of metabolite cycles on constraining overall cell metabolism. We complement this with measurement of NAD(P)H autofluorescence in real time in yeast and HeLA cells. The ultimate aim is to understand role of cycled metabolite pools in determining metabolic dynamics, and in particular overflow metabolism.

2. Feedbacks between metabolism, community dynamics and spatial organisation in microbial communities (funded by Gordon and Betty Moore Foundation). We study a spatially organised microbial community, derived from Nature but cultured in the laboratory. We determine the metabolic interactions in this ~15-species system and aim to decipher the role of spatial organisation in the stability of those interactions and species co-existence. In this project, we make extensive use of temporal metagenomics (in collaboration with Christopher Quince), targeted metabolomics, and time-lapse microscopy.

3. Membrane potential and cellular metabolism (in collaboration with Munehiro Asally). In both prokaryotic and eukaryotic cells, the redox processes and maintenance of cellular co-substrate pools is tightly interlinked with membrane potential and respiration. These observations raise the possibility that control of redox balances could provide a means to control cellular metabolism. We are currently exploring the use of redox mediators and electric fields (together with micro-fluidics) to study and influence relations between cellular metabolic fluxes, membrane potential, and cellular redox balance. This work focuses on mammalian cells (HeLa) and yeast (S. cerevisiae).

4. Modelling of metabolic dynamics (in collaboration with Elisenda Feliu and Alex Fletcher). Composed of a myriad of interconnected reactions, and involving shared conserved moieties and regulatory mechanisms, metabolism is a complex dynamical system. We are interested in understanding the early emergence of such metabolic systems as well their possible dynamical determinants. Currently, we are developing mathematical models to try and understand how specific biochemical and biophysical mechanisms can emerge and determine the dynamics in small metabolic systems.

Publications

For a full list of publications, see WRAP

Education

  • 2000 - 2004 PhD, University of Michigan, Ann Arbor, MI, USA.
  • 1993 - 2000 BSc in Chemistry, Bogazici University (ed. language: English), Istanbul, Turkey.
  • 1985 - 1993 German Abitur, Istanbul Erkek Lisesi (ed. language: German), Istanbul, Turkey.

Appointments

  • 2013 - Prof. of Sys. Biology, University of Warwick, Coventry, UK
  • 2011 - 2013 Senior Lecturer in Sys. Biology, University of Exeter; Exeter, UK.
  • 2009 - 2011 Lecturer in Sys. Biology, University of Exeter; Exeter, UK.
  • 2006 - 2009 Researcher, CoSBi (Microsoft Research & University of Trento Centre for Computational and Systems Biology); Trento, Italy.
  • 2004 - 2006 Postdoctoral Research Assistant with Prof. Sebastian Bonhoeffer, Theoretical Biology, ETH (Swiss Federal Institute of Technology); Z├╝rich, Switzerland.

Honorary Appointments

  • 2014 - 2015 Fellow, Wissenschaftskolleg zu Berlin, Institute for Advanced Study; Berlin,Germany.
  • 2010 - 2015 Senior Research Fellow, ESRC Centre for Genomics in Soc. (Egenis); Exeter, UK.