Professor Orkun Soyer

Professor

Email: O.Soyer@warwick.ac.uk

Phone: 024 765 72968

Office: M131.1

Twitter: @osslab

See more info on group page

Research Clusters

Quantitative, Systems & Engineering Biology (Cluster 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 cyanobacterial microbial communities, capable of macro-scale spatial organisation. In the former domain, we study metabolism at the single-cell level, using a model eukaryote; baker's yeast.

Since 2020, I am one of the 15 world-wide recipientsLink opens in a new window of the Gordon and Betty Moore FoundationLink opens in a new window 6-year investigator awards, which funds our research on cyanobacteria communities. In addition, I currently hold a LeverhulmeLink opens in a new window project grant, funding our work on cellular metabolism. Over the years, my research has been funded by BBSRC, EPSRC, NSF, and Cancer Research, UK.

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 at Y3 level, and one module, introducing computational biology, at Y1 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 Leverhulme, and previously by NSF/BBSRC). 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. 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, targeted metabolomics, and time-lapse microscopy.

3. Membrane potential and cellular metabolism. 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. 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.

Biography

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); Zürich, Switzerland.

Honorary Appointments

2026, Fellow, Tokyo Science, Earth Life Science Institute, Tokyo, Japan.
2026, Fellow, Kavli Institute for Theoretical Physics; Santa Barbara, CA, USA
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.

Publications

Rosko, Jerko, Poon, Rebecca N., Cremin, Kelsey, Locatelli, Emanuele, Coates, Mary, Duxbury, Sarah J. N., Randall, Kieran, Croft, Katie, Valeriani, Chantal, Polin, Marco and Soyer, Orkun S. (2025) Cellular coordination underpins rapid reversals in gliding filamentous cyanobacteria and its loss results in plectonemes. eLife, 13 . RP100768. doi:10.7554/eLife.100768.3 ISSN 2050-084X.

Cremin, Kelsey, Meloni, Gabriel N., Soyer, Orkun S. and Unwin, Patrick R. (2025) Single-cell analysis with spatiotemporal control of local pH. ACS Measurement Science Au, 5 (1). pp. 120-129. doi:10.1021/acsmeasuresciau.4c00079 ISSN 2694-250X.

Duxbury, Sarah Jennifer Nicola, Raguideau, Sebastien, Cremin, Kelsey, Richards, Luke, Medvecky, Matej, Rosko, Jerko, Coates, Mary, Randall, Kieran, Chen, Jing, Quince, Christopher and Soyer, Orkun S. (2025) Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community. The ISME Journal, 19 (1). wraf126. doi:10.1093/ismejo/wraf126 ISSN 1751-7362.

Prakash, Praneet, Jiang, Xue, Richards, Luke, Schofield, Zoe, Schäfer, Patrick, Polin, Marco, Soyer, Orkun S. and Asally, Munehiro (2024) Emergence of synchronised growth oscillations in filamentous fungi. Journal of The Royal Society Interface, 21 (219). 20240574. doi:10.1098/rsif.2024.0574 ISSN 1742-5689.

Richards, Luke, Cremin, Kelsey, Coates, Mary E., Vigor, Finley, Schäfer, Patrick and Soyer, Orkun S. (2024) Ammonia leakage can underpin nitrogen-sharing among soil microorganisms. ISME Journal, 18 (1). wrae171. doi:10.1093/ismejo/wrae171 ISSN 1751-7362.

Skates, Emily, Delattre, Hadrien, Schofield, Zoe, Asally, Munehiro and Soyer, Orkun S. (2023) Thioflavin T indicates mitochondrial membrane potential in mammalian cells. Biophysical Reports, 3 (4). 100134. doi:10.1016/j.bpr.2023.100134 ISSN 2667-0747.

Cremin, Kelsey , Meloni, Gabriel N., Valavanis, Dimitrios, Soyer, Orkun S. and Unwin, Patrick R. (2023) Can single cell respiration be measured by scanning electrochemical microscopy (SECM)? ACS Measurement Science Au, 3 (5). pp. 361-370. doi:10.1021/acsmeasuresciau.3c00019 ISSN 2694-250X.

West, Robert, Delattre, Hadrien, Noor, Elad, Feliu, Elisenda and Soyer, Orkun S. (2023) Dynamics of co-substrate pools can constrain and regulate metabolic fluxes. eLife, 12 . 12:e84379. doi:10.7554/eLife.84379 ISSN 2050-084X.

Cremin, Kelsey , Duxbury, Sarah J. N., Rosko, Jerko and Soyer, Orkun S. (2023) Formation and emergent dynamics of spatially organized microbial systems. Interface Focus, 13 (2). 20220062. doi:10.1098/rsfs.2022.0062 ISSN 2042-8898.

Johnson, Connah G. M., Fletcher, Alexander G. and Soyer, Orkun S. (2022) ChemChaste : simulating spatially inhomogeneous biochemical reaction–diffusion systems for modeling cell–environment feedbacks. GigaScience, 11 . giac051. doi:10.1093/gigascience/giac051 ISSN 2047-217X.

Hayes, Clarmyra, Feliu, Elisenda and Soyer, Orkun S. (2022) Multisite enzymes as a mechanism for bistability in reaction networks. ACS Synthetic Biology, 11 (2). pp. 596-607. doi:10.1021/acssynbio.1c00272 ISSN 2161-5063.

Quince, Christopher , Nurk, Sergey, Raguideau, Sébastien, James, Robert, Soyer, Orkun S., Summers, J. Kimberly, Limasset, Antoine, Eren, A. Murat, Chikhi, Rayan and Darling, Aaron E. (2021) STRONG : metagenomics strain resolution on assembly graphs. Genome Biology, 22 (1). 214. doi:10.1186/s13059-021-02419-7 ISSN 1474-7596.

Delattre, Hadrien, Sasidharan, Kalesh and Soyer, Orkun S. (2021) Inhibiting the reproduction of SARS-CoV-2 through perturbations in human lung cell metabolic network. Life Science Alliance, 4 (1). e202000869. doi:10.26508/lsa.202000869 ISSN 2575-1077.

Johnson, Connah, Delattre, Hadrien, Hayes, Clarmyra and Soyer, Orkun S. (2021) An evolutionary systems biology view on metabolic system structure and dynamics. In: Crombach, Anton, (ed.) Evolutionary Systems Biology : Advances, Questions, and Opportunities. Cham : Springer International Publishing, pp. 159-196. ISBN 9783030717360

Cremin, Kelsey , Jones, Bryn, Teahan, James, Meloni, Gabriel N., Perry, David, Zerfass, Christian, Asally, Munehiro, Soyer, Orkun S. and Unwin, Patrick R. (2020) Scanning ion conductance microscopy reveals differences in the ionic environments of gram-positive and negative bacteria. Analytical Chemistry, 92 (24). pp. 16024-16032. doi:10.1021/acs.analchem.0c03653 ISSN 0003-2700.

Morcrette, Helen, Kovacs-Simon, Andrea, Tennant, Richard K., Love, John, Wagley, Sariqa, Yang, Zheng R., Studholme, David J., Soyer, Orkun S., Champion, Olivia L., Butler, Clive S. and Titball, Richard W. (2020) Campylobacter jejuni 11168H exposed to penicillin forms persister cells and cells with altered redox protein activity. Frontiers in Cellular and Infection Microbiology, 10 . 565975. doi:10.3389/fcimb.2020.565975 ISSN 2235-2988.

Schofield, Zoe, Meloni, Gabriel N., Tran, Peter, Zerfass, Christian, Sena, Giovanni, Hayashi, Yoshikatsu, Grant, Murray R., Contera, Sonia A., Minteer, Shelley D., Kim, Minsu, Prindle, Arthur, Rocha, Paulo, Djamgoz, Mustafa B. A., Pilizota, Teuta, Unwin, Patrick R., Asally, Munehiro and Soyer, Orkun S. (2020) Bioelectrical understanding and engineering of cell biology. Journal of The Royal Society Interface, 17 (166). 20200013. doi:10.1098/rsif.2020.0013 ISSN 1742-5689.

Delattre, Hadrien, Chen, Jing, Wade, Matthew J. and Soyer, Orkun S. (2020) Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis. Journal of The Royal Society Interface, 17 (166). 20200053. doi:10.1098/rsif.2020.0053 ISSN 1742-5689.

Chen, Jing, Wade, Matthew J., Dolfing, Jan and Soyer, Orkun S. (2019) Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulfate reducer. Journal of The Royal Society Interface, 16 (154). 20190129. doi:10.1098/rsif.2019.0129 ISSN 1742-5689.

Feng, Song and Soyer, Orkun S. (2019) In silico evolution of signaling networks using rule-based models : bistable response dynamics. Methods in molecular biology, 1945 . pp. 315-339. doi:10.1007/978-1-4939-9102-0_15 ISSN 1940-6029.

Zerfaß, Christian, Asally, Munehiro and Soyer, Orkun S. (2019) Interrogating metabolism as an electron flow system. Current Opinion in Systems Biology, 13 . pp. 59-67. doi:10.1016/j.coisb.2018.10.001 ISSN 2452-3100.

Zerfaß, Christian, Christie-Oleza, Joseph A., Soyer, Orkun S. and Master, Emma R. (2019) Manganese oxide biomineralization provides protection against nitrite toxicity in a cell-density-dependent manner. Applied and Environmental Microbiology, 85 (2). e02129-18. doi:10.1128/AEM.02129-18 ISSN 0099-2240.

Martinez-Vernon, Andrea, Farrell, Frederick and Soyer, Orkun S. (2018) MetQy – an R package to query metabolic functions of genes and genomes. Bioinformatics, 34 (23). pp. 4134-4137. doi:10.1093/bioinformatics/bty447 ISSN 1367-4803.

Zerfaß, Christian, Christie-Oleza, Joseph Alexander and Soyer, Orkun S. (2018) Manganese oxide biomineralization is a social trait protecting. Applied and Environmental Microbiology, 85 (92). e02129-18. doi:10.1128/AEM.02129-18 ISSN 0099-2240.

Sierocinski, Pawel, Bayer, Florian, Yvon-Durocher, Gabriel, Burdon, Melia, Großkopf, Tobias, Alston, Mark, Swarbreck, David, Hobbs, Phil J., Soyer, Orkun S. and Buckling, Angus (2018) Biodiversity-function relationships in methanogenic communities. Molecular Ecology, 27 (22). pp. 4641-4651. doi:10.1111/mec.14895 ISSN 0962-1083.

Aller, Sean, Scott, Andrew, Sarkar-Tyson, Mitali and Soyer, Orkun S. (2018) Integrated human-virus metabolic stoichiometric modelling predicts host-based antiviral targets against Chikungunya, Dengue and Zika viruses. Journal of The Royal Society Interface, 15 (146). 20180125. doi:10.1098/rsif.2018.0125 ISSN 1742-5689.

Zerfaß, Christian, Chen, Jing and Soyer, Orkun S. (2018) Engineering microbial communities using thermodynamic principles and electrical interfaces. Current Opinion in Biotechnology, 50 . pp. 121-127. ISSN 0958-1669.

Jiang, Xue, Zerfaß, Christian, Eichmann, Ruth, Asally, Munehiro, Schäfer, Patrick and Soyer, Orkun S. (2018) Impact of spatial organization on a novel auxotrophic interaction among soil microbes. ISME Journal, 12 . pp. 1443-1456. doi:10.1038/s41396-018-0095-z ISSN 1751-7370.

Sierocinski, Pawel, Milferstedt, Kim, Bayer, Florian, Großkopf, Tobias, Alston, Mark, Bastkowski, Sarah, Swarbreck, David, Hobbs, Phil J., Soyer, Orkun S., Hamelin, Jérôme and Buckling, Angus (2017) A single community dominates structure and function of a mixture of multiple methanogenic communities. Current Biology, 27 (21). 3390-3395.e4. doi:10.1016/j.cub.2017.09.056 ISSN 0960-9822.

Jiang, Xue, Zerfaß, Christian, Eichmann, Ruth, Asally, Munehiro, Schäfer, P. (Patrick) and Soyer, Orkun S. (2017) Impact of spatial organization on a novel auxotrophic interaction among soil microbes. UNSPECIFIED. BioRxiv: Cold Spring Harbour Laboratories. (Submitted)

Cavaliere, Matteo, Feng, Song, Soyer, Orkun S. and Jiménez, José I. (2017) Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology, 19 (8). pp. 2949-2963. doi:10.1111/1462-2920.13767 ISSN 1462-2912.

Senior, Nicola J., Sasidharan, Kalesh, Saint, Richard J., Scott, Andrew E., Sarkar-Tyson, Mitali, Ireland, Philip M., Bullifent, Helen L, Rong Yang, Z., Moore, Karen, Oyston, Petra C. F., Atkins, Timothy P., Atkins, Helen S., Soyer, Orkun S. and Titball, Richard W. (2017) An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions. BMC Microbiology, 17 (1). 163. doi:10.1186/s12866-017-1073-8 ISSN 1471-2180.

Großkopf, Tobias, Zenobi, Simone, Alston, Mark, Folkes, Leighton, Swarbreck, David and Soyer, Orkun S. (2016) A stable genetic polymorphism underpinning microbial syntrophy. The ISME Journal, 10 . pp. 2844-2853. doi:10.1038/ismej.2016.80 ISSN 1751-7362.

Widder, Stefanie, Allen, Rosalind, Pfeiffer, Thomas, Curtis, Thomas P., Wiuf, Carsten, Sloan, William T., Cordero, Otto X., Brown, Sam P., Momeni, Babak, Shou, Wenying et al.

(2016) Challenges in microbial ecology : building predictive understanding of community function and dynamics. The ISME Journal, 2016 (10). pp. 2557-2568. doi:10.1038/ismej.2016.45 ISSN 1751-7362.

Großkopf, Tobias and Soyer, Orkun S. (2016) Microbial diversity arising from thermodynamic constraints. The ISME Journal, 10 . pp. 2725-2733. doi:10.1038/ismej.2016.49 ISSN 1751-7362.

Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S. and Schneider, Dominique (2016) Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. BMC Evolutionary Biology, 16 (1). doi:10.1186/s12862-016-0733-x ISSN 1471-2148.

Montefusco, Francesco, Akman, Ozgur E., Soyer, Orkun S. and Bates, Declan (2016) Ultrasensitive negative feedback control : a natural approach for the design of synthetic controllers. PLoS One, 11 (8). e0161605. doi:10.1371/journal.pone.0161605 ISSN 1932-6203.

Feng, Song, Sáez, Meritxell, Wiuf, Carsten, Feliu, Elisenda and Soyer, Orkun S. (2016) Core signalling motif displaying multistability through multi-state enzymes. Journal of The Royal Society Interface, 13 (123). 20160524. doi:10.1098/rsif.2016.0524 ISSN 1742-5689.

Feng, Song, Ollivier, Julien F. and Soyer, Orkun S. (2016) Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks. PLoS Computational Biology, 12 (5). e1004918. doi:10.1371/journal.pcbi.1004918 ISSN 1553-7358.

Steinacher, Arno, Bates, Declan, Akman, Ozgur E. and Soyer, Orkun S. (2016) Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels. PLoS One, 11 (4). e0153295. doi:10.1371/journal.pone.0153295 ISSN 1932-6203.

Cizmeci, Deniz, Dempster, Emma L., Champion, Olivia L., Wagley, Sariqa, Akman, Ozgur E., Prior, Joann L., Soyer, Orkun S., Mill, Jonathan and Titball, Richard W. (2016) Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection. Scientific Reports, 6 . 30861. doi:10.1038/srep30861 ISSN 2045-2322.

Feng, Song, Ollivier, Julien F., Swain, Peter S. and Soyer, Orkun S. (2015) BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Research, 43 (19). e123. doi:10.1093/nar/gkv595 ISSN 0305-1048.

Kothamachu, Varun B., Feliu, Elisenda, Cardelli, Luca and Soyer, Orkun S. (2015) Unlimited multistability and Boolean logic in microbial signalling. Journal of The Royal Society Interface, Volume 12 (Number 108). pp. 1-9. Article number 20150234. doi:10.1098/rsif.2015.0234 ISSN 1742-5689.

Calcott, Brett, Levy, Arnon, Siegal, Mark L., Soyer, Orkun S. and Wagner, Andreas (2015) Engineering and biology : counsel for a continued relationship. Biological Theory, 10 (1). pp. 50-59. doi:10.1007/s13752-014-0198-3 ISSN 1555-5542.

O’Malley, Maureen A., Soyer, Orkun S. and Siegal, Mark L. (2015) A philosophical perspective on evolutionary systems biology. Biological Theory, Volume 10 (Number 1). pp. 6-17. doi:10.1007/s13752-015-0202-6 ISSN 1555-5542.

Amin, Munia, Kothamachu, Varun B., Feliu, Elisenda, Scharf, Birgit E., Porter, Steven L. and Soyer, Orkun S. (2014) Phosphate sink containing two-component signaling systems as tunable threshold devices. PLoS Computational Biology, Volume 10 (Number 10). Article number e1003890. doi:10.1371/journal.pcbi.1003890 ISSN 1553-7358.

Hemsley, Claudia M., Luo, Jamie X., Andreae, Clio A., Butler, Clive S., Soyer, Orkun S. and Titball, Richard W. (2014) Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation but not anaerobic respiration. Antimicrobial Agents and Chemotherapy, Volume 58 (Number 10). pp. 5775-5783. doi:10.1128/AAC.02793-14 ISSN 0066-4804.

Großkopf, Tobias and Soyer, Orkun S. (2014) Synthetic microbial communities. Current Opinion in Microbiology, Volume 18 . pp. 72-77. doi:10.1016/j.mib.2014.02.002 ISSN 1369-5274.

Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca and Soyer, Orkun S. (2013) Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, Volume 9 (Number 11). Article number e1003322. doi:10.1371/journal.pcbi.1003322 ISSN 1553-7358.

Soyer, Orkun S. and Swain, Peter S. (2013) Systems and synthetic biology underpinning biotechnology. Current Opinion in Biotechnology, 24 (4). pp. 735-736. ISSN 0958-1669 doi:10.1016/j.copbio.2013.06.002

Soyer, Orkun S. and O'Malley, Maureen A. (2013) Evolutionary systems biology : what it is and why it matters. BioEssays, Volume 35 (Number 8). pp. 696-705. doi:10.1002/bies.201300029 ISSN 0265-9247.

Amin, Munia, Porter, Steven L. and Soyer, Orkun S. (2013) Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks. PLoS Computational Biology, Volume 9 (Number 3). Article no. e1002949. doi:10.1371/journal.pcbi.1002949 ISSN 1553-7358.

Kuwahara, Hiroyuki and Soyer, Orkun S. (2012) Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology, Volume 8 (Number 564). Article no. 564. doi:10.1038/msb.2011.98 ISSN 1744-4292.

Soyer, Orkun S. and Goldstein, Richard A. (2011) Evolution of response dynamics underlying bacterial chemotaxis. BMC Evolutionary Biology, 11 (1). 240. doi:10.1186/1471-2148-11-240 ISSN 1471-2148.

O’Malley, Maureen A. and Soyer, Orkun S. (2011) The roles of integration in molecular systems biology. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 43 (1). pp. 58-68. doi:10.1016/j.shpsc.2011.10.006 ISSN 1369-8486.

Csikasz-Nagy, A., Cardelli, L. and Soyer, Orkun S. (2010) Response dynamics of phosphorelays suggest their potential utility in cell signalling. Journal of The Royal Society Interface, 8 (57). pp. 480-488. doi:10.1098/rsif.2010.0336 ISSN 1742-5689.

Soyer, Orkun S. and Pfeiffer, Thomas (2010) Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Computational Biology, Volume 6 (Number 8). Article no. e1000907. doi:10.1371/journal.pcbi.1000907 ISSN 1553-7358.

Salathé, Marcel and Soyer, Orkun S. (2008) Parasites lead to evolution of robustness against gene loss in host signaling networks. Molecular Systems Biology, Volume 4 . Article no. 202. doi:10.1038/msb.2008.44 ISSN 1744-4292.

Research Projects

Title	Funder	Award start	Award end
Cofactors as emerging key regulators of global metabolism (outline Ideate record 79682)	Leverhulme Trust	06 January 2025	05 January 2028
Symbiosis in Aquatic Systems Investigator Award: Understanding interplay between microbial interactions and spatial organisation	Gordon and Betty Moore Foundation	01 April 2020	01 April 2027
Gordon and Betty Moore Foundation Supplement (Linked to Award 63619 and Outline 80742)	Gordon and Betty Moore Foundation	01 April 2024	31 March 2027
A broadly accessible and versatile spinning disc microscope to probe biological processes across temporal and spatial scales (BBSRC Alert 2025)	BBSRC	01 August 2025	31 July 2026
Understanding the origin and evolution of metabolic interactions using synthetic microbial communities. full stage	BBSRC	02 September 2019	08 April 2024
WISB extension Oct 21 - March 22	BBSRC	01 October 2021	31 March 2022
Warwick Integrative Synthetic Biology Centre (WISB) extension - related to 46082	BBSRC	01 April 2020	31 March 2022
Collaboration Agreement with Oxford - for extra funds for NPIF studentship (Alan Reed) under the SynBioCDT	EPSRC	01 October 2019	30 September 2021
BBSRC equipment MPFLIM	BBSRC	10 November 2020	09 June 2021
Electrical control of cancer merabolism	Cancer Research UK	01 January 2019	30 April 2021
Warwick Integrative Synthetic Biology Centre (WISB)	BBSRC	14 November 2014	31 May 2020
ESPRC and BBSRC Centre for Doctoral Training in Synthetic Biology	University of Oxford	01 July 2014	30 June 2019
Bioelectrochemical conversion of cellulosic biomass into methane and organic acids - BBSRC NIBB BIV costing	BBSRC	01 December 2018	31 January 2019
BBSRC IBBE (Led by Southampton)	BBSRC	01 February 2014	31 January 2019
BBSRC LoLA: Engineering Synthetic Microbial Communities for Biomethane Production	BBSRC	25 May 2013	30 November 2018
Predictive Temporal Analysis of Functional Microbiomes in UK's Anerobic Digestion Reactors	BBSRC	01 July 2016	07 March 2018
Electrical control of anaerobic digestion microbial communities	BBSRC	01 September 2017	28 February 2018
Towards engineering microbial communities to treat a defined waste stream	BBSRC	01 February 2017	31 July 2017
Via Southampton: Engineering a semmi-biotic immune system	EPSRC	25 May 2013	31 January 2016
Transfer from Exeter: Evolving controllers and controlling evolution	EPSRC	24 May 2013	23 March 2014

Teaching / Student Supervision

I am the module lead and teacher on the 3rd year module "Dynamics of biological systems - LF305", which focuses on cellular system dynamics.

I also teach on the 3rd year module "Synthetic Biology - LF306" and 1st year module "Computational Biology - LF132".

In addition, I contribute to teaching at Masters and PhD programs, and am involved in a multi-national open-book project

I offer UG, final year projects focusing on microbial communities, cellular metabolism, and cell physiology. Projects in these areas can be computational or experimental. The former would involve modelling and simulation using Python or MATLAB, or bioinformatics analyses using Python. The latter would involve microbial cultures, measurements using fluorescent microscopy and quantifying metabolites.

I am also happy to receive enquires about PG Research projects in my group, please contact me at the above email address.