Research Interests
Biology is a result of evolution. This fact is at the core of research ideas pursued at OSSlab. Headed by Orkun S. Soyer, the lab is interested in understanding the structure and response dynamics of biological systems from an evolutionary perspective and using this understanding to (re)design de novo biological systems. In other words, we are after evolutionary and ecological principles that can explain the structure and dynamics of biological systems and utilising these principles in systems and synthetic biology.
Our science is mostly driven by a desire to follow novel and interesting ideas. Consequently, we work on a broad set of questions and systems. We are a dry/wet lab working both through experiments done in theoretical models and computer simulations, and in real biological systems. On the latter domain, we currently focus on microbial systems, with two key research areas being the analysis and design of signaling and metabolic networks, and understanding and engineering of microbial communities.
We are part of the University of Warwick, School of Life Sciences (SLS), Warwick Centre for Integrative Synthetic Biology (WISB), and the EPSRC/BBSRC Centre for Doctoral Training in Synthetic Biology (SynBioCDT).
Biography
- BSC Chemistry. Bogazici University, Istanbul, Turkey
- PhD University of Michigan, USA
- Quince, Christopher, Nurk, Sergey, Raguideau, Sébastien, James, Robert, Soyer, Orkun S., Summers, J. Kimberly, Limasset, Antoine, Eren, A. Murat, Chikhi, Rayan, Darling, Aaron E., 2021. STRONG : metagenomics strain resolution on assembly graphs. Genome Biology, 22 (1)
- Delattre, Hadrien, Sasidharan, Kalesh, Soyer, Orkun S., 2021. Inhibiting the reproduction of SARS-CoV-2 through perturbations in human lung cell metabolic network. Life Science Alliance, 4 (1)
- Delattre, Hadrien, Chen, Jing, Wade, Matthew J., 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)
- 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, Soyer, Orkun S., 2020. Bioelectrical understanding and engineering of cell biology. Journal of The Royal Society Interface, 17 (166)
- Cremin, Kelsey, Jones, Bryn, Teahan, James, Meloni, Gabriel N., Perry, David, Zerfass, Christian, Asally, Munehiro, Soyer, Orkun S., 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
- 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., 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
- Feng, Song, 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
- Chen, Jing, Wade, Matthew J., Dolfing, Jan, 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)
- Zerfaß, Christian, Asally, Munehiro, Soyer, Orkun S., 2019. Interrogating metabolism as an electron flow system. Current Opinion in Systems Biology, 13, pp. 59-67
- Zerfaß, Christian, Christie-Oleza, Joseph A., Soyer, Orkun S., Master, Emma R., 2019. Manganese oxide biomineralization provides protection against nitrite toxicity in a cell-density-dependent manner. Applied and Environmental Microbiology, 85 (2)
- Jiang, Xue, Zerfaß, Christian, Eichmann, Ruth, Asally, Munehiro, Schäfer, Patrick, Soyer, Orkun S., 2018. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. ISME Journal, 12, pp. 1443-1456
- Aller, Sean, Scott, Andrew, Sarkar-Tyson, Mitali, 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)
- Sierocinski, Pawel, Bayer, Florian, Yvon-Durocher, Gabriel, Burdon, Melia, Großkopf, Tobias, Alston, Mark, Swarbreck, David, Hobbs, Phil J., Soyer, Orkun S., Buckling, Angus, 2018. Biodiversity-function relationships in methanogenic communities. Molecular Ecology, 27 (22), pp. 4641-4651
- Martinez-Vernon, Andrea, Farrell, Frederick, Soyer, Orkun S., 2018. MetQy ? an R package to query metabolic functions of genes and genomes. Bioinformatics, 34 (23), pp. 4134-4137
- Zerfaß, Christian, Christie-Oleza, Joseph Alexander, Soyer, Orkun S., 2018. Manganese oxide biomineralization is a social trait protecting. Applied and Environmental Microbiology, 85 (92)
- Zerfaß, Christian, Chen, Jing, Soyer, Orkun S., 2018. Engineering microbial communities using thermodynamic principles and electrical interfaces. Current Opinion in Biotechnology, 50, pp. 121-127
- 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., 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)
- Sierocinski, Pawel, Milferstedt, Kim, Bayer, Florian, Großkopf, Tobias, Alston, Mark, Bastkowski, Sarah, Swarbreck, David, Hobbs, Phil J., Soyer, Orkun S., Hamelin, Jérôme, Buckling, Angus, 2017. A single community dominates structure and function of a mixture of multiple methanogenic communities. Current Biology, 27 (21), pp. 3390-3395.e4
- Cavaliere, Matteo, Feng, Song, Soyer, Orkun S., Jiménez, José I., 2017. Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology, 19 (8), pp. 2949-2963
- Großkopf, Tobias, Zenobi, Simone, Alston, Mark, Folkes, Leighton, Swarbreck, David, Soyer, Orkun S., 2016. A stable genetic polymorphism underpinning microbial syntrophy. The ISME Journal, 10, pp. 2844-2853
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Widder, Stefanie, Allen, Rosalind, Pfeiffer, Thomas, Curtis, Thomas P., Wiuf, Carsten, Sloan, William T., Cordero, Otto X., Brown, Sam P., Momeni, Babak, Shou, Wenying, Kettle, Helen, Flint, Harry J., Haas, Andreas F., Laroche, Beatrice, Kreft, Jan-Ulrich, Rainey, Paul B., Freilich, Shiri, Schuster, Stefan, Milferstedt, Kim, van der Meer, Jan R. et al (Select to open full list), 2016. Challenges in microbial ecology : building predictive understanding of community function and dynamics. The ISME Journal, 2016 (10), pp. 2557-2568
- Feng, Song, Sáez, Meritxell, Wiuf, Carsten, Feliu, Elisenda, Soyer, Orkun S., 2016. Core signalling motif displaying multistability through multi-state enzymes. Journal of The Royal Society Interface, 13 (123)
- Feng, Song, Ollivier, Julien F., Soyer, Orkun S., 2016. Enzyme sequestration as a tuning point in controlling response dynamics of signalling networks. PLoS Computational Biology, 12 (5)
- Cizmeci, Deniz, Dempster, Emma L., Champion, Olivia L., Wagley, Sariqa, Akman, Ozgur E., Prior, Joann L., Soyer, Orkun S., Mill, Jonathan, 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
- Großkopf, Tobias, Consuegra, Jessika, Gaffé, Joël, Willison, John C., Lenski, Richard E., Soyer, Orkun S., 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)
- Großkopf, Tobias, Soyer, Orkun S., 2016. Microbial diversity arising from thermodynamic constraints. The ISME Journal, 10, pp. 2725-2733
- Steinacher, Arno, Bates, Declan, Akman, Ozgur E., Soyer, Orkun S., 2016. Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels. PLoS One, 11 (4)
- Montefusco, Francesco, Akman, Ozgur E., Soyer, Orkun S., Bates, Declan, 2016. Ultrasensitive negative feedback control : a natural approach for the design of synthetic controllers. PLoS One, 11 (8)
- O'Malley, Maureen A., Soyer, Orkun S., Siegal, Mark L., 2015. A philosophical perspective on evolutionary systems biology. Biological Theory, 10 (1), pp. 6-17
- Feng, Song, Ollivier, Julien F., Swain, Peter S., Soyer, Orkun S., 2015. BioJazz : In silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Research, 43 (19)
- Calcott, Brett, Levy, Arnon, Siegal, Mark L., Soyer, Orkun S., Wagner, Andreas, 2015. Engineering and biology : counsel for a continued relationship. Biological Theory, 10 (1), pp. 50-59
- Kothamachu, Varun B., Feliu, Elisenda, Cardelli, Luca, Soyer, Orkun S., 2015. Unlimited multistability and Boolean logic in microbial signalling. Journal of The Royal Society Interface, 12 (108), pp. 1-9
- Großkopf, Tobias, Soyer, Orkun S., 2014. Synthetic microbial communities. Current Opinion in Microbiology, 18, pp. 72-77
- Amin, Munia, Kothamachu, Varun B., Feliu, Elisenda, Scharf, Birgit E., Porter, Steven L., Soyer, Orkun S., 2014. Phosphate sink containing two-component signaling systems as tunable threshold devices. PLoS Computational Biology, 10 (10)
- Hemsley, Claudia M., Luo, Jamie X., Andreae, Clio A., Butler, Clive S., Soyer, Orkun S., Titball, Richard W., 2014. Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation but not anaerobic respiration. Antimicrobial Agents and Chemotherapy, 58 (10), pp. 5775-5783
- Soyer, Orkun S., O'Malley, Maureen A., 2013. Evolutionary systems biology : what it is and why it matters. BioEssays, 35 (8), pp. 696-705
- Amin, Munia, Porter, Steven L., Soyer, Orkun S., 2013. Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks. PLoS Computational Biology, 9 (3)
- Kothamachu, Varun B., Feliu, Elisenda, Wiuf, Carsten, Cardelli, Luca, Soyer, Orkun S., 2013. Phosphorelays provide tunable signal processing capabilities for the cell. PLoS Computational Biology, 9 (11)
- Kuwahara, Hiroyuki, Soyer, Orkun S., 2012. Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology, 8 (564)
- Soyer, Orkun S., Goldstein, Richard A., 2011. Evolution of response dynamics underlying bacterial chemotaxis. BMC Evolutionary Biology, 11 (1)
- O'Malley, Maureen A., 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
- Soyer, Orkun S., Pfeiffer, Thomas, 2010. Evolution under fluctuating environments explains observed robustness in metabolic networks. PLoS Computational Biology, 6 (8)
- Csikasz-Nagy, A., Cardelli, L., 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
- Salathé, Marcel, Soyer, Orkun S., 2008. Parasites lead to evolution of robustness against gene loss in host signaling networks. Molecular Systems Biology, 4
- Johnson, Connah, Delattre, Hadrien, Hayes, Clarmyra, 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
- Jiang, Xue, Zerfaß, Christian, Eichmann, Ruth, Asally, Munehiro, Schäfer, P. (Patrick), Soyer, Orkun S., 2017. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. Bio, Cold Spring Harbour Laboratories
- Soyer, Orkun S., Swain, Peter S., 2013. Systems and synthetic biology underpinning biotechnology. Current Opinion in Biotechnology, Elsevier Ltd, pp. 735-736
| Title | Funder | Award start | Award end |
|---|---|---|---|
| Symbiosis in Aquatic Systems Investigator Award: Understanding interplay between microbial interactions and spatial organisation | Gordon and Betty Moore Foundation | 01 Apr 2020 | 31 Mar 2025 |
| Understanding the origin and evolution of metabolic interactions using synthetic microbial communities. full stage | BBSRC | 02 Sep 2019 | 01 Sep 2023 |
| WISB extension Oct 21 - March 22 | BBSRC | 01 Oct 2021 | 31 Mar 2022 |
| Warwick Integrative Synthetic Biology Centre (WISB) extension - related to 46082 | BBSRC | 01 Apr 2020 | 31 Mar 2022 |
| Collaboration Agreement with Oxford - for extra funds for NPIF studentship (Alan Reed) under the SynBioCDT | EPSRC | 01 Oct 2019 | 30 Sep 2021 |
| BBSRC equipment MPFLIM | BBSRC | 10 Nov 2020 | 09 Jun 2021 |
| Electrical control of cancer merabolism | Cancer Research UK | 01 Jan 2019 | 30 Apr 2021 |
| Warwick Integrative Synthetic Biology Centre (WISB) | BBSRC | 14 Nov 2014 | 31 May 2020 |
| ESPRC and BBSRC Centre for Doctoral Training in Synthetic Biology | University of Oxford | 01 Jul 2014 | 30 Jun 2019 |
| Bioelectrochemical conversion of cellulosic biomass into methane and organic acids - BBSRC NIBB BIV costing | BBSRC | 01 Dec 2018 | 31 Jan 2019 |
| BBSRC IBBE (Led by Southampton) | BBSRC | 01 Feb 2014 | 31 Jan 2019 |
| BBSRC LoLA: Engineering Synthetic Microbial Communities for Biomethane Production | BBSRC | 25 May 2013 | 30 Nov 2018 |
| Predictive Temporal Analysis of Functional Microbiomes in UK's Anerobic Digestion Reactors | BBSRC | 01 Jul 2016 | 07 Mar 2018 |
| Electrical control of anaerobic digestion microbial communities | BBSRC | 01 Sep 2017 | 28 Feb 2018 |
| Towards engineering microbial communities to treat a defined waste stream | BBSRC | 01 Feb 2017 | 31 Jul 2017 |
| Via Southampton: Engineering a semmi-biotic immune system | EPSRC | 25 May 2013 | 31 Jan 2016 |
| Transfer from Exeter: Evolving controllers and controlling evolution | EPSRC | 24 May 2013 | 23 Mar 2014 |