Richards, Luke, Cremin, Kelsey, Coates, Mary, 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.
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 . ISSN 1742-5689. (Submitted)
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.