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Journals


  • 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, View
  • 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), View
  • Zerfaß, Christian, Asally, Munehiro, Soyer, Orkun S.. 2019. Interrogating metabolism as an electron flow system. Current Opinion in Systems Biology, 13, pp. 59-67, View
  • 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, View
  • 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, View
  • 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), View
  • 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, View
  • 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, View
  • Zerfaß, Christian, Christie-Oleza, Joseph Alexander, Soyer, Orkun S.. 2018. Manganese oxide biomineralization is a social trait protecting. Applied and Environmental Microbiology, 85 (92), View
  • Zerfaß, Christian, Asally, Munehiro, Soyer, Orkun S.. 2018. Interrogating metabolism as an electron flow system. Current Opinion in Systems Biology, 13, pp. 59-67, View
  • 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), View
  • 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, View
  • 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, View
  • 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), View
  • 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), View
  • 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, View
  • 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), View
  • Großkopf, Tobias, Soyer, Orkun S.. 2016. Microbial diversity arising from thermodynamic constraints. The ISME Journal, 10, pp. 2725-2733, View
  • 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, View
  • 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., Großkopf, Tobias, Huisman, Jef, Free, Andrew, Picioreanu, Cristian, Quince, Christopher, Klapper, Isaac, Labarthe, Simon, Smets, Barth F., Wang, Harris, Soyer, Orkun S., Allison, Steven D., Chong, James, Cosentino-Lagomarsino, Marco, Croze, Ottavio A., Hamelin, Jérôme, Harmand, Jérôme, Hoyle, Rebecca, Hwa, Terence T., Jin, Qusheng, Johnson, David R., de Lorenzo, Và­ctor, Mobilia, Mauro, Murphy, Barry, Peaudecerf, François, Prosser, James I., Quinn, Robert A., Ralser, Markus, Smith, Alison G., Steyer, Jean-Philippe, Swainston, Neil, Tarnita, Corina E., Trably, Eric, Warren, Patrick B., Wilmes, Paul. 2016. Challenges in microbial ecology : building predictive understanding of community function and dynamics. The ISME Journal, 2016 (10), pp. 2557-2568, View
  • 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), View
  • 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), View
  • 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, Volume 12 (Number 108), pp. 1-9, View
  • O'Malley, Maureen A., Soyer, Orkun S., Siegal, Mark L.. 2015. A philosophical perspective on evolutionary systems biology. Biological Theory, Volume 10 (Number 1), pp. 6-17, View
  • 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, View
  • 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), View
  • 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, Volume 58 (Number 10), pp. 5775-5783, View
  • 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, Volume 10 (Number 10), View
  • Großkopf, Tobias, Soyer, Orkun S.. 2014. Synthetic microbial communities. Current Opinion in Microbiology, Volume 18, pp. 72-77, View
  • Amin, Munia, Porter, Steven L., Soyer, Orkun S.. 2013. Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks. PLoS Computational Biology, Volume 9 (Number 3), View


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