Publications (and most recent Preprints)
Cell Physiology |
Microbial Communities |
Theory
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Thioflavin T indicates membrane potential in mammalian cells and can affect it in a blue light dependent manner2020Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteriaCampylobacter jejuni 11168H exposed to penicillin forms persister cells and cells with altered redox protein activityHelen Morcrette, Andrea Kovacs-Simon, Richard Kenneth Tennant, John Love, Sariqa Wagley, Zheng R Yang, David J. Studholme, Orkun S Soyer, Olivia L Champion, Clive S Butler, Richard Titball Frontiers in Cellular and Infection Microbiology, (2020) 10:583 LinkLink opens in a new window Bioelectrical understanding and engineering of cell biologyZoe Schofield, Gabriel N. Meloni, Peter Tran, Christian Zerfass, Giovanni Sena, Yoshikatsu Hayashi, Murray Grant, Sonia A. Contera, Shelley D. Minteer, Minsu Kim, Arthur Prindle, Paulo Rocha, Mustafa B. A. Djamgoz,Teuta Pilizota, Patrick R. Unwin, Munehiro Asally and Orkun S. Soyer (2020) 17:20200013 LinkLink opens in a new window 2019Interrogating metabolism as an electron flow systemChristian Zerfass, Munehiro Asally, Orkun S Soyer Manganese oxide biomineralization provides protection against nitrite toxicity in a cell density dependent mannerChristian Zerfass, Joseph-Christie Oleza, Orkun S Soyer 2017An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions.Nicola J. Senior, Kalesh Sasidharan, et al, Orkun S. Soyer and Richard W. Titball 2016Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection.Deniz Cizmeci, Emma L. Dempster, Olivia L. Champion, Sariqa Wagley, Ozgur E. Akman, Joann L. Prior, Orkun S. Soyer, Jonathan Mill, and Richard W. Titball 2015A philosophical perspective on evolutionary systems biology.Maureen A. O'Malley, Orkun S. Soyer, and Mark L. Siegal. 2014Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation, but not anaerobic respiration.Claudia M. Hemsley, Jamie X. Luo, Clio A. Andreae, Clive S. Butler, Orkun S. Soyer, and Richard W. Titball Phosphate sink containing two-component signaling systems as tunable threshold devices.Munia Amin, Varun B. Kothamachu, Elisenda Feliu, Birgit E. Scharf, Steven L. Porter, and Orkun S. Soyer 2013Systems and synthetic biology underpinning biotechnology.Orkun S. Soyer and Peter Swain Evolutionary Systems Biology: What it is and why it matters.Maureen O'Malley and Orkun S Soyer Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks.Amin Munia, Steve Porter, and Orkun S. Soyer 2012Evolutionary principles underlying structure and response dynamics of cellular networks.Arno Steinacher and Orkun Soyer In Soyer O.S. (ed.). Evolutionary Systems Biology: Adv. in Exp. Medicine and Biology. Springer, (2012) The roles of integration in molecular systems biology.Maureen A. O'Malley and Orkun S. Soyer 2010The promise of evolutionary systems biology: Lessons from bacterial chemotaxis.Orkun S. Soyer |
Reproducible spatial structure formation and stable community composition in the cyanosphere predicts metabolic interactionsNovel microbial syntrophies identified by longitudinal metagenomics2023Formation and emergent dynamics of spatially organized microbial systemsKelsey Cremin, Sarah J. N. Duxbury, Jerko Rosko and Orkun S Soyer Interface Focus (2023) 13:20220062 LinkLink opens in a new window 2021STRONG: metagenomics strain resolution on assembly graphsQuince, C., Nurk, S., Raguideau, S., James R., Soyer OS., Summers JK., Limasset A., Eren AM., Chikhi R & Darling A. Genome Biol 22, 214 (2021) 2020Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis
2019Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulphate reducerJing Chen, Matthew J Wade, Jan Dolfing, Orkun S Soyer 2018Biodiversity function relationships in methanogenic communitiesPawel Sierocinski, Florian Bayer, Gabriel Yvon Durocher, Melia Burdon, Tobias Großkopf, Mark Alston, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Angus Buckling MetQy an R package to query metabolic functions of genes and genomesAndrea Martinez-Vernon, Frederick Farrell, Orkun S Soyer Impact of spatial organization on a novel auxotrophic interaction among soil microbesXue Jiang, Christian Zerfass, Song Feng, Ruth Eichmann, Munehiro Asally, Patrick Schaefer, Orkun S Soyer 2017Engineering microbial communities using thermodynamic principles and electrical interfaces.Christian Zerfass, Jing Chen, Orkun S Soyer, A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities.Pawel Sierocinski, Kim Milferstedt, Florian Bayer, Tobias Großkopf, Mark Alston, Sarah Bastkowski, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Jerome Hamelin, Angus Buckling Cooperation in microbial communities and their biotechnological applications.Matteo Cavaliere, Song Feng, Orkun S. Soyer, Jose I. Jimenez 2016A stable genetic polymorphism underpinning microbial syntrophy.Tobias Großkopf, Simone Zenobi, Mark Alston, Leighton Folkes, David Swarbreck, and Orkun S Soyer Microbial diversity arising from thermodynamic constraints.Tobias Großkopf and Orkun S. Soyer Metabolic modelling in an evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.Tobias Grosskopf, Jessika Consuegra, Joel Gaffe, John C. Willison, Richard E. Lenski, Orkun S. Soyer, and Dominique Schneider Challenges in microbial ecology: building predictive understanding of community function and dynamics.Stefanie Widder, Rosalind Allen, et al, and Orkun S. Soyer 2014Synthetic microbial communities.Tobias Grosskopf and Orkun S. Soyer |
2023Dynamics of co-substrate pools can constrain and regulate metabolic fluxes2022ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks
our GithubLink opens in a new windowLink opens in a new window page or ZenodoLink opens in a new windowLink opens in a new window Multi-site enzymes as a mechanism for bistability in reaction networks2021An evolutionary systems biology view on metabolic system structure and dynamicsJohnson C, Delattre H, Hayes C and Soyer, OS (2021). In: Crombach, Anton, (ed.) Evolutionary Systems Biology : Advances, Questions, and Opportunities. Springer Cham. Chapter LinkLink opens in a new window 2020Inhibiting the reproduction of COVID-19-causing SARS-CoV-2 through perturbations in human cell metabolic networkHadrien Delattre, Kalesh Sasidharan, Orkun Soyer
2019In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response DynamicsSong Feng, Orkun S Soyer In: Hlavacek W. S. (ed.) Methods in Molecular Biology: Modeling Biomolecular Site Dynamics. Springer (2019). Series InfoLink opens in a new window 2018Integrated Human-Virus Metabolic Stoichiometric Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika VirusesSean Aller, Andrew E Scott, Mitali Sarkar-Tyson, Orkun S Soyer 2016Core signalling motif displaying multistability through multi-state enzymes.Song Feng, Meritxell Sez, Carsten Wiuf, Elisenda Feliu, and Orkun S. Soyer Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling NetworksSong Feng, Julien F. Ollivier, and Orkun S. Soyer Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers.Francesco Montefusco, Ozgur E. Akman, Orkun S. Soyer, and Declan Bates Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levelsArno Steinacher, Declan G. Bates, Ozgur E. Akman, and Orkun S. Soyer 2015BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modelingSong Feng, Julien Ollivier, Peter S. Swain, and Orkun S. Soyer Unlimited multistability and Boolean logic in microbial signalingVarun B. Kothamachu, Elisenda Feliu, Luca Cardelli, and Orkun S. Soyer Engineering and biology: Counsel for a continued relationshipBrett Calcott, Arnon Levy, Mark L. Siegal, Orkun S. Soyer, and Andreas Wagner. 2013Metabolic Tinker: An online tool for guiding the design of synthetic metabolic pathways.Kent McClymont and Orkun S. Soyer Phosphorelays provide tunable signal processing capabilities for the cell.Varun B. Kothamachu, Elisenda Feliu, Carsten Wuif, Luca Cardelli, and Orkun S. Soyer 2012Bistability in feedback circuits as a byproduct of evolution of evolvability.Hiroaki Kuwahara and Orkun S Soyer 2011Evolution of response dynamics underlying bacterial chemotaxis.Orkun S. Soyer and Richard A. Goldstein 2010Response dynamics of phosphorelays suggest their potential utility in cell signaling.Attila Csiksz-Nagy, Luca Cardelli, and Orkun S. Soyer Evolution under fluctuating environments explains observed robustness in metabolic networks.Orkun S. Soyer and Thomas Pfeiffer Fate of a duplicate gene in a network context.Orkun S. Soyer 2009Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses.Orkun S. Soyer, Hiroaki Kuwahara, and Attila Csiksz-Nagy 2008Evolution of taxis responses in bacteria: nonadaptive dynamics.Richard A. Goldstein and Orkun S. Soyer Parasites lead to evolution of robustness against gene loss in host signaling networks.Marcel Salathe and Orkun S. Soyer Adaptive dynamics with a single two state protein.Attila Csiksz-Nagy and Orkun S. Soyer Evolving BlenX programs to simulate the evolution of biological networks.Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer 2007Emergence and maintenance of functional modules in signaling pathways.Orkun S Soyer A formal and integrated framework to simulate evolution of biological pathways.Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer 2006Evolution of complexity in signaling pathways.Orkun S. Soyer and Sebastian Bonhoeffer Simulating the evolution of signal transduction pathways.Orkun S Soyer, Thomas Pfeiffer, and Sebastian Bonhoeffer Signal transduction networks: topology, response, and biochemical reactions.Orkun S. Soyer Marcel Salathe, and Sebastian Bonhoeffer 2005Evolution of connectivity in metabolic networks.Thomas Pfeiffer, Orkun S. Soyer, and Sebastian Bonhoeffer 2004Predicting functional sites in proteins: Site specific evolutionary models and their application to neurotransmitter transporters.Orkun S. Soyer and Richard A. Goldstein 2003Probing conformational changes in neurotransmitter transporters in a structural context.Naomi R. Goldberg, Thijs Beuming, Orkun S. Soyer, Richard A. Goldstein, Harel Weinstein, and Jonathan A. Javitch Dimerization in aminergic G-protein coupled receptors: Application of a hidden site-class model of protein evolution.Orkun S. Soyer, Matt W. Dimmic, Richard R. Neubig, and Richard A. Goldstein Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMsBin Qian, Orkun S. Soyer, Richard R. Neubig, and Richard A. Goldstein 2002NMR Structure of the second intracellular loop of the alpha2a adrenergic receptor: Evidence for a novel cytoplasmic helix.Duane A. Chung, Erik R. P. Zuiderweg, Carol B. Fowler, Orkun S. Soyer, Henry I. Mosberg, and Richard R. Neubig Using evolutionary methods to study G-protein coupled receptors.Orkun S. Soyer, Matt W. Dimmic, Richard R. Neubig, and Richard A. Golstein |
