Publications (and most recent Preprints)

Cell Physiology	Microbial Communities	Theory
2024 Emergence of synchronized growth oscillations in filamentous fungi Prakash Praneet, Jiang Xue, Richards Luke, Schofield Zoe, Schäfer Patrick, Polin Marco, Soyer Orkun S. and Asally Munehiro 2024 J. R. Soc. Interface 21:20240574 \| LinkLink opens in a new window Cellular coordination underpins rapid reversals in gliding filamentous cyanobacteria and its loss results in plectonemes Jerko Rosko, Kelsey Cremin, Emanuele Locatelli, Mary Coates, Sarah JN Duxbury, Kieran Randall, Katie Croft, Chantal Valeriani, Marco Polin, Orkun S Soyer eLife 13:RP100768 \| LinkLink opens in a new window 2023 Thioflavin T indicates membrane potential in mammalian cells Emily Skates, Hadrien Delattre, Zoe Schofield, Munehiro Asally, Orkun S. Soyer Biophysical Reports (2023), 3(4):100134 \| LinkLink opens in a new window Can Single Cell Respiration be Measured by Scanning Electrochemical Microscopy (SECM)? Kelsey Cremin, Gabriel N. Meloni, Dimitrios Valavanis, Orkun S. Soyer, and Patrick R. Unwin ACS Meas. Sci. Au (2023), 3, 5, 361–370 \| LinkLink opens in a new window 2020 Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteria Kelsey Cremin, Bryn Jones, James Teahan, Gabriel N. Meloni, David Perry, Christian Zerfass, Munehiro Asally, Orkun S. Soyer, Patrick R. Unwin Analytical Chemistry (2020) \| LinkLink opens in a new window \| Featured in Bioelectricity BuzzLink opens in a new window Campylobacter jejuni 11168H exposed to penicillin forms persister cells and cells with altered redox protein activity Helen 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 biology Zoe 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 Journal of the Royal Society Interface (2020) 17:20200013 \| LinkLink opens in a new window 2019 Interrogating metabolism as an electron flow system Christian Zerfass, Munehiro Asally, Orkun S Soyer Current Opinion in Systems Biology 13: 59-67 (2019). LinkLink opens in a new window Manganese oxide biomineralization provides protection against nitrite toxicity in a cell density dependent manner Christian Zerfass, Joseph-Christie Oleza, Orkun S Soyer Applied and Environmental Microbiology 85(2). pii: e02129-18 (2019). LinkLink opens in a new window 2017 An 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 BMC Microbiology 17:163 (2017). LinkLink opens in a new window 2016 Mapping 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 Scientific Reports 6:30861 (2016). LinkLink opens in a new window 2015 A philosophical perspective on evolutionary systems biology. Maureen A. O'Malley, Orkun S. Soyer, and Mark L. Siegal. Biological Theory 10(1):6-17 (2015). LinkLink opens in a new window 2014 Bacterial 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 Antimicrobial Agents and Chemotherapy 58(10):5775-83 (2014). LinkLink opens in a new window 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 PLoS Computational Biology 10(10):e1003890 (2014). LinkLink opens in a new window 2013 Systems and synthetic biology underpinning biotechnology. Orkun S. Soyer and Peter Swain Current Opinion Biotechnology 24(4):735-6 (2013). LinkLink opens in a new window Evolutionary Systems Biology: What it is and why it matters. Maureen O'Malley and Orkun S Soyer BioEssays 35(8):696-705 (2013). LinkLink opens in a new window Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks. Amin Munia, Steve Porter, and Orkun S. Soyer PLoS Computational Biology 9(3): e1002949 (2013). LinkLink opens in a new window \| 2012 Evolutionary principles underlying structure and response dynamics of cellular networks. Arno Steinacher and Orkun Soyer Advances in Experimental Medicine and Biology 751 (2012). LinkLink opens in a new window In Soyer O.S. (ed.). Evolutionary Systems Biology: Adv. in Exp. Medicine and Biology. Springer, (2012) Book InfoLink opens in a new window The roles of integration in molecular systems biology. Maureen A. O'Malley and Orkun S. Soyer Studies in History and Philosophy of Biological and Biomedical Sciences 43:1 (2012). LinkLink opens in a new window \| In "top download list" at ScienceDirect subject website. 2010 The promise of evolutionary systems biology: Lessons from bacterial chemotaxis. Orkun S. Soyer Science Signaling 3:128, pe23 (2010). Link	Reproducible spatial structure formation and stable community composition in the cyanosphere predicts metabolic interactions Sarah J. N. Duxbury, Sebastien Raguideau, Jerko Rosko, Kelsey Cremin, Mary Coates, Christopher Quince, Orkun S Soyer Posted December 13, 2022 \| bioRxiv linkLink opens in a new window 2024 Ammonia leakage can underpin nitrogen-sharing among soil microorganisms Luke Richards, Kelsey Cremin, Mary Coates, Finley Vigor, Patrick Schaefer, Orkun S Soyer. Accepted for publication Sep 2024 The ISME Journal, wrae171\| LinkLink opens in a new window 2023 Formation and emergent dynamics of spatially organized microbial systems Kelsey Cremin, Sarah J. N. Duxbury, Jerko Rosko and Orkun S Soyer Interface Focus (2023) 13:20220062 \| LinkLink opens in a new window 2021 STRONG: metagenomics strain resolution on assembly graphs Quince, C., Nurk, S., Raguideau, S., James R., Soyer OS., Summers JK., Limasset A., Eren AM., Chikhi R & Darling A. Genome Biol 22, 214 (2021) \| LinkLink opens in a new window 2020 Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis Hadrien Delattre, Jing Chen, Matthew Wade, Orkun S Soyer Journal of the Royal Society Interface (2020) 17:20200053. LinkLink opens in a new window \| GitHub - MicodymoraLink opens in a new window 2019 Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulphate reducer Jing Chen, Matthew J Wade, Jan Dolfing, Orkun S Soyer Journal of the Royal Society Interface 16: 20190129 (2019) LinkLink opens in a new window 2018 Biodiversity function relationships in methanogenic communities Pawel Sierocinski, Florian Bayer, Gabriel Yvon Durocher, Melia Burdon, Tobias Großkopf, Mark Alston, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Angus Buckling Molecular Ecology 27(22):4641-4651 (2018). LinkLink opens in a new window MetQy an R package to query metabolic functions of genes and genomes Andrea Martinez-Vernon, Frederick Farrell, Orkun S Soyer Bioinformatics 34(23):4134-4137 (2018). LinkLink opens in a new window \| GitHub - MetQyLink opens in a new window Impact of spatial organization on a novel auxotrophic interaction among soil microbes Xue Jiang, Christian Zerfass, Song Feng, Ruth Eichmann, Munehiro Asally, Patrick Schaefer, Orkun S Soyer The ISME Journal 12(6):1443-1456 (2018). LinkLink opens in a new window \| 2017 Engineering microbial communities using thermodynamic principles and electrical interfaces. Christian Zerfass, Jing Chen, Orkun S Soyer, Current Opinion in Biotechnology 50:121-127 (2017). LinkLink opens in a new window 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 Current Biology 27(21):3390-3395 (2017). LinkLink opens in a new window \| CommentaryLink opens in a new window Cooperation in microbial communities and their biotechnological applications. Matteo Cavaliere, Song Feng, Orkun S. Soyer, Jose I. Jimenez Environmental Microbiology 19:8 (2017). LinkLink opens in a new window 2016 A stable genetic polymorphism underpinning microbial syntrophy. Tobias Großkopf, Simone Zenobi, Mark Alston, Leighton Folkes, David Swarbreck, and Orkun S Soyer The ISME Journal 10:12 (2016). LinkLink opens in a new window \| Sequence DataLink opens in a new window \| Microbial diversity arising from thermodynamic constraints. Tobias Großkopf and Orkun S. Soyer The ISME Journal 10:11 (2016). LinkLink opens in a new window \| Resource 10Link opens in a new window 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 BMC Evolutionary Biology 16(1):163 (2016). LinkLink opens in a new window \| Resource 12 (evoFBA)Link opens in a new window Challenges in microbial ecology: building predictive understanding of community function and dynamics. Stefanie Widder, Rosalind Allen, et al, and Orkun S. Soyer The ISME Journal 10:11 (2016). LinkLink opens in a new window \| In "top download list" at ISME website. 2014 Synthetic microbial communities. Tobias Grosskopf and Orkun S. Soyer Current Opinion in Microbiology 18:72-77 (2014). LinkLink opens in a new window \| In "top download list" at Current Opinion in Microbiology website.	2023 Dynamics of co-substrate pools can constrain and regulate metabolic fluxes Robert West, Hadrien Delattre, Elad Noor, Elisenda Feliu and Orkun S Soyer eLife 12:e84379 \| LinkLink opens in a new window 2022 ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks Connah G. M. Johnson, Alexander G. Fletcher, Orkun S. Soyer GigaScience (2022), Volume 11: giac051 \| LinkLink opens in a new window \| code available via 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 networks Clarmyra Hayes, Elisenda Feliu, Orkun S Soyer ACS Synth. Biol. 2022 , 11 , 2 , 596–607 \| LinkLink opens in a new window 2021 An evolutionary systems biology view on metabolic system structure and dynamics Johnson 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 2020 Inhibiting the reproduction of COVID-19-causing SARS-CoV-2 through perturbations in human cell metabolic network Hadrien Delattre, Kalesh Sasidharan, Orkun Soyer Life Science Alliance Nov 2020, 4 (1) e202000869 \| LinkLink opens in a new window \| SBML model \| GitHub - FBAhv 2019 In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics Song Feng, Orkun S Soyer Methods in Molecular Biology 1945:315-339 (2019). LinkLink opens in a new window In: Hlavacek W. S. (ed.) Methods in Molecular Biology: Modeling Biomolecular Site Dynamics. Springer (2019). Series InfoLink opens in a new window 2018 Integrated Human-Virus Metabolic Stoichiometric Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses Sean Aller, Andrew E Scott, Mitali Sarkar-Tyson, Orkun S Soyer Royal Society Interface 12;15:146 (2018). LinkLink opens in a new window \| Resource 13 (ViraNet)Link opens in a new window 2016 Core signalling motif displaying multistability through multi-state enzymes. Song Feng, Meritxell Sez, Carsten Wiuf, Elisenda Feliu, and Orkun S. Soyer Royal Society Interface 13:123 (2016). LinkLink opens in a new window Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks Song Feng, Julien F. Ollivier, and Orkun S. Soyer PLoS Computational Biology 12(5):e1004918 (2016). LinkLink opens in a new window \| Resource 11Link opens in a new window Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers. Francesco Montefusco, Ozgur E. Akman, Orkun S. Soyer, and Declan Bates PLoS One 18;11(8):e0161605 (2016). LinkLink opens in a new window Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels Arno Steinacher, Declan G. Bates, Ozgur E. Akman, and Orkun S. Soyer PLoS One 11(4):e0153295 (2016). LinkLink opens in a new window 2015 BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling Song Feng, Julien Ollivier, Peter S. Swain, and Orkun S. Soyer Nucleic Acid Research 43(19):e123 (2015). LinkLink opens in a new window \| GitHub - BioJazzLink opens in a new window Unlimited multistability and Boolean logic in microbial signaling Varun B. Kothamachu, Elisenda Feliu, Luca Cardelli, and Orkun S. Soyer Royal Society Interface 12:108 (2015). LinkLink opens in a new window Engineering and biology: Counsel for a continued relationship Brett Calcott, Arnon Levy, Mark L. Siegal, Orkun S. Soyer, and Andreas Wagner. Biological Theory 10(1):50-59 (2015) LinkLink opens in a new window 2013 Metabolic Tinker: An online tool for guiding the design of synthetic metabolic pathways. Kent McClymont and Orkun S. Soyer Nucleic Acid Research 41(11):e113 (2013). LinkLink opens in a new window \| Resource 8Link opens in a new window Phosphorelays provide tunable signal processing capabilities for the cell. Varun B. Kothamachu, Elisenda Feliu, Carsten Wuif, Luca Cardelli, and Orkun S. Soyer PLoS Computational Biology 9(11):e1003322 (2013). LinkLink opens in a new window 2012 Bistability in feedback circuits as a byproduct of evolution of evolvability. Hiroaki Kuwahara and Orkun S Soyer Molecular Systems Biology 8:564 (2012). LinkLink opens in a new window \| Resource 7Link opens in a new window \| In "top download list" at Nature MSB website. 2011 Evolution of response dynamics underlying bacterial chemotaxis. Orkun S. Soyer and Richard A. Goldstein BMC Evolutionary Biology 11:240 (2011). LinkLink opens in a new window 2010 Response dynamics of phosphorelays suggest their potential utility in cell signaling. Attila Csiksz-Nagy, Luca Cardelli, and Orkun S. Soyer Journal of Royal Society Interface 8:57 (2010). Link \| Resource 5Link opens in a new window Evolution under fluctuating environments explains observed robustness in metabolic networks. Orkun S. Soyer and Thomas Pfeiffer PLoS Computational Biology 6(8): e1000907 (2010). LinkLink opens in a new window Fate of a duplicate gene in a network context. Orkun S. Soyer Invited chapter in "Evolution After Gene Duplication", Dittmar K., Liberles D.A. (eds.) Wiley and Sons, ISBN: 978-0-470-59382-0, October 2010. Book DescriptionLink opens in a new window 2009 Regulating 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 FEBS Journal, 276:12 (2009). LinkLink opens in a new window 2008 Evolution of taxis responses in bacteria: nonadaptive dynamics. Richard A. Goldstein and Orkun S. Soyer PLoS Computational Biology, 4:5, e1000084 (2008). LinkLink opens in a new window \| Resource 3, 4Link opens in a new window Parasites lead to evolution of robustness against gene loss in host signaling networks. Marcel Salathe and Orkun S. Soyer Molecular Systems Biology, 4:202 (2008). LinkLink opens in a new window \| Resource 2Link opens in a new window \| Featured in NatureLink opens in a new window \| Top ten download at Nature MSB website. Adaptive dynamics with a single two state protein. Attila Csiksz-Nagy and Orkun S. Soyer Royal Society Interface, 5:Suppl 1, S41-7 (2008). LinkLink opens in a new window Evolving BlenX programs to simulate the evolution of biological networks. Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer Theoretical Computer Science, 408:1 (2008). LinkLink opens in a new window 2007 Emergence and maintenance of functional modules in signaling pathways. Orkun S Soyer BMC Evolutionary Biology, 7:205 (2007). LinkLink opens in a new window A formal and integrated framework to simulate evolution of biological pathways. Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer Proceedings of the Fifth International Conference on Computational Methods in Systems Biology (CMSB) 106-120 (2007). LinkLink opens in a new window 2006 Evolution of complexity in signaling pathways. Orkun S. Soyer and Sebastian Bonhoeffer Proc. Natl. Acad. Sci. USA (PNAS), 103:44 (2006). LinkLink opens in a new window Simulating the evolution of signal transduction pathways. Orkun S Soyer, Thomas Pfeiffer, and Sebastian Bonhoeffer Journal of Theoretical Biology, 241:2 (2006). LinkLink opens in a new window Signal transduction networks: topology, response, and biochemical reactions. Orkun S. Soyer Marcel Salathe, and Sebastian Bonhoeffer Journal of Theoretical Biology, 238:2 (2006). LinkLink opens in a new window \| Resource 1Link opens in a new window 2005 Evolution of connectivity in metabolic networks. Thomas Pfeiffer, Orkun S. Soyer, and Sebastian Bonhoeffer PLoS Biology, 3:7 (2005). LinkLink opens in a new window \| Featured in Journal of Cell BiologyLink opens in a new window 2004 Predicting functional sites in proteins: Site specific evolutionary models and their application to neurotransmitter transporters. Orkun S. Soyer and Richard A. Goldstein Journal of Molecular Biology, 339:1 (2004). LinkLink opens in a new window 2003 Probing 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 European Journal of Pharmacology, 479:1-3 (2003). LinkLink opens in a new window 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 Biochemistry, 42:49 (2003). LinkLink opens in a new window Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs Bin Qian, Orkun S. Soyer, Richard R. Neubig, and Richard A. Goldstein FEBS Letters, 554:1-2 (2003). LinkLink opens in a new window 2002 NMR 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 Biochemistry, 41:11 (2002). LinkLink opens in a new window Using evolutionary methods to study G-protein coupled receptors. Orkun S. Soyer, Matt W. Dimmic, Richard R. Neubig, and Richard A. Golstein Pacific Symposium on Biocomputing (PSB) 625-36 (2002). LinkLink opens in a new window

Cell Physiology

Microbial Communities

Theory

2024

Emergence of synchronized growth oscillations in filamentous fungi

Prakash Praneet, Jiang Xue, Richards Luke, Schofield Zoe, Schäfer Patrick, Polin Marco, Soyer Orkun S. and Asally Munehiro 2024

J. R. Soc. Interface 21:20240574 | LinkLink opens in a new window

Cellular coordination underpins rapid reversals in gliding filamentous cyanobacteria and its loss results in plectonemes

Jerko Rosko, Kelsey Cremin, Emanuele Locatelli, Mary Coates, Sarah JN Duxbury, Kieran Randall, Katie Croft, Chantal Valeriani, Marco Polin, Orkun S Soyer

eLife 13:RP100768 | LinkLink opens in a new window

2023

Thioflavin T indicates membrane potential in mammalian cells

Emily Skates, Hadrien Delattre, Zoe Schofield, Munehiro Asally, Orkun S. Soyer
Biophysical Reports (2023), 3(4):100134 | LinkLink opens in a new window

Can Single Cell Respiration be Measured by Scanning Electrochemical Microscopy (SECM)?

Kelsey Cremin, Gabriel N. Meloni, Dimitrios Valavanis, Orkun S. Soyer, and Patrick R. Unwin

ACS Meas. Sci. Au (2023), 3, 5, 361–370 | LinkLink opens in a new window

2020

Scanning ion conductance microscopy reveals differences in the ionic environments of gram positive and negative bacteria

Kelsey Cremin, Bryn Jones, James Teahan, Gabriel N. Meloni, David Perry, Christian Zerfass, Munehiro Asally, Orkun S. Soyer, Patrick R. Unwin
Analytical Chemistry (2020) | Link | Featured in Bioelectricity Buzz

Campylobacter jejuni 11168H exposed to penicillin forms persister cells and cells with altered redox protein activity

Helen 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 biology

Zoe 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
Journal of the Royal Society Interface (2020) 17:20200013 | LinkLink opens in a new window

2019

Interrogating metabolism as an electron flow system

Christian Zerfass, Munehiro Asally, Orkun S Soyer
Current Opinion in Systems Biology 13: 59-67 (2019). LinkLink opens in a new window

Manganese oxide biomineralization provides protection against nitrite toxicity in a cell density dependent manner

Christian Zerfass, Joseph-Christie Oleza, Orkun S Soyer
Applied and Environmental Microbiology 85(2). pii: e02129-18 (2019). LinkLink opens in a new window

2017

An 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
BMC Microbiology 17:163 (2017). LinkLink opens in a new window

2016

Mapping 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
Scientific Reports 6:30861 (2016). LinkLink opens in a new window

2015

A philosophical perspective on evolutionary systems biology.

Maureen A. O'Malley, Orkun S. Soyer, and Mark L. Siegal.
Biological Theory 10(1):6-17 (2015). LinkLink opens in a new window

2014

Bacterial 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
Antimicrobial Agents and Chemotherapy 58(10):5775-83 (2014). LinkLink opens in a new window

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
PLoS Computational Biology 10(10):e1003890 (2014). LinkLink opens in a new window

2013

Systems and synthetic biology underpinning biotechnology.

Orkun S. Soyer and Peter Swain
Current Opinion Biotechnology 24(4):735-6 (2013). LinkLink opens in a new window

Evolutionary Systems Biology: What it is and why it matters.

Maureen O'Malley and Orkun S Soyer
BioEssays 35(8):696-705 (2013). LinkLink opens in a new window

Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks.

Amin Munia, Steve Porter, and Orkun S. Soyer
PLoS Computational Biology 9(3): e1002949 (2013). LinkLink opens in a new window |

2012

Evolutionary principles underlying structure and response dynamics of cellular networks.

Arno Steinacher and Orkun Soyer
Advances in Experimental Medicine and Biology 751 (2012). LinkLink opens in a new window

In Soyer O.S. (ed.). Evolutionary Systems Biology: Adv. in Exp. Medicine and Biology. Springer, (2012)
Book InfoLink opens in a new window

The roles of integration in molecular systems biology.

Maureen A. O'Malley and Orkun S. Soyer
Studies in History and Philosophy of Biological and Biomedical Sciences 43:1 (2012). LinkLink opens in a new window | In "top download list" at ScienceDirect subject website.

2010

The promise of evolutionary systems biology: Lessons from bacterial chemotaxis.

Orkun S. Soyer
Science Signaling 3:128, pe23 (2010). Link

Reproducible spatial structure formation and stable community composition in the cyanosphere predicts metabolic interactions

Sarah J. N. Duxbury, Sebastien Raguideau, Jerko Rosko, Kelsey Cremin, Mary Coates, Christopher Quince, Orkun S Soyer
Posted December 13, 2022 | bioRxiv linkLink opens in a new window

2024

Ammonia leakage can underpin nitrogen-sharing among soil microorganisms

Luke Richards, Kelsey Cremin, Mary Coates, Finley Vigor, Patrick Schaefer, Orkun S Soyer.

Accepted for publication Sep 2024 The ISME Journal, wrae171| LinkLink opens in a new window

2023

Formation and emergent dynamics of spatially organized microbial systems

Kelsey Cremin, Sarah J. N. Duxbury, Jerko Rosko and Orkun S Soyer
Interface Focus (2023) 13:20220062 | LinkLink opens in a new window

2021

STRONG: metagenomics strain resolution on assembly graphs

Quince, C., Nurk, S., Raguideau, S., James R., Soyer OS., Summers JK., Limasset A., Eren AM., Chikhi R & Darling A.
Genome Biol 22, 214 (2021) | LinkLink opens in a new window

2020

Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis

Hadrien Delattre, Jing Chen, Matthew Wade, Orkun S Soyer
Journal of the Royal Society Interface (2020) 17:20200053. LinkLink opens in a new window | GitHub - MicodymoraLink opens in a new window

2019

Increasing sulfate levels show a differential impact on synthetic communities comprising different methanogens and a sulphate reducer

Jing Chen, Matthew J Wade, Jan Dolfing, Orkun S Soyer
Journal of the Royal Society Interface 16: 20190129 (2019) LinkLink opens in a new window

2018

Biodiversity function relationships in methanogenic communities

Pawel Sierocinski, Florian Bayer, Gabriel Yvon Durocher, Melia Burdon, Tobias Großkopf, Mark Alston, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Angus Buckling
Molecular Ecology 27(22):4641-4651 (2018). LinkLink opens in a new window

MetQy an R package to query metabolic functions of genes and genomes

Andrea Martinez-Vernon, Frederick Farrell, Orkun S Soyer
Bioinformatics 34(23):4134-4137 (2018). LinkLink opens in a new window | GitHub - MetQyLink opens in a new window

Impact of spatial organization on a novel auxotrophic interaction among soil microbes

Xue Jiang, Christian Zerfass, Song Feng, Ruth Eichmann, Munehiro Asally, Patrick Schaefer, Orkun S Soyer
The ISME Journal 12(6):1443-1456 (2018). LinkLink opens in a new window |

2017

Engineering microbial communities using thermodynamic principles and electrical interfaces.

Christian Zerfass, Jing Chen, Orkun S Soyer,
Current Opinion in Biotechnology 50:121-127 (2017). LinkLink opens in a new window

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
Current Biology 27(21):3390-3395 (2017). LinkLink opens in a new window | CommentaryLink opens in a new window

Cooperation in microbial communities and their biotechnological applications.

Matteo Cavaliere, Song Feng, Orkun S. Soyer, Jose I. Jimenez
Environmental Microbiology 19:8 (2017). LinkLink opens in a new window

2016

A stable genetic polymorphism underpinning microbial syntrophy.

Tobias Großkopf, Simone Zenobi, Mark Alston, Leighton Folkes, David Swarbreck, and Orkun S Soyer
The ISME Journal 10:12 (2016). LinkLink opens in a new window | Sequence DataLink opens in a new window |

Microbial diversity arising from thermodynamic constraints.

Tobias Großkopf and Orkun S. Soyer
The ISME Journal 10:11 (2016). LinkLink opens in a new window | Resource 10Link opens in a new window

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
BMC Evolutionary Biology 16(1):163 (2016). LinkLink opens in a new window | Resource 12 (evoFBA)Link opens in a new window

Challenges in microbial ecology: building predictive understanding of community function and dynamics.

Stefanie Widder, Rosalind Allen, et al, and Orkun S. Soyer
The ISME Journal 10:11 (2016). LinkLink opens in a new window | In "top download list" at ISME website.

2014

Synthetic microbial communities.

Tobias Grosskopf and Orkun S. Soyer
Current Opinion in Microbiology 18:72-77 (2014). LinkLink opens in a new window | In "top download list" at Current Opinion in Microbiology website.

2023

Dynamics of co-substrate pools can constrain and regulate metabolic fluxes

, , , and

2022

ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks

Connah G. M. Johnson, Alexander G. Fletcher, Orkun S. Soyer
GigaScience (2022), Volume 11: giac051 | LinkLink opens in a new window | code available via 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 networks

, , ACS Synth. Biol. 2022 , 11 , 2 , 596–607 | Link

2021

An evolutionary systems biology view on metabolic system structure and dynamics

Johnson 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

2020

Inhibiting the reproduction of COVID-19-causing SARS-CoV-2 through perturbations in human cell metabolic network

Hadrien Delattre, Kalesh Sasidharan, Orkun Soyer
Life Science Alliance Nov 2020, 4 (1) e202000869 | LinkLink opens in a new window | SBML model | GitHub - FBAhv

2019

In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics

Song Feng, Orkun S Soyer
Methods in Molecular Biology 1945:315-339 (2019). LinkLink opens in a new window
In: Hlavacek W. S. (ed.) Methods in Molecular Biology: Modeling Biomolecular Site Dynamics. Springer (2019). Series InfoLink opens in a new window

2018

Integrated Human-Virus Metabolic Stoichiometric Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses

Sean Aller, Andrew E Scott, Mitali Sarkar-Tyson, Orkun S Soyer
Royal Society Interface 12;15:146 (2018). LinkLink opens in a new window | Resource 13 (ViraNet)Link opens in a new window

2016

Core signalling motif displaying multistability through multi-state enzymes.

Song Feng, Meritxell Sez, Carsten Wiuf, Elisenda Feliu, and Orkun S. Soyer
Royal Society Interface 13:123 (2016). LinkLink opens in a new window

Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks

Song Feng, Julien F. Ollivier, and Orkun S. Soyer
PLoS Computational Biology 12(5):e1004918 (2016). LinkLink opens in a new window | Resource 11Link opens in a new window

Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers.

Francesco Montefusco, Ozgur E. Akman, Orkun S. Soyer, and Declan Bates
PLoS One 18;11(8):e0161605 (2016). LinkLink opens in a new window

Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels

Arno Steinacher, Declan G. Bates, Ozgur E. Akman, and Orkun S. Soyer
PLoS One 11(4):e0153295 (2016). LinkLink opens in a new window

2015

BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling

Song Feng, Julien Ollivier, Peter S. Swain, and Orkun S. Soyer
Nucleic Acid Research 43(19):e123 (2015). LinkLink opens in a new window | GitHub - BioJazzLink opens in a new window

Unlimited multistability and Boolean logic in microbial signaling

Varun B. Kothamachu, Elisenda Feliu, Luca Cardelli, and Orkun S. Soyer
Royal Society Interface 12:108 (2015). LinkLink opens in a new window

Engineering and biology: Counsel for a continued relationship

Brett Calcott, Arnon Levy, Mark L. Siegal, Orkun S. Soyer, and Andreas Wagner.
Biological Theory 10(1):50-59 (2015) LinkLink opens in a new window

2013

Metabolic Tinker: An online tool for guiding the design of synthetic metabolic pathways.

Kent McClymont and Orkun S. Soyer
Nucleic Acid Research 41(11):e113 (2013). LinkLink opens in a new window | Resource 8Link opens in a new window

Phosphorelays provide tunable signal processing capabilities for the cell.

Varun B. Kothamachu, Elisenda Feliu, Carsten Wuif, Luca Cardelli, and Orkun S. Soyer
PLoS Computational Biology 9(11):e1003322 (2013). LinkLink opens in a new window

2012

Bistability in feedback circuits as a byproduct of evolution of evolvability.

Hiroaki Kuwahara and Orkun S Soyer
Molecular Systems Biology 8:564 (2012). LinkLink opens in a new window | Resource 7Link opens in a new window | In "top download list" at Nature MSB website.

2011

Evolution of response dynamics underlying bacterial chemotaxis.

Orkun S. Soyer and Richard A. Goldstein
BMC Evolutionary Biology 11:240 (2011). LinkLink opens in a new window

2010

Response dynamics of phosphorelays suggest their potential utility in cell signaling.

Attila Csiksz-Nagy, Luca Cardelli, and Orkun S. Soyer
Journal of Royal Society Interface 8:57 (2010). Link | Resource 5Link opens in a new window

Evolution under fluctuating environments explains observed robustness in metabolic networks.

Orkun S. Soyer and Thomas Pfeiffer
PLoS Computational Biology 6(8): e1000907 (2010). LinkLink opens in a new window

Fate of a duplicate gene in a network context.

Orkun S. Soyer
Invited chapter in "Evolution After Gene Duplication", Dittmar K., Liberles D.A. (eds.) Wiley and Sons, ISBN: 978-0-470-59382-0, October 2010. Book DescriptionLink opens in a new window

2009

Regulating 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
FEBS Journal, 276:12 (2009). LinkLink opens in a new window

2008

Evolution of taxis responses in bacteria: nonadaptive dynamics.

Richard A. Goldstein and Orkun S. Soyer
PLoS Computational Biology, 4:5, e1000084 (2008). LinkLink opens in a new window | Resource 3, 4Link opens in a new window

Parasites lead to evolution of robustness against gene loss in host signaling networks.

Marcel Salathe and Orkun S. Soyer
Molecular Systems Biology, 4:202 (2008). LinkLink opens in a new window | Resource 2Link opens in a new window | Featured in NatureLink opens in a new window | Top ten download at Nature MSB website.

Adaptive dynamics with a single two state protein.

Attila Csiksz-Nagy and Orkun S. Soyer
Royal Society Interface, 5:Suppl 1, S41-7 (2008). LinkLink opens in a new window

Evolving BlenX programs to simulate the evolution of biological networks.

Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer
Theoretical Computer Science, 408:1 (2008). LinkLink opens in a new window

2007

Emergence and maintenance of functional modules in signaling pathways.

Orkun S Soyer
BMC Evolutionary Biology, 7:205 (2007). LinkLink opens in a new window

A formal and integrated framework to simulate evolution of biological pathways.

Lorenzo Dematte, Corado Priami, Alfonso Romanel, and Orkun S. Soyer
Proceedings of the Fifth International Conference on Computational Methods in Systems Biology (CMSB) 106-120 (2007). LinkLink opens in a new window

2006

Evolution of complexity in signaling pathways.

Orkun S. Soyer and Sebastian Bonhoeffer
Proc. Natl. Acad. Sci. USA (PNAS), 103:44 (2006). LinkLink opens in a new window

Simulating the evolution of signal transduction pathways.

Orkun S Soyer, Thomas Pfeiffer, and Sebastian Bonhoeffer
Journal of Theoretical Biology, 241:2 (2006). LinkLink opens in a new window

Signal transduction networks: topology, response, and biochemical reactions.

Orkun S. Soyer Marcel Salathe, and Sebastian Bonhoeffer
Journal of Theoretical Biology, 238:2 (2006). LinkLink opens in a new window | Resource 1Link opens in a new window

2005

Evolution of connectivity in metabolic networks.

Thomas Pfeiffer, Orkun S. Soyer, and Sebastian Bonhoeffer
PLoS Biology, 3:7 (2005). LinkLink opens in a new window | Featured in Journal of Cell BiologyLink opens in a new window

2004

Predicting functional sites in proteins: Site specific evolutionary models and their application to neurotransmitter transporters.

Orkun S. Soyer and Richard A. Goldstein
Journal of Molecular Biology, 339:1 (2004). LinkLink opens in a new window

2003

Probing 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
European Journal of Pharmacology, 479:1-3 (2003). LinkLink opens in a new window

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
Biochemistry, 42:49 (2003). LinkLink opens in a new window

Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs

Bin Qian, Orkun S. Soyer, Richard R. Neubig, and Richard A. Goldstein
FEBS Letters, 554:1-2 (2003). LinkLink opens in a new window

2002

NMR 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
Biochemistry, 41:11 (2002). LinkLink opens in a new window

Using evolutionary methods to study G-protein coupled receptors.

Orkun S. Soyer, Matt W. Dimmic, Richard R. Neubig, and Richard A. Golstein
Pacific Symposium on Biocomputing (PSB) 625-36 (2002). LinkLink opens in a new window