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Publications (and most recent Preprints)

Cell Physiology
Microbial Communities
Theory
Thioflavin T indicates membrane potential in mammalian cells and can affect it in a blue light dependent manner
Emily Skates, Hadrien Delattre, Zoe Schofield, Munehiro Asally, Orkun S. Soyer
Posted October 22, 2021 | bioRxiv 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

Novel microbial syntrophies identified by longitudinal metagenomics
Sebastien Raguideau, Anna Trego, Fred Farrell, Gavin Collins, Christopher Quince, Orkun S Soyer

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)


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 | Faculty Opinions Logo


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 | Faculty Opinions LogoLink 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.


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 Synthetic Biology (2022) 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 (2020) 4(1): published online November 24 2020 | 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. Faculty Opinions LogoLink opens in a new window


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