Skip to main content Skip to navigation


Quick links:
Articles | Pre Prints | Books


65. 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)

64. 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
63. 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 | Link | SBML model | GitHub - FBAhv

62. 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. Link

61. 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. Link

60. 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. Link | GitHub - Micodymora

59. 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) Link

58. 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) Link
57. 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). Link

56. Interrogating metabolism as an electron flow system

Christian Zerfass, Munehiro Asally, Orkun S Soyer
Current Opinion in Systems Biology 13: 59-67 (2019). Link

55. 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). Link

54. 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). Link | GitHub - MetQy

53. 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). Link | Resource 13 (ViraNet)

52. 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). Link | Faculty Opinions Logo

51. Engineering microbial communities using thermodynamic principles and electrical interfaces.

Christian Zerfass, Jing Chen, Orkun S Soyer,
Current Opinion in Biotechnology 50:121-127 (2017). Link

50. 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). Link | Commentary

49. Cooperation in microbial communities and their biotechnological applications.

Matteo Cavaliere, Song Feng, Orkun S. Soyer, Jose I. Jimenez
Environmental Microbiology 19:8 (2017). Link

48. 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). Link
47. 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). Link | Resource 12 (evoFBA)
46. 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). Link | Sequence Data | Faculty Opinions Logo
45. 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). Link
44. 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). Link | Resource 11
43. Microbial diversity arising from thermodynamic constraints.
Tobias Großkopf and Orkun S. Soyer
The ISME Journal 10:11 (2016). Link| Resource 10
42. 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). Link | In "top download list" at ISME website.

41. 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). Link
40. 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). Link
39. 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). Link
38. 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). Link | GitHub - BioJazz
37. 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). Link
36. 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) PDF
35. 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). PDF
34. 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). PDF
33. 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). PDF
32. Synthetic microbial communities.

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

31. 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). PDF

30. Systems and synthetic biology underpinning biotechnology.

Orkun S. Soyer and Peter Swain
Current Opinion Biotechnology 24(4):735-6 (2013).

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

Maureen O'Malley and Orkun S Soyer
BioEssays 35(8):696-705 (2013).

28. 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). PDF | Resource 8

27. 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). PDF | Faculty Opinions Logo

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

Hiroaki Kuwahara and Orkun S Soyer
Molecular Systems Biology 8:564 (2012). PDF | Resource 7 | In "top download list" at Nature MSB website. Faculty Opinions Logo

25. Evolutionary principles underlying structure and response dynamics of cellular networks.

Arno Steinacher and Orkun Soyer
Advances in Experimental Medicine and Biology 751 (2012).

24. 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). PDF | In "top download list" at ScienceDirect subject website.

23. Evolution of response dynamics underlying bacterial chemotaxis.

Orkun S. Soyer and Richard A. Goldstein
BMC Evolutionary Biology 11:240 (2011). PDF

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

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

21. Duplicate retention in signaling proteins and constraints from network dynamics.

Chris J. Creevey and Orkun S. Soyer
Journal of Evolutionary Biology 23:11 (2010). Link | Resource 6

20. 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). PDF | Resource 5

19. Evolution under fluctuating environments explains observed robustness in metabolic networks.

Orkun S. Soyer and Thomas Pfeiffer
PLoS Computational Biology 6(8): e1000907 (2010). PDF

18. 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 Description

17. 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). Link

16. Evolution of taxis responses in bacteria: nonadaptive dynamics.

Richard A. Goldstein and Orkun S. Soyer
PLoS Computational Biology, 4:5, e1000084 (2008). Link | Resource 3, 4

15. 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). Link | Resource 2 | Featured in Nature | Top ten download at Nature MSB website.

14. Adaptive dynamics with a single two state protein.

Attila Csiksz-Nagy and Orkun S. Soyer
Royal Society Interface, 5:Suppl 1, S41-7 (2008). Link

13. 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).

12. Emergence and maintenance of functional modules in signaling pathways.

Orkun S Soyer
BMC Evolutionary Biology, 7:205 (2007). Link

11. 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).

10. Evolution of complexity in signaling pathways.

Orkun S. Soyer and Sebastian Bonhoeffer
Proc. Natl. Acad. Sci. USA (PNAS), 103:44 (2006). Link

9. Simulating the evolution of signal transduction pathways.

Orkun S Soyer, Thomas Pfeiffer, and Sebastian Bonhoeffer
Journal of Theoretical Biology, 241:2 (2006).

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

Orkun S. Soyer Marcel Salathe, and Sebastian Bonhoeffer
Journal of Theoretical Biology, 238:2 (2006). Resource 1

7. Evolution of connectivity in metabolic networks.

Thomas Pfeiffer, Orkun S. Soyer, and Sebastian Bonhoeffer
PLoS Biology, 3:7 (2005). Link | Featured in Journal of Cell Biology

6. 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).

5. 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).

4. 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).

3. Depict a proteins two faces: Using phylogenetic tree based HMMs for G-protein coupled receptor classification.

Bin Qian, Orkun S. Soyer, Richard R. Neubig, and Richard A. Goldstein
FEBS Letters, 554:1-2 (2003).

2. 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).

1. 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).

Pre Prints

Listed here are currently unpublished manuscripts deposited at biorxiv or Authorea. Previous manuscripted deposited at biorxiv/Authorea which were then published in a peer-reviewed journal are now listed under Articles.

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

Connah G. M. Johnson, Alexander G. Fletcher, Orkun S. Soyer

Posted October 22, 2021 | bioRxiv link

5. 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 link
4. Novel microbial syntrophies identified by longitudinal metagenomics
Sebastien Raguideau, Anna Trego, Fred Farrell, Gavin Collins, Christopher Quince, Orkun S Soyer
Posted July 05, 2021 | bioRxiv link
3. Multi-site enzymes as a mechanism for bistability in reaction networks
Clarmyra Hayes, Elisenda Feliu, Orkun S Soyer
Posted May 07, 2021 | bioRxiv link
2. A low-cost DIY device for high resolution, continuous measurement of microbial growth dynamics.
Kalesh Sasidharan, Andrea S Martinez-Vernon, Jing Chen, Tiantian Fu, Orkun Soyer
Posted Sept 04, 2018 | bioRxiv link
1. Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes.

Fred Farrell, Orkun S Soyer, Christopher Quince
Posted April 25, 2018 | bioRxiv link


4. 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-Nature. (In Press)

Chapter Link

evolutionary systems biology book image
3. In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics

Feng S and Soyer OS (2019)

In: Hlavacek W. S. (ed.) Methods in Molecular Biology: Modeling Biomolecular Site Dynamics. Springer (2019)

Series Info
methods in molecular biology
2. Evolutionary Principles Underlying Structure and Response Dynamics of Cellular Networks

Steinacher A and Soyer OS (2012)

In Soyer O.S. (ed.). Evolutionary Systems Biology: Adv. in Exp. Medicine and Biology. Springer, (2012)
Book Info
evosysbio cover
1. Fate of a Duplicate in a Network Context

Soyer OS (2011)

In: Dittmar K. and Liberles D. (eds.). Evolution after Gene Duplication. Wiley-Blackwell, (2011)
Book Info