Articles

59. Increasing sulphate 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 Royal Society Interface 16: 20190129 (2019) PDF
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). PDF
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). PDF
56. Interrogating metabolism as an electron flow system. Christian Zerfass, Munehiro Asally, Orkun S Soyer Current Opinion in Systems Biology 13: 59-67 (2019). PDF
55. Biodiversity function relationships in methanogenic communities. Pawel Sierocinski, Florian Bayer, Gabriel YvonDurocher, Melia Burdon, Tobias Grokopf, Mark Alston, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Angus Buckling Molecular Ecology 27(22):4641-4651 (2018). PDF
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). PDF \| Resource 14 (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). PDF \| Resource 13 (ViraNet)
52. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. Xue Jiang, Christian Zerfa, Song Feng, Ruth Eichmann, Munehiro Asally, Patrick Schaefer, Orkun S Soyer The ISME Journal 12(6):1443-1456 (2018). PDF \|
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). PDF
50. A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities. Pawel Sierocinski, Kim Milferstedt, Florian Bayer, Tobias Grokopf, Mark Alston, Sarah Bastkowski, David Swarbreck, Phil J Hobbs, Orkun S Soyer, Jerome Hamelin, Angus Buckling Current Biology 27(21):3390-3395 (2017). PDF \| Commentary
49. Cooperation in microbial communities and their biotechnological applications. Matteo Cavaliere, Song Feng, Orkun S. Soyer, Jose I. Jimenez Environmental Microbiology Environ Microbiol. 19:8 (2017). PDF
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, Richard J. Saint, Andrew E. Scott, Mitali Sarkar-Tyson, Philip M. Ireland,Helen L Bullifent, Z. Rong Yang, Karen Moore, Petra C. F. Oyston, Timothy P. Atkins, Helen S. Atkins, Orkun S. Soyer and Richard W. Titball BMC Microbiology 17:163 (2017). PDF
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). PDF \| 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) PDF \| Sequence Data \|
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). PDF
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). PDF \| Resource 11
43. Microbial diversity arising from thermodynamic constraints. Tobias Grosskopf and Orkun S. Soyer The ISME Journal 10:11 (2016) PDF \| Resource 10
42. Challenges in microbial ecology: building predictive understanding of community function and dynamics. Stefanie Widder, Rosalind Allen, Thomas Pfeiffer, Thomas P. Curtis, Carsten Wiuf, William T. Sloan, Otto X. Cordero, Sam P. Brown, Babak Momeni, Wenying Shou, Helen Kettle, Harry J. Flint, Andreas F. Haas, Batrice Laroche, Jan-Ulrich Kreft, Paul B. Rainey, Shiri Freilich, Stefan Schuster, Kim Milferstedt, Jan R. van der Meer, Tobias Grosskopf, Jef Huisman, Andrew Free, Cristian Picioreanu, Christopher Quince, Isaac Klapper, Simon Labarthe, Barth F. Smets, Harris Wang, Isaac Newton Institute Fellows*, and Orkun S. Soyer The ISME Journal 10:11 (2016) PDF \| 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). PDF
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). PDF
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) PDF
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). PDF \| BioJazz \| Resource 9
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). PDF
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 \|
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.
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). Abstract \| 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). Abstract
16. Evolution of taxis responses in bacteria: nonadaptive dynamics. Richard A. Goldstein and Orkun S. Soyer PLoS Computational Biology, 4:5, e1000084 (2008). PDF \| 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). PDF \| 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). PDF
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). PDF
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). PDF
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). PDF \| 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).

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

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

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

56. Interrogating metabolism as an electron flow system.

55. Biodiversity function relationships in methanogenic communities.

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

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

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

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

50. A Single Community Dominates Structure and Function of a Mixture of Multiple Methanogenic Communities.

49. Cooperation in microbial communities and their biotechnological applications.

48. An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions.

47. Metabolic modelling in an evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

46. A stable genetic polymorphism underpinning microbial syntrophy.

45. Core signalling motif displaying multistability through multi-state enzymes.

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

43. Microbial diversity arising from thermodynamic constraints.

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

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

40. Mapping epigenetic changes to the host cell genome induced by Burkholderia pseudomallei reveals pathogen-specific and pathogen-generic signatures of infection.

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

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

37. Unlimited multistability and Boolean logic in microbial signaling

36. Engineering and biology: Counsel for a continued relationship

35. A philosophical perspective on evolutionary systems biology.

34. Phosphate sink containing two-component signaling systems as tunable threshold devices.

33. Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation, but not anaerobic respiration.

32. Synthetic microbial communities.

31. Phosphorelays provide tunable signal processing capabilities for the cell.

30. Systems and synthetic biology underpinning biotechnology.

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

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

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

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

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

24. The roles of integration in molecular systems biology.

23. Evolution of response dynamics underlying bacterial chemotaxis.

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

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

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

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

18. Fate of a duplicate gene in a network context.

17. Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses.

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

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

14. Adaptive dynamics with a single two state protein.

13. Evolving BlenX programs to simulate the evolution of biological networks.

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

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

10. Evolution of complexity in signaling pathways.

9. Simulating the evolution of signal transduction pathways.

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

7. Evolution of connectivity in metabolic networks.

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

5. Probing conformational changes in neurotransmitter transporters in a structural context.

4. Dimerization in aminergic G-protein coupled receptors: Application of a hidden site-class model of protein evolution.

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

2. NMR Structure of the second intracellular loop of the alpha2a adrenergic receptor: Evidence for a novel cytoplasmic helix.

1. Using evolutionary methods to study G-protein coupled receptors.