37. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling
Song Feng, Julien F. Ollivier, Peter S. Swain and Orkun S. Soyer
Nucleic Acid Research, in print (2015)
36. Unlimited multistability and Boolean logic in microbial signaling
Varun B. Kothamachu, Elisenda Feliu, Luca Cardelli and Orkun S. Soyer
Royal Society Interface, in print (2015)
35. A philosophical perspective on evolutionary systems biology.
Maureen A. O’Malley, Orkun S. Soyer, and Mark L. Siegal.
Biological Theorys 10.1007/s13752-015-0202-6 (2015).
34. Phosphate sink containing two-component signaling systems as tunable threshold devices.
Amin M., Kothamachu V.B., Feliu E., Scharf B.E., Porter S.L., and Soyer O. S.
PLoS Computational Biology 10(10):e1003890 (2014).
33. Bacterial drug tolerance under clinical conditions is governed by anaerobic adaptation, but not anaerobic respiration.
Hemsley C. M., Luo J. X., Andreae C. A., Butler C. S., Soyer O. S., and Titball R. W.
Antimicrobial Agents and Chemotherapy 58(10):5775-83 (2014).
32. Synthetic microbial communities.
Groβkopf T. and Soyer O.S.
Current Opinion in Microbiology 18:72-77 (2014).
31. Phosphorelays provide tunable signal processing capabilities for the cell.
Kothamachu V.B., Feliu E., Wiuf C., Cardelli L. and Soyer O.S.
PLoS Computational Biology 9(11):e1003322 (2013).
30. Systems and synthetic biology underpinning biotechnology.
Soyer O.S and Swain P.
Current Opinion Biotechnology 24(4):735-6 (2013).
29. Evolutionary Systems Biology: What it is and why it matters.
Soyer O.S and O'Malley M.
BioEssays 35(8):696-705 (2013).
28. Metabolic Tinker: An online tool for guiding the design of synthetic metabolic pathways.
McClymont K. and Soyer O.S.
Nucleic Acid Research 41(11):e113 (2013).
PDF | Tinker
27. Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks.
Munia A., Porter S. and Soyer O.S.
PLoS Computational Biology 9(3): e1002949 (2013).
26. Bistability in feedback circuits as a byproduct of evolution of evolvability.
Kuwahara H. and Soyer O.S.
Molecular Systems Biology 8:564 (2012).
PDF | Resource | In "top download list" at Nature MSB website.
25. Evolutionary principles underlying structure and response dynamics of cellular networks.
Steinacher A. and Soyer O.S.
Advances in Experimental Medicine and Biology 751 (2012).
24. The roles of integration in molecular systems biology.
O'Malley M.A and Soyer O.S.
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.
Soyer O.S. and Goldstein R.A.
BMC Evolutionary Biology 11:240 (2011).
22. The promise of evolutionary systems biology: Lessons from bacterial chemotaxis.
Soyer O.S.
Science Signaling 3:128, pe23 (2010).
21. Duplicate retention in signaling proteins and constraints from network dynamics.
Creevey C.J. and Soyer O.S.
Journal of Evolutionary Biology 23:11 (2010).
Abstract | Resource
20. Response dynamics of phosphorelays suggest their potential utility in cell signaling.
Csikász-Nagy A., Cardelli L., Soyer O. S.
Journal of Royal Society Interface 8:57 (2010).
PDF | Resource
19. Evolution under fluctuating environments explains observed robustness in metabolic networks.
Soyer O.S. and Pfeiffer T.
PLoS Computational Biology 6(8): e1000907 (2010).
18. Fate of a duplicate gene in a network context.
Soyer O.S.
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.
Soyer O.S., Kuwahara H., Csik·sz-Nagy A.
FEBS Journal, 276:12 (2009).
16. Parasites lead to evolution of robustness against gene loss in host signaling networks.
SalathË M. and Soyer O.S.
Molecular Systems Biology, 4:202 (2008).
PDF | Resource | Featured in Nature | Top ten download at Nature MSB website.
15. Evolution of taxis responses in bacteria: nonadaptive dynamics.
Goldstein R.A. and Soyer O.S.
PLoS Computational Biology, 4:5, e1000084 (2008).
PDF | Resource
14. Adaptive dynamics with a single two state protein.
Csik·sz-Nagy A., Soyer O.S.
Royal Society Interface, 5:Suppl 1, S41-7 (2008).
13. Evolving BlenX programs to simulate the evolution of biological networks.
DemattÈ L., Priami C., Romanel A., Soyer O.S.
Theoretical Computer Science, 408:1 (2008).
12. Emergence and maintenance of functional modules in signaling pathways.
Soyer O.S.
BMC Evolutionary Biology, 7:205 (2007).
11. A formal and integrated framework to simulate evolution of biological pathways.
DemattÈ L., Priami C., Romanel A., Soyer O.S.
Proceedings of the Fifth International Conference on Computational Methods in Systems Biology (CMSB) 106-120 (2007).
10. Evolution of complexity in signaling pathways.
Soyer O.S. and Bonhoeffer S.
Proc. Natl. Acad. Sci. USA (PNAS), 103:44 (2006).
9. Simulating the evolution of signal transduction pathways.
Soyer O.S., Pfeiffer T., Bonhoeffer S.
Journal of Theoretical Biology, 241:2 (2006).
8. Signal transduction networks: topology, response, and biochemical reactions.
Soyer O.S., SalathË M., Bonhoeffer S.
Journal of Theoretical Biology, 238:2 (2006).
PDF | Resource
7. Evolution of connectivity in metabolic networks.
Pfeiffer T., Soyer O.S., Bonhoeffer S.
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.
Soyer O.S. and Goldstein R.A.
Journal of Molecular Biology, 339:1 (2004).
5. Probing conformational changes in neurotransmitter transporters in a structural context.
Goldberg N.R., Beuming T., Soyer O.S., Goldstein R.A., Weinstein H., Javitch J.A.
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.
Soyer O.S., Dimmic M.W., Neubig R.R., Goldstein R.A.
Biochemistry, 42:49 (2003).
3. Depict a protein’s two faces: Using phylogenetic tree based HMMs for G-protein coupled receptor classification.
Qian B., Soyer O.S., Neubig R.R., Goldstein R.A.
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.
Chung D.A., Zuiderweg E.R.P., Fowler C.B., Soyer O.S., Mosberg H.I., Neubig R.R.
Biochemistry, 41:11 (2002).
1. Using evolutionary methods to study G-protein coupled receptors.
Soyer O.S., Dimmic M.W., Neubig R.R., Golstein R.A.
Pacific Symposium on Biocomputing (PSB) 625-36 (2002).