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Orkun S. Soyer - Publications

Affiliations: 
University of Warwick, Coventry, England, United Kingdom 
Area:
Computational biology, systems biology, synthetic biology, evolution
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50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Cremin K, Duxbury SJN, Rosko J, Soyer OS. Formation and emergent dynamics of spatially organized microbial systems. Interface Focus. 13: 20220062. PMID 36789239 DOI: 10.1098/rsfs.2022.0062  0.708
2020 Schofield Z, Meloni GN, Tran P, Zerfass C, Sena G, Hayashi Y, Grant M, Contera SA, Minteer SD, Kim M, Prindle A, Rocha PRF, Djamgoz MBA, Pilizota T, Unwin PR, ... ... Soyer OS, et al. Correction to 'Bioelectrical understanding and engineering of cell biology'. Journal of the Royal Society, Interface. 17: 20200435. PMID 32546111 DOI: 10.1098/Rsif.2020.0435  0.649
2020 Schofield Z, Meloni GN, Tran P, Zerfass C, Sena G, Hayashi Y, Grant M, Contera SA, Minteer SD, Kim M, Prindle A, Rocha P, Djamgoz MBA, Pilizota T, Unwin PR, ... ... Soyer OS, et al. Bioelectrical understanding and engineering of cell biology. Journal of the Royal Society, Interface. 17: 20200013. PMID 32429828 DOI: 10.1098/Rsif.2020.0013  0.683
2020 Delattre H, Chen J, Wade MJ, Soyer OS. Thermodynamic modelling of synthetic communities predicts minimum free energy requirements for sulfate reduction and methanogenesis. Journal of the Royal Society, Interface. 17: 20200053. PMID 32370691 DOI: 10.1098/Rsif.2020.0053  0.372
2019 Zerfaß C, Asally M, Soyer OS. Interrogating metabolism as an electron flow system. Current Opinion in Systems Biology. 13: 59-67. PMID 31008413 DOI: 10.1016/J.Coisb.2018.10.001  0.322
2019 Feng S, Soyer OS. In Silico Evolution of Signaling Networks Using Rule-Based Models: Bistable Response Dynamics. Methods in Molecular Biology (Clifton, N.J.). 1945: 315-339. PMID 30945254 DOI: 10.1007/978-1-4939-9102-0_15  0.67
2018 Sierocinski P, Bayer F, Yvon-Durocher G, Burdon M, Großkopf T, Alston M, Swarbreck D, Hobbs PJ, Soyer OS, Buckling A. Biodiversity-function relationships in methanogenic communities. Molecular Ecology. PMID 30307662 DOI: 10.1111/Mec.14895  0.303
2018 Jiang X, Zerfaß C, Feng S, Eichmann R, Asally M, Schäfer P, Soyer OS. Impact of spatial organization on a novel auxotrophic interaction among soil microbes. The Isme Journal. PMID 29572468 DOI: 10.1038/S41396-018-0095-Z  0.631
2017 Zerfaß C, Chen J, Soyer OS. Engineering microbial communities using thermodynamic principles and electrical interfaces. Current Opinion in Biotechnology. 50: 121-127. PMID 29268107 DOI: 10.1016/J.Copbio.2017.12.004  0.346
2017 Cavaliere M, Feng S, Soyer O, Jimenez JI. Cooperation in microbial communities and their biotechnological applications. Environmental Microbiology. PMID 28447371 DOI: 10.1111/1462-2920.13767  0.639
2016 Feng S, Sáez M, Wiuf C, Feliu E, Soyer OS. Core signalling motif displaying multistability through multi-state enzymes. Journal of the Royal Society, Interface. 13. PMID 27733693 DOI: 10.1098/Rsif.2016.0524  0.624
2016 Großkopf T, Consuegra J, Gaffé J, Willison JC, Lenski RE, Soyer OS, Schneider D. Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment. Bmc Evolutionary Biology. 16: 163. PMID 27544664 DOI: 10.1186/S12862-016-0733-X  0.365
2016 Montefusco F, Akman OE, Soyer OS, Bates DG. Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers. Plos One. 11: e0161605. PMID 27537373 DOI: 10.1371/Journal.Pone.0161605  0.361
2016 Großkopf T, Zenobi S, Alston M, Folkes L, Swarbreck D, Soyer OS. A stable genetic polymorphism underpinning microbial syntrophy. The Isme Journal. PMID 27258948 DOI: 10.1038/Ismej.2016.80  0.304
2016 Feng S, Ollivier JF, Soyer OS. Enzyme Sequestration as a Tuning Point in Controlling Response Dynamics of Signalling Networks. Plos Computational Biology. 12: e1004918. PMID 27163612 DOI: 10.1371/Journal.Pcbi.1004918  0.674
2016 Steinacher A, Bates DG, Akman OE, Soyer OS. Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels. Plos One. 11: e0153295. PMID 27082741 DOI: 10.1371/Journal.Pone.0153295  0.341
2016 Großkopf T, Soyer OS. Microbial diversity arising from thermodynamic constraints. The Isme Journal. PMID 27035705 DOI: 10.1038/Ismej.2016.49  0.371
2016 Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, ... ... Soyer OS, et al. Challenges in microbial ecology: building predictive understanding of community function and dynamics. The Isme Journal. PMID 27022995 DOI: 10.1038/Ismej.2016.45  0.386
2015 Feng S, Ollivier JF, Swain PS, Soyer OS. BioJazz: in silico evolution of cellular networks with unbounded complexity using rule-based modeling. Nucleic Acids Research. PMID 26101250 DOI: 10.1093/Nar/Gkv595  0.662
2015 O'Malley MA, Soyer OS, Siegal ML. A Philosophical Perspective on Evolutionary Systems Biology. Biological Theory. 10: 6-17. PMID 26085823 DOI: 10.1007/S13752-015-0202-6  0.375
2015 Kothamachu VB, Feliu E, Cardelli L, Soyer OS. Unlimited multistability and Boolean logic in microbial signalling. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 26040599 DOI: 10.1098/Rsif.2015.0234  0.409
2014 Amin M, Kothamachu VB, Feliu E, Scharf BE, Porter SL, Soyer OS. Phosphate sink containing two-component signaling systems as tunable threshold devices. Plos Computational Biology. 10: e1003890. PMID 25357192 DOI: 10.1371/Journal.Pcbi.1003890  0.364
2014 Grosskopf T, Soyer OS. Synthetic microbial communities. Current Opinion in Microbiology. 18: 72-7. PMID 24632350 DOI: 10.1016/J.Mib.2014.02.002  0.33
2013 Kothamachu VB, Feliu E, Wiuf C, Cardelli L, Soyer OS. Phosphorelays provide tunable signal processing capabilities for the cell. Plos Computational Biology. 9: e1003322. PMID 24244132 DOI: 10.1371/Journal.Pcbi.1003322  0.353
2013 Soyer OS, Swain PS. Systems and synthetic biology underpinning biotechnology. Current Opinion in Biotechnology. 24: 735-6. PMID 23810372 DOI: 10.1016/J.Copbio.2013.06.002  0.34
2013 Soyer OS, O'Malley MA. Evolutionary systems biology: what it is and why it matters. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 35: 696-705. PMID 23681824 DOI: 10.1002/Bies.201300029  0.417
2013 Amin M, Porter SL, Soyer OS. Split histidine kinases enable ultrasensitivity and bistability in two-component signaling networks. Plos Computational Biology. 9: e1002949. PMID 23505358 DOI: 10.1371/Journal.Pcbi.1002949  0.338
2012 Steinacher A, Soyer OS. Evolutionary principles underlying structure and response dynamics of cellular networks. Advances in Experimental Medicine and Biology. 751: 225-47. PMID 22821461 DOI: 10.1007/978-1-4614-3567-9_11  0.465
2012 O'Malley MA, Soyer OS. The roles of integration in molecular systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences. 43: 58-68. PMID 22326073 DOI: 10.1016/J.Shpsc.2011.10.006  0.315
2012 Kuwahara H, Soyer OS. Bistability in feedback circuits as a byproduct of evolution of evolvability. Molecular Systems Biology. 8: 564. PMID 22252387 DOI: 10.1038/Msb.2011.98  0.367
2011 Soyer OS, Goldstein RA. Evolution of response dynamics underlying bacterial chemotaxis. Bmc Evolutionary Biology. 11: 240. PMID 21846396 DOI: 10.1186/1471-2148-11-240  0.555
2011 Csikász-Nagy A, Cardelli L, Soyer OS. Response dynamics of phosphorelays suggest their potential utility in cell signalling. Journal of the Royal Society, Interface / the Royal Society. 8: 480-8. PMID 20702449 DOI: 10.1098/Rsif.2010.0336  0.354
2010 Soyer OS, Pfeiffer T. Evolution under fluctuating environments explains observed robustness in metabolic networks. Plos Computational Biology. 6. PMID 20865149 DOI: 10.1371/Journal.Pcbi.1000907  0.352
2010 Soyer OS, Creevey CJ. Duplicate retention in signalling proteins and constraints from network dynamics. Journal of Evolutionary Biology. 23: 2410-21. PMID 20825548 DOI: 10.1111/J.1420-9101.2010.02101.X  0.404
2010 Soyer OS. The promise of evolutionary systems biology: lessons from bacterial chemotaxis. Science Signaling. 3: pe23. PMID 20587804 DOI: 10.1126/Scisignal.3128Pe23  0.426
2009 Soyer OS, Kuwahara H, Csikász-Nagy A. Regulating the total level of a signaling protein can vary its dynamics in a range from switch like ultrasensitivity to adaptive responses. The Febs Journal. 276: 3290-8. PMID 19438711 DOI: 10.1111/J.1742-4658.2009.07054.X  0.393
2008 Salathé M, Soyer OS. Parasites lead to evolution of robustness against gene loss in host signaling networks. Molecular Systems Biology. 4: 202. PMID 18628743 DOI: 10.1038/Msb.2008.44  0.355
2008 Goldstein RA, Soyer OS. Evolution of taxis responses in virtual bacteria: non-adaptive dynamics. Plos Computational Biology. 4: e1000084. PMID 18483577 DOI: 10.1371/Journal.Pcbi.1000084  0.566
2008 Csikász-Nagy A, Soyer OS. Adaptive dynamics with a single two-state protein. Journal of the Royal Society, Interface / the Royal Society. 5: S41-7. PMID 18445552 DOI: 10.1098/Rsif.2008.0099.Focus  0.434
2007 Soyer OS. Emergence and maintenance of functional modules in signaling pathways. Bmc Evolutionary Biology. 7: 205. PMID 17974002 DOI: 10.1186/1471-2148-7-205  0.362
2006 Soyer OS, Bonhoeffer S. Evolution of complexity in signaling pathways. Proceedings of the National Academy of Sciences of the United States of America. 103: 16337-42. PMID 17060629 DOI: 10.1073/Pnas.0604449103  0.562
2006 Soyer OS, Pfeiffer T, Bonhoeffer S. Simulating the evolution of signal transduction pathways. Journal of Theoretical Biology. 241: 223-32. PMID 16403533 DOI: 10.1016/J.Jtbi.2005.11.024  0.589
2006 Soyer OS, Salathé M, Bonhoeffer S. Signal transduction networks: topology, response and biochemical processes. Journal of Theoretical Biology. 238: 416-25. PMID 16045939 DOI: 10.1016/J.Jtbi.2005.05.030  0.588
2005 Pfeiffer T, Soyer OS, Bonhoeffer S. The evolution of connectivity in metabolic networks. Plos Biology. 3: e228. PMID 16000019 DOI: 10.1371/Journal.Pbio.0030228  0.557
2004 Soyer OS, Goldstein RA. Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters. Journal of Molecular Biology. 339: 227-42. PMID 15123434 DOI: 10.1016/J.Jmb.2004.03.025  0.53
2003 Soyer OS, Dimmic MW, Neubig RR, Goldstein RA. Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution. Biochemistry. 42: 14522-31. PMID 14661965 DOI: 10.1021/Bi035097R  0.734
2003 Goldberg NR, Beuming T, Soyer OS, Goldstein RA, Weinstein H, Javitch JA. Probing conformational changes in neurotransmitter transporters: a structural context. European Journal of Pharmacology. 479: 3-12. PMID 14612133 DOI: 10.1016/J.Ejphar.2003.08.052  0.474
2003 Qian B, Soyer OS, Neubig RR, Goldstein RA. Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs. Febs Letters. 554: 95-9. PMID 14596921 DOI: 10.1016/S0014-5793(03)01112-8  0.642
2002 Soyer O, Dimmic MW, Neubig RR, Goldstein RA. Using evolutionary methods to study G-protein coupled receptors. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 625-36. PMID 11928514  0.73
2002 Chung DA, Zuiderweg ER, Fowler CB, Soyer OS, Mosberg HI, Neubig RR. NMR structure of the second intracellular loop of the alpha 2A adrenergic receptor: evidence for a novel cytoplasmic helix. Biochemistry. 41: 3596-604. PMID 11888275 DOI: 10.1021/Bi015811+  0.313
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