Orkun S Soyer

Summary

Affiliation: Swiss Federal Institute of Technology
Country: Switzerland

Publications

  1. ncbi request reprint Signal transduction networks: topology, response and biochemical processes
    Orkun S Soyer
    Theoretical Biology Group, Ecology and Evolution, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
    J Theor Biol 238:416-25. 2006
  2. ncbi request reprint Simulating the evolution of signal transduction pathways
    Orkun S Soyer
    Theoretical Biology Group, Ecology and Evolution, CH 8092, Zurich, Switzerland
    J Theor Biol 241:223-32. 2006
  3. pmc Evolution of complexity in signaling pathways
    Orkun S Soyer
    Theoretical Biology Group, Institute for Integrative Biology, Swiss Federal Institute of Technology ETH, Universitatsstrasse 16, ETH Zentrum, CHN K12 2, CH 8092 Zurich, Switzerland
    Proc Natl Acad Sci U S A 103:16337-42. 2006
  4. pmc The evolution of connectivity in metabolic networks
    Thomas Pfeiffer
    Computational Laboratory, ETH Zurich, Zurich, Switzerland
    PLoS Biol 3:e228. 2005
  5. pmc Emergence and maintenance of functional modules in signaling pathways
    Orkun S Soyer
    The Microsoft Research University of Trento Centre for Computational and Systems Biology CoSBi, Piazza Manci 17, 38100 Povo Trento, Italy
    BMC Evol Biol 7:205. 2007
  6. ncbi request reprint Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters
    Orkun S Soyer
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    J Mol Biol 339:227-42. 2004
  7. pmc Adaptive dynamics with a single two-state protein
    Attila Csikasz-Nagy
    Microsoft Research University of Trento Centre for Computational and Systems Biology, Piazza Manci 17, Povo Trento, Italy
    J R Soc Interface 5:S41-7. 2008
  8. ncbi request reprint Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs
    Bin Qian
    Biophysics Research Division, University of Michigan, Ann Arbor, MI 48105, USA
    FEBS Lett 554:95-9. 2003
  9. ncbi request reprint Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution
    Orkun S Soyer
    Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
    Biochemistry 42:14522-31. 2003
  10. ncbi request reprint Probing conformational changes in neurotransmitter transporters: a structural context
    Naomi R Goldberg
    Center for Molecular Recognition, Columbia University, P and S 11 401, Box 7, 630 West 168th Street, New York, NY 10032, USA
    Eur J Pharmacol 479:3-12. 2003

Collaborators

Detail Information

Publications11

  1. ncbi request reprint Signal transduction networks: topology, response and biochemical processes
    Orkun S Soyer
    Theoretical Biology Group, Ecology and Evolution, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
    J Theor Biol 238:416-25. 2006
    ..Furthermore it shows that network topology plays a key role on determining response type and properties and that proper representation of network topology is crucial to discover and understand so-called building blocks of large networks...
  2. ncbi request reprint Simulating the evolution of signal transduction pathways
    Orkun S Soyer
    Theoretical Biology Group, Ecology and Evolution, CH 8092, Zurich, Switzerland
    J Theor Biol 241:223-32. 2006
    ..We conclude that simulating the evolution of signal transduction networks to mediate a certain behavior may be a promising approach for understanding the general properties of the natural pathway for that behavior...
  3. pmc Evolution of complexity in signaling pathways
    Orkun S Soyer
    Theoretical Biology Group, Institute for Integrative Biology, Swiss Federal Institute of Technology ETH, Universitatsstrasse 16, ETH Zentrum, CHN K12 2, CH 8092 Zurich, Switzerland
    Proc Natl Acad Sci U S A 103:16337-42. 2006
    ..This leads to the counterintuitive conclusion that simple response requirements on a pathway would facilitate its evolution toward higher complexity...
  4. pmc The evolution of connectivity in metabolic networks
    Thomas Pfeiffer
    Computational Laboratory, ETH Zurich, Zurich, Switzerland
    PLoS Biol 3:e228. 2005
    ..Specifically, our simulations indicate that group transfer reactions are essential for the emergence of hubs...
  5. pmc Emergence and maintenance of functional modules in signaling pathways
    Orkun S Soyer
    The Microsoft Research University of Trento Centre for Computational and Systems Biology CoSBi, Piazza Manci 17, 38100 Povo Trento, Italy
    BMC Evol Biol 7:205. 2007
    ..e. environment) in order for modularity to emerge. Here, we provide an alternative and simpler explanation using a realistic model of biological signaling pathways and simulating their evolution...
  6. ncbi request reprint Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters
    Orkun S Soyer
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    J Mol Biol 339:227-42. 2004
    ..Based on this application we present testable hypotheses regarding the mechanism of action of these proteins...
  7. pmc Adaptive dynamics with a single two-state protein
    Attila Csikasz-Nagy
    Microsoft Research University of Trento Centre for Computational and Systems Biology, Piazza Manci 17, Povo Trento, Italy
    J R Soc Interface 5:S41-7. 2008
    ..The analysis of coupled BioNetUnits will show how the presented dynamics at single unit will change upon increased system complexity and how such systems would mediate biological functions...
  8. ncbi request reprint Depicting a protein's two faces: GPCR classification by phylogenetic tree-based HMMs
    Bin Qian
    Biophysics Research Division, University of Michigan, Ann Arbor, MI 48105, USA
    FEBS Lett 554:95-9. 2003
    ..In this study we used the method to generate common features of G protein-coupled receptors (GPCRs). The profile generated by T-HMM gives high accuracy in GPCR function classification, both by ligand and by coupled G protein...
  9. ncbi request reprint Dimerization in aminergic G-protein-coupled receptors: application of a hidden-site class model of evolution
    Orkun S Soyer
    Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
    Biochemistry 42:14522-31. 2003
    ..On the basis of these findings, we propose an experimentally testable dimerization mechanism, involving interactions among different combinations of these helices in different families of aminergic GPCRs...
  10. ncbi request reprint Probing conformational changes in neurotransmitter transporters: a structural context
    Naomi R Goldberg
    Center for Molecular Recognition, Columbia University, P and S 11 401, Box 7, 630 West 168th Street, New York, NY 10032, USA
    Eur J Pharmacol 479:3-12. 2003
    ....
  11. pmc Evolution of taxis responses in virtual bacteria: non-adaptive dynamics
    Richard A Goldstein
    Mathematical Biology, National Institute for Medical Research, London, United Kingdom
    PLoS Comput Biol 4:e1000084. 2008
    ....