Subsections

Publications

Books

  1. C. O. Wilke. Evolutionary Dynamics in Time-Dependent Environments. Shaker Verlag, Aachen, 1999. ISBN 3-8265-6199-6. (PhD Thesis, Ruhr-Universität Bochum)

    Download: PhD.ps.gz (3.3 MB)

  2. C. Wilke, S. Altmeyer, and T. Martinetz, editors. Third German Workshop on Artificial Life. Verlag Harri Deutsch, Thun, Frankfurt a.M., 1998. ISBN 3-8171-1591-1.
    (order form)

Articles

Several of the manuscripts provided through links are preprints and may differ in details from the published papers. In case of doubt, please refer to the published version.

  1. É. Brunet, I. M. Rouzine, and C. O. Wilke. The stochastic edge in adaptive evolution. Genetics, in press.
  2. T. Zhou, D. A. Drummond, and C. O. Wilke. Contact density affects protein evolutionary rate from bacteria to animals. J. Mol. Evol., in press.
  3. R. N. Dutta, I. M. Rouzine, S. D. Smith, C. O. Wilke, and I. S. Novella. Rapid adaptive amplification of preexisting variation in an RNA virus. J. Virol., in press.
  4. A. R. Sedaghat, J. B. Dinoso, L. Shen, C. O. Wilke, and R. F. Siliciano. Decay dynamics of HIV-1 depend on the inhibited stages of the viral life cycle. Proc. Natl. Acad. Sci. USA, in press.
  5. J. J. Bull, R. Sanjuán, and C. O. Wilke. Lethal mutagenesis. In E. Domingo, C. R. Parrish, and J. J. Holland, eds., Origin and Evolution of Viruses, 2nd ed. Elsevier, in press.
  6. I. M. Rouzine, É. Brunet, and C. O. Wilke. The traveling wave approach to asexual evolution: Muller's ratchet and speed of adaptation. Theor. Popul. Biol. 73:24-46, 2008.
  7. A. R. Sedaghat, R. F. Siliciano, and C. O. Wilke. Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART. BMC Infect. Dis. 8:2, 2008.
  8. A. R. Sedaghat, J. D. Siliciano, T. P. Brennan, C. O. Wilke, and R. F. Siliciano. Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART. PLoS Pathogens 3:e122, 2007.
  9. R. Forster and C. O. Wilke. Frequency-dependent selection in a periodic environment. Physica A 381:255-264, 2007.
  10. J. D. Bloom, F. H. Arnold, and C. O. Wilke. Breaking proteins with mutations: threads and thresholds in evolution. Mol. Syst. Biol. 3:76, 2007.
  11. J. J. Bull, R. Sanjuán, and C. O. Wilke. Theory of lethal mutagenesis for viruses. J. Virol. 81:2930-2939, 2007.
  12. S. F. Elena, C. O. Wilke, C. Ofria, and R. E. Lenski. Effects of population size and mutation rate on the evolution of mutational robustness. Evolution 61:666-674, 2007.
  13. J. D. Bloom, A. Raval, and C. O. Wilke. Thermodynamics of neutral protein evolution. Genetics 175:255-266, 2007.
  14. R. Foster, C. Adami, and C. O. Wilke. Selection for mutational robustness in finite populations. J. Theor. Biol. 243:181-190, 2006.
  15. C. O. Wilke. Biology through the robustness lens. BioScience 56:695-696, 2006. (book review)
  16. J. D. Bloom, D. A. Drummond, F. H. Arnold, and C. O. Wilke. Structural determinants of the rate of protein evolution in yeast. Mol. Biol. Evol. 23:1751-1761, 2006.
  17. J. R. Bailey, A. R. Sedaghat, T. Kieffer, T. Brennan, P. K. Lee, M. Wind-Rotolo, C. M. Haggerty, A. R. Kamireddi, Y. Liu, J. Lee, D. Persaud, J. E. Gallant, J. Cofrancesco, Jr., T. C. Quinn, C. O. Wilke, S. C. Ray, J. D. Siliciano, R. E. Nettles, and R. F. Siliciano. Residual Human Immunodeficiency Virus Type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4 T cells. J. Virol. 80:6441-6457, 2006.
  18. C. O. Wilke and D. Allan Drummond. Population genetics of translational robustness. Genetics 173:473-481, 2006.
  19. D. A. Drummond, A. Raval, and C. O. Wilke. A Single Determinant Dominates the Rate of Yeast Protein Evolution. Mol. Biol. Evol. 23:327-337, 2006.
  20. C. O. Wilke, R. Forster, and I. S. Novella. Quasispecies in time-dependent environments. Curr. Topics Microbiol. Immun. 299:33-50, 2006.
  21. R. Forster and C. O. Wilke. Tradeoff between short-term and long-term adaptation in a changing environment. Phys. Rev. E 72:041922, 2005.
  22. C. O. Wilke, J. D. Bloom, D. A. Drummond, and A. Raval. Predicting the tolerance of proteins to random amino acid substitution. Biophys. J. 89:3714-3720, 2005.
  23. D. A. Drummond, J. D. Bloom, C. Adami, C. O. Wilke, and F. H. Arnold. Why highly expressed proteins evolve slowly. Proc. Natl. Acad. Sci. USA 102:14338-14343, 2005.
  24. C. O. Wilke. Quasispecies theory in the context of population genetics. BMC Evol. Biol. 5:44, 2005.
  25. C. O. Wilke. The heavy, the cold and the slow. Heredity 95:115, 2005.
  26. D. A. Drummond, J. J. Silberg, M. M. Meyer, C. O. Wilke, and F. H. Arnold. On the conservative nature of intragenic recombination. Proc. Natl. Acad. Sci. USA 102:5380-5385, 2005.
  27. J. D. Bloom, J. J. Silberg, C. O. Wilke, D. A. Drummond, C. Adami, and F. H. Arnold. Thermodynamic prediction of protein neutrality. Proc. Natl. Acad. Sci. USA 102:606-611, 2005.
  28. C. Ofria and C. O. Wilke. Avida: Evolution experiments with self-replicating computer programs. In A. Adamatzky and M. Komosinski, eds. Artificial Life Models in Software. Springer, 2005, pp. 3-36.
  29. C. O. Wilke and S. S. Chow. Exploring the evolution of ecosystems with digital organisms. In M. Pascual and J. Dunne, eds. Ecological Networks. Linking Structure to Dynamics in Food Webs. Oxford University Press, 2005.
  30. C. O. Wilke. Molecular clock in neutral protein evolution. BMC Genetics 5:25, 2004.
  31. C. O. Wilke. Supplementary materials need the right format. Nature 430:291, 2004.
  32. S. S. Chow*, C. O. Wilke*, C. Ofria, R. E. Lenski, and C. Adami. Adaptive Radiation from Resource Competition in Digital Organisms. Science 305:84-86, 2004. *Joint first authorship.
  33. R. Froissart, C. O. Wilke, R. Montville, S. K. Remold, L. Chao, and P. E. Turner. Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics 168:9-19, 2004.
  34. C. O. Wilke. The speed of adaptation in large asexual populations. Genetics 167:2045-2053, 2004.
  35. J. D. Bloom, C. O. Wilke, F. H. Arnold, and C. Adami. Stability and the evolvability of function in a model protein. Biophys. J. 86:2758-2764, 2004.
  36. I. S. Novella, D. D. Reissig, and C. O. Wilke. Density-dependent selection in vesicular stomatitis virus. J. Virol. 78:5799-5804, 2004.
  37. C. O. Wilke, D. D. Reissig, and I. S. Novella. Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations. Evolution 58:900-905, 2004.
  38. C. Adami and C. O. Wilke. Experiments in Evolution. Artificial Life 10:117-122, 2004.
  39. Y. Li and C. O. Wilke. Digital Evolution in Time-Dependent Fitness Landscapes. Artificial Life 10:123-134, 2004.
  40. T. J. Johnson and C. O. Wilke. Evolution of Resource Competition Between Mutually Dependent Digital Organisms. Artificial Life 10:145-156, 2004.
  41. C. Ofria and C. O. Wilke. Avida: A Software Platform for Research in Computational Evolutionary Biology. Artificial Life 10:191-229, 2004.
  42. P. R. A. Campos, C. Adami, and C. O. Wilke. Modeling Stochastic Clonal Interference. In G. Ciobanu and G. Rozenberg, eds., Modeling in Molecular Biology. Springer Series in Natural Computing, 2004. pp. 21-39.
  43. C. O. Wilke and I. S. Novella. Phenotypic mixing and hiding may contribute to memory in viral quasispecies. BMC Microbiology 3:11, 2003.
  44. C. O. Wilke. Does the Red Queen reign in the kingdom of digital organisms?. Lect. Notes. Artif. Int. 2801:405-414, 2003.
  45. C. O. Wilke. Probability of fixation of an advantageous mutant in a viral quasispecies. Genetics 163:467-474, 2003.
  46. C. O. Wilke, R. E. Lenski, and C. Adami. Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding. BMC Evolutionary Biology 3:3, 2003.
  47. C. O. Wilke, C. Adami. Evolution of mutational robustness. Mut. Res. 522:3-11, 2003.
  48. C. Kamp, C. O. Wilke, C. Adami and S. Bornholdt. Viral evolution under the pressure of an adaptive immune system - optimal mutation rates for viral escape. Complexity 8:28-33, 2002.
  49. C. O. Wilke, C. Adami. The biology of digital organisms. Trends. Ecol. Evol. 17:528-532, 2002.
  50. C. O. Wilke, P. R. A. Campos, and J. F. Fontanari. The genealogical process in a correlated fitness landscape. J. exp. Zool. (Mol. Dev. Evol.) 294:274-284, 2002.
  51. C. O. Wilke. Maternal effects in molecular evolution. Phys. Rev. Lett. 88:078101, 2002.
  52. P. R. A. Campos, C. Adami, and C. O. Wilke. Optimal adaptive performance and delocalization in NK fitness landscapes. Physica A 304:495-506, 2002. Erratum: Physica A 318:637, 2003.
  53. C. O. Wilke. Selection for fitness vs. selection for robustness in RNA secondary structure folding. Evolution 55:2412-2420, 2001.
  54. C. O. Wilke, J. L. Wang, C. Ofria, R. E. Lenski, and C. Adami. Evolution of digital organisms at high mutation rate leads to survival of the flattest. Nature 412:331-333, 2001.
  55. C. O. Wilke. Adaptive evolution on neutral networks. Bull. Math. Biol. 63:715-730, 2001.
  56. C. O. Wilke and C. Adami. Interaction between directional epistasis and average mutational effects. Proc. R. Soc. London B 268:1469-1474, 2001.
  57. C. O. Wilke, C. Ronnewinkel and T. Martinetz. Dynamic fitness landscapes in molecular evolution. Phys. Rep. 349:395-446, 2001.
  58. C. O. Wilke and C. Ronnewinkel. Dynamic fitness landscapes: Expansions for small mutation rates. Physica A 290:475-490, 2001.
  59. C. Ronnewinkel, C. O. Wilke and T. Martinetz. Genetic algorithms in time-dependent environments. In L. Kallel, B. Naudts and A. Rogers, editors, Theoretical Aspects of Evolutionary Computing, 2001, pp. 261-285. Natural Computing, Springer Verlag.
  60. C. O. Wilke. Dynamische Fitnesslandschaften. KI 14:20-25, 2000 (in german).
  61. C. O. Wilke and T. Martinetz. Adaptive walks on time-dependent fitness landscapes Phys. Rev. E 60:2154-2159, 1999.
  62. C. O. Wilke and T. Martinetz. Lifetimes of agents under external stress Phys. Rev. E Rapid Communications 59:R2512-R2515, 1999.
  63. C. O. Wilke, C. Ronnewinkel, and T. Martinetz. Molecular Evolution in Time Dependent Environments. In D. Floreano, J.-D. Nicoud and F. Mondada, editors, Advances in Artificial Life, ECAL'99, Lausanne, Switzerland, 1999. Lect. Notes. Artif. Int. 1674:417-421, 1999.
  64. C. Wilke and T. Martinetz. Hierarchical noise in large systems of independent agents. Phys. Rev. E 58:7101-7108, 1998.
  65. C. Wilke, S. Altmeyer, and T. Martinetz. Aftershocks in Coherent-Noise Models. Physica D, 120:401-417, 1998.
  66. S. Altmeyer, C. Wilke, and T. Martinetz. How fast do structures emerge in hypercycle systems? In C. Wilke, S. Altmeyer, and T. Martinetz, editors, Third German Workshop on Artificial Life, 1998. Verlag Harri Deutsch.
  67. C. Wilke, S. Altmeyer, and T. Martinetz. Large-scale evolution and extinction in a hierarchically structured environment. In C. Adami, R. Belew, H. Kitano, and C. Taylor, editors, Proc. of ''Artificial Life VI'', Los Angeles, June 26-29 1998. MIT Press.
  68. C. Wilke and T. Martinetz. Simple model of evolution with variable system size. Phys. Rev. E 56:7128-7131, 1997.
  69. M. Kachelrieß, C. Wilke, and G. Wunner. Axion cyclotron emissivity of magnetized white dwarfs and neutron stars. Phys. Rev. D 56:1313-1319, 1997.
  70. C. Wilke and G. Wunner. Photon splitting in strong magnetic fields: asymptotic approximation formulae vs. accurate numerical results. Phys. Rev. D 55:997-1000, 1997.

Technical reports or unpublished

  1. T. Schoenmeyr and C. O. Wilke. Finite genome size can halt Muller's ratchet. Unpublished.
  2. C. O. Wilke. Evolution in time-dependent fitness landscapes. Internal Report No IR-INI 98-09, Nov. 1998. Institut für Neuroinformatik, Ruhr-Universität Bochum. ISSN 0943-2752.
  3. C. Wilke and T. Martinetz. A coarse-grained model of evolution with variable system size. In P. Dittrich, H. Rauhe, W. Banzhaf, editors, 2nd German Workshop on Artificial Life, Dortmund, 1998. ''SYS Report'', Internal Report of Systems Analysis Research Group, University of Dortmund, Department of Computer Science, D-44221 Dortmund, Germany.
  4. C. Wilke. Untersuchung des Photon-Splitting-Prozesses, speziell im Grenzfall eines extrem starken Magnetfeldes. Diploma thesis (in german), Ruhr-Universität Bochum, 1996.


Claus Wilke 2008-03-04