C O Wilke

Summary

Affiliation: California Institute of Technology
Country: USA

Publications

  1. pmc Interaction between directional epistasis and average mutational effects
    C O Wilke
    Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Biol Sci 268:1469-74. 2001
  2. pmc Phenotypic mixing and hiding may contribute to memory in viral quasispecies
    Claus O Wilke
    Digital Life Laboratory, California Institute of Technology, Mail Code 136 93, Pasadena, California 91125, USA
    BMC Microbiol 3:11. 2003
  3. pmc Probability of fixation of an advantageous mutant in a viral quasispecies
    Claus O Wilke
    Digital Life Laboratory, Caltech, Pasadena, California 91125, USA
    Genetics 163:467-74. 2003
  4. pmc Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding
    Claus O Wilke
    Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Evol Biol 3:3. 2003
  5. ncbi request reprint Evolution of mutational robustness
    Claus O Wilke
    Digital Life Laboratory, California Institute of Technology, Mail Code 136 93, Pasadena, CA 91125, USA
    Mutat Res 522:3-11. 2003
  6. ncbi request reprint Genealogical process on a correlated fitness landscape
    Claus O Wilke
    Digital Life Lab, California Institute of Technology, Pasadena, California 91125, USA
    J Exp Zool 294:274-84. 2002
  7. ncbi request reprint Maternal effects in molecular evolution
    Claus O Wilke
    Digital Life Laboratory, Mail Code 136 93, Pasadena, California 91125, USA
    Phys Rev Lett 88:078101. 2002
  8. ncbi request reprint Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations
    Claus O Wilke
    Digital Life Laboratory, California Institute of Technology, Mail Code 136 93, Pasadena, California 91125, USA
    Evolution 58:900-5. 2004
  9. ncbi request reprint Evolution of digital organisms at high mutation rates leads to survival of the flattest
    C O Wilke
    Digital Life Laboratory, Mail Code 136 93, California Institute of Technology, Pasadena, California 91125, USA
    Nature 412:331-3. 2001
  10. ncbi request reprint Adaptive evolution on neutral networks
    C O Wilke
    Digital Life Lab, California Institute of Technology, Pasadena 91125, USA
    Bull Math Biol 63:715-30. 2001

Collaborators

Detail Information

Publications42

  1. pmc Interaction between directional epistasis and average mutational effects
    C O Wilke
    Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Biol Sci 268:1469-74. 2001
    ....
  2. pmc Phenotypic mixing and hiding may contribute to memory in viral quasispecies
    Claus O Wilke
    Digital Life Laboratory, California Institute of Technology, Mail Code 136 93, Pasadena, California 91125, USA
    BMC Microbiol 3:11. 2003
    ..While the quasispecies theory predicts the existence of these memory genomes, there is a disagreement between the expected and observed mutant frequency values. Therefore, the origin of quasispecies memory is not fully understood...
  3. pmc Probability of fixation of an advantageous mutant in a viral quasispecies
    Claus O Wilke
    Digital Life Laboratory, Caltech, Pasadena, California 91125, USA
    Genetics 163:467-74. 2003
    ..The performance of these two approximations is compared to the exact fixation probability on a network of RNA sequences with identical secondary structure...
  4. pmc Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure folding
    Claus O Wilke
    Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
    BMC Evol Biol 3:3. 2003
    ..However, in a number of recent studies, a prevalence of antagonistic epistasis (the tendency of multiple mutations to have a mitigating rather than reinforcing effect) has been observed...
  5. ncbi request reprint Evolution of mutational robustness
    Claus O Wilke
    Digital Life Laboratory, California Institute of Technology, Mail Code 136 93, Pasadena, CA 91125, USA
    Mutat Res 522:3-11. 2003
    ..We discuss empirical evidence for the evolution of mutational robustness, and speculate on its relevance for higher organisms...
  6. ncbi request reprint Genealogical process on a correlated fitness landscape
    Claus O Wilke
    Digital Life Lab, California Institute of Technology, Pasadena, California 91125, USA
    J Exp Zool 294:274-84. 2002
    ..It resembles the one for high mutation rates in that the population drifts rapidly, but nevertheless selection still shapes the distribution of fitness values...
  7. ncbi request reprint Maternal effects in molecular evolution
    Claus O Wilke
    Digital Life Laboratory, Mail Code 136 93, Pasadena, California 91125, USA
    Phys Rev Lett 88:078101. 2002
    ..In addition to biological applications, our model is important for understanding the dynamics of self-replicating computer programs...
  8. ncbi request reprint Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populations
    Claus O Wilke
    Digital Life Laboratory, California Institute of Technology, Mail Code 136 93, Pasadena, California 91125, USA
    Evolution 58:900-5. 2004
    ..Our results suggest that frequency-dependent selection may be common in typical evolution experiments with viruses...
  9. ncbi request reprint Evolution of digital organisms at high mutation rates leads to survival of the flattest
    C O Wilke
    Digital Life Laboratory, Mail Code 136 93, California Institute of Technology, Pasadena, California 91125, USA
    Nature 412:331-3. 2001
    ..These genotypes, although they occupied lower fitness peaks, were located in flatter regions of the fitness surface and were therefore more robust with respect to mutations...
  10. ncbi request reprint Adaptive evolution on neutral networks
    C O Wilke
    Digital Life Lab, California Institute of Technology, Pasadena 91125, USA
    Bull Math Biol 63:715-30. 2001
    ..The transitions between epochs, however, are generally accompanied by a significant increase in the average fitness. We verify our theoretical considerations with two analytically tractable bitstring models...
  11. ncbi request reprint Selection for fitness versus selection for robustness in RNA secondary structure folding
    C O Wilke
    Digital Life Laboratory, California Institute of Technology, Pasadena 91125, USA
    Evolution 55:2412-20. 2001
    ..The analytical results are in excellent agreement with flow-reactor simulations of replicating RNA sequences...
  12. ncbi request reprint Tradeoff between short-term and long-term adaptation in a changing environment
    Robert Forster
    Digital Life Laboratory, California Institute of Technology, Pasadena, California 91125, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 72:041922. 2005
    ..Our model is relevant for arboviruses, which alternate between different host species on a regular basis...
  13. pmc On the conservative nature of intragenic recombination
    D Allan Drummond
    Program in Computation and Neural Systems, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 102:5380-5. 2005
    ....
  14. pmc Thermodynamic prediction of protein neutrality
    Jesse D Bloom
    Division of Chemistry and Chemical Engineering 210 41, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 102:606-11. 2005
    ..Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications...
  15. ncbi request reprint Adaptive radiation from resource competition in digital organisms
    Stephanie S Chow
    Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
    Science 305:84-6. 2004
    ..A diverse pool of limiting resources is sufficient to cause adaptive radiation, which is manifest by the origin and maintenance of phenotypically and phylogenetically distinct groups of organisms...
  16. pmc Why highly expressed proteins evolve slowly
    D Allan Drummond
    Program in Computation and Neural Systems and Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 4100, USA
    Proc Natl Acad Sci U S A 102:14338-43. 2005
    ..Our results suggest that proteins evolve at rates largely unrelated to their functions and can explain why highly expressed proteins evolve slowly across the tree of life...
  17. ncbi request reprint Digital evolution in time-dependent fitness landscapes
    Ye Li
    California Institute of Technology, Pasadena, CA 91125, USA
    Artif Life 10:123-34. 2004
    ..Finally, we witness long-term adaptation to fluctuating environments not anticipated in previous theoretical work...
  18. ncbi request reprint Evolution of resource competition between mutually dependent digital organisms
    Tyler J Johnson
    California Institute of Technology, Pasadena, CA 91125, USA
    Artif Life 10:145-56. 2004
    ..In this case, the relative fitness of the organisms in the presence of resources plays an important role in the time-averaged abundance levels as well...
  19. pmc Stability and the evolvability of function in a model protein
    Jesse D Bloom
    Department of Chemistry, California Institute of Technology, Pasadena, California 91125, USA
    Biophys J 86:2758-64. 2004
    ..Our model also demonstrates that even in the absence of a fundamental biophysical tradeoff between stability and function, the speed with which function can evolve is limited by the stability requirement imposed on the protein...
  20. ncbi request reprint Selection for mutational robustness in finite populations
    Robert Forster
    Digital Life Laboratory, California Institute of Technology, Pasadena, CA 91125, USA
    J Theor Biol 243:181-90. 2006
    ..Our results show that quasispecies effects and neutral drift can occur concurrently, and that the relative importance of each is determined by the product of population size and mutation rate...
  21. pmc Thermodynamics of neutral protein evolution
    Jesse D Bloom
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
    Genetics 175:255-66. 2007
    ..All our theoretical predictions are confirmed by simulations with lattice proteins. Our work provides a mathematical foundation for understanding how protein biophysics shapes the process of evolution...
  22. ncbi request reprint Structural determinants of the rate of protein evolution in yeast
    Jesse D Bloom
    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
    Mol Biol Evol 23:1751-61. 2006
    ..Our results provide evidence that protein structure plays an important role in shaping the rate of sequence evolution and provide evidence to support recent theoretical advances linking structural designability to contact density...
  23. pmc The speed of adaptation in large asexual populations
    Claus O Wilke
    Digital Life Laboratory, California Institute of Technology, Pasadena, California 91125, USA
    Genetics 167:2045-53. 2004
    ..Moreover, I derive a simple formula that determines whether at given N beneficial mutations are expected to compete with each other or go to fixation independently. Finally, I verify all results with numerical simulations...
  24. ncbi request reprint A single determinant dominates the rate of yeast protein evolution
    D Allan Drummond
    Program in Computation and Neural Systems, California Institute of Technology, Pasadena, USA
    Mol Biol Evol 23:327-37. 2006
    ..Our results support the hypothesis that translational selection governs the rate of synonymous and protein sequence evolution in yeast...
  25. pmc Rapid adaptive amplification of preexisting variation in an RNA virus
    Ranendra N Dutta
    Department of Medical Microbiology and Immunology, University of Toledo Health Science Campus, Toledo, OH 43614, USA
    J Virol 82:4354-62. 2008
    ..39, 9%, and 0.06%, respectively. The method can be generalized and applied easily to other rapidly evolving microbes, including both asexual microorganisms and those with recombination...
  26. pmc Population genetics of translational robustness
    Claus O Wilke
    Section of Integrative Biology and Center for Computational Biology and Bioinformatics, University of Texas, Austin 78712, USA
    Genetics 173:473-81. 2006
    ..Here, we study a simple theoretical model of translational robustness that allows us to gain analytic insight into how this paradoxical behavior arises...
  27. ncbi request reprint Effects of population size and mutation rate on the evolution of mutational robustness
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, 46022 Valencia, Spain
    Evolution 61:666-74. 2007
    ..These results are independent of whether genomes were constrained to their original length or allowed to change in size...
  28. pmc Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    D Allan Drummond
    FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
    Cell 134:341-52. 2008
    ....
  29. pmc Predicting the tolerance of proteins to random amino acid substitution
    Claus O Wilke
    Keck Graduate Institute of Applied Life Sciences, Claremont, California, USA
    Biophys J 89:3714-20. 2005
    ..We test the accuracy of all approximations against our simulation results, and find good overall agreement between the approximations and the simulation measurements...
  30. pmc Quasispecies theory in the context of population genetics
    Claus O Wilke
    BMC Evol Biol 5:44. 2005
    ..A number of recent papers have cast doubt on the applicability of the quasispecies concept to virus evolution, and have argued that population genetics is a more appropriate framework to describe virus evolution than quasispecies theory...
  31. ncbi request reprint Avida: a software platform for research in computational evolutionary biology
    Charles Ofria
    Department of Computer Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
    Artif Life 10:191-229. 2004
    ..We explain the general principles on which Avida is built, as well as its main components and their interactions. We also explain how experiments are set up, carried out, and analyzed...
  32. pmc Molecular clock in neutral protein evolution
    Claus O Wilke
    Keck Graduate Institute of Applied Life Sciences, 535 Watson Drive, Claremont, California 91711, USA
    BMC Genet 5:25. 2004
    ..However, the simulation method of Bastolla et al. is representative only for cases in which the product of mutation rate micro and population size Ne is small. How the substitution process behaves when micro Ne is large is not known...
  33. pmc The stochastic edge in adaptive evolution
    Eric Brunet
    Laboratoire de Physique Statistique, Ecole Normale Superieure, 75230 Paris Cedex 05, France
    Genetics 179:603-20. 2008
    ..Our results are compatible with predictions made using a different analytical approach (Rouzine et al.) and agree well with numerical simulations...
  34. pmc The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptation
    Igor M Rouzine
    Department of Molecular Biology and Microbiology, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
    Theor Popul Biol 73:24-46. 2008
    ..We predict the adaptation rate to grow logarithmically in the population size until the population size is extremely large...
  35. doi request reprint Contact density affects protein evolutionary rate from bacteria to animals
    Tong Zhou
    Center for Computational Biology and Bioinformatics, Section of Integrative Biology, University of Texas at Austin, Austin, TX 78731, USA
    J Mol Evol 66:395-404. 2008
    ..Our study provides evidence that contact density can increase evolutionary rates, and that it acts similarly on the level of entire proteins and of individual protein domains...
  36. pmc Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAART
    Ahmad R Sedaghat
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore Maryland 21205, USA
    BMC Infect Dis 8:2. 2008
    ..However, the mechanism underlying the long half-life of the latent reservoir is unknown. The most likely potential mechanisms are low-level viral replication and the intrinsic stability of latently infected cells...
  37. pmc Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAART
    Ahmad R Sedaghat
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
    PLoS Pathog 3:e122. 2007
    ..Thus, intensification of standard HAART regimens should have minimal effects on the decay of the latent reservoir...
  38. pmc Breaking proteins with mutations: threads and thresholds in evolution
    Jesse D Bloom
    Mol Syst Biol 3:76. 2007
  39. pmc 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
    Justin R Bailey
    Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    J Virol 80:6441-57. 2006
    ..The sequences have been deposited in GenBank. The accession numbers are DQ 391282 to DQ 391351 (for env) and DQ 391352 to DQ 392955 (for RT)...
  40. pmc Co-infection weakens selection against epistatic mutations in RNA viruses
    Remy Froissart
    Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut 06520, USA
    Genetics 168:9-19. 2004
    ..We discuss our results in light of virus disease management and the evolutionary advantage of haploidy in biological populations...
  41. ncbi request reprint Supplementary materials need the right format
    Claus O Wilke
    Nature 430:291. 2004
  42. pmc Density-dependent selection in vesicular stomatitis virus
    Isabel S Novella
    Department of Microbiology and Immunology, Medical College of Ohio, 3055 Arlington Ave, Toledo, OH 43614, USA
    J Virol 78:5799-804. 2004
    ..We found good agreement between our experimental results and the model predictions, which suggests that the wild type and MARM N freely share all of their gene products under coinfection...