Research Topics
| C O WilkeSummaryAffiliation: California Institute of Technology Country: USA Publications
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Detail Information
Publications
Interaction between directional epistasis and average mutational effectsC O Wilke
Digital Life Laboratory 136 93, California Institute of Technology, Pasadena, CA 91125, USA
Proc Biol Sci 268:1469-74. 2001....
Phenotypic mixing and hiding may contribute to memory in viral quasispeciesClaus 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...- Probability of fixation of an advantageous mutant in a viral quasispeciesClaus 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... - Compensatory mutations cause excess of antagonistic epistasis in RNA secondary structure foldingClaus 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... 
Evolution of mutational robustnessClaus 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...- Genealogical process on a correlated fitness landscapeClaus 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... - Maternal effects in molecular evolutionClaus 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... - Replication at periodically changing multiplicity of infection promotes stable coexistence of competing viral populationsClaus 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... - Evolution of digital organisms at high mutation rates leads to survival of the flattestC 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... - Adaptive evolution on neutral networksC 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... - Selection for fitness versus selection for robustness in RNA secondary structure foldingC 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... - Tradeoff between short-term and long-term adaptation in a changing environmentRobert 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... - On the conservative nature of intragenic recombinationD 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.... - Thermodynamic prediction of protein neutralityJesse 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... - Adaptive radiation from resource competition in digital organismsStephanie 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... - Why highly expressed proteins evolve slowlyD 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... - Digital evolution in time-dependent fitness landscapesYe 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... - Evolution of resource competition between mutually dependent digital organismsTyler 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... - Stability and the evolvability of function in a model proteinJesse 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... - Selection for mutational robustness in finite populationsRobert 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... - Thermodynamics of neutral protein evolutionJesse 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... - Structural determinants of the rate of protein evolution in yeastJesse 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... - The speed of adaptation in large asexual populationsClaus 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... - A single determinant dominates the rate of yeast protein evolutionD 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... - Rapid adaptive amplification of preexisting variation in an RNA virusRanendra 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... - Population genetics of translational robustnessClaus 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... - Effects of population size and mutation rate on the evolution of mutational robustnessSantiago 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... - Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolutionD Allan Drummond
FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
Cell 134:341-52. 2008.... - Predicting the tolerance of proteins to random amino acid substitutionClaus 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... - Quasispecies theory in the context of population geneticsClaus O Wilke
BMC Evol Biol 5:44. 2005.... - Avida: a software platform for research in computational evolutionary biologyCharles 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... - Molecular clock in neutral protein evolutionClaus 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... - The stochastic edge in adaptive evolutionEric 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... - The traveling-wave approach to asexual evolution: Muller's ratchet and speed of adaptationIgor 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... 
Contact density affects protein evolutionary rate from bacteria to animalsTong 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...- Low-level HIV-1 replication and the dynamics of the resting CD4+ T cell reservoir for HIV-1 in the setting of HAARTAhmad 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... - Limits on replenishment of the resting CD4+ T cell reservoir for HIV in patients on HAARTAhmad 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... - Breaking proteins with mutations: threads and thresholds in evolutionJesse D Bloom
Mol Syst Biol 3:76. 2007 - 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 cellsJustin 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)... - Co-infection weakens selection against epistatic mutations in RNA virusesRemy 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... - Supplementary materials need the right formatClaus O Wilke
Nature 430:291. 2004 - Density-dependent selection in vesicular stomatitis virusIsabel 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...