Publications

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2007

• Who watches the watcher?;
  C. Adami, Science 316 (2007)
• Evolution of virtual creatures and catapults;
  N. Chaumont, R. Egli, and C. Adami, Artificial Life 13 (2007) 139-157.
• Biological programming;
  C. Adami, Nature 446 (2007) 263-264.
• Thermodynamics of neutral protein evolution;
  J.D. Bloom, A. Raval, and C.O. Wilke, Genetics 175 (2007) 255-266.

2006

• What do robots dream of?;
  C. Adami, Science 314 (2006) 1093-1094
• Selection for mutational robustness in finite populations;
  R. Forster, C. Adami, and C.O. Wilke, J. theor. Biol. 243 (2006) 181-190.
• Reducible complexity;
  C. Adami, Science 312 (2006) 61-63.
• Evolving virtual catapults;
  N. Chaumont, R. Egli, and C. Adami, Proc. Artificial Life X, L.M. Rocha et al, eds. (MIT Press, 2006) pp. 262-268.
• Structural determinants of the rate of protein evolution in Yeast;
  J.D. Bloom, D.A. Drummond, F.H. Arnold, and C.O. Wilke, Mol. Biol. Evol. 23 (2006) 1751-1761.
• Population genetics of translational robustness;
  C.O. Wilke and D.A. Drummond, Genetics 173 (2006).
• Digital genetics: Unravelling the genetic basis of evolution;
  C. Adami, Nature Reviews Genetics 7 (2006) 109-118.
• A single determinant dominates the rate of protein evolution;
  D. A. Drummond, A. Raval, and C.O. Wilke, Mol. Biol. Evol. 22 (2006) 327-337.

2005

• Predicting the tolerance of proteins to random amino acid substitution;
  C.O. Wilke, J.D. Bloom, D.A. Drummond, and A. Raval, Biophys. J. 89 (2005) 3714-3720.
• Tradeoff between short-term and long-term adaptation in a changing environment;
  R. Forster and C.O. Wilke, Phys. Rev. E 72 (2005) 041922.
• Quasispecies theory in the context of population genetics;
  C.O. Wilke, BMC Evol. Biol. 5 (2005) 44.
• Why highly expressed proteins evolve slowly;
  D.A. Drummond, J.D. Bloom, C. Adami, C.O. Wilke, and F.H. Arnold, Proc. Natl. Acad. Sci. USA 102 (2005) 14338-14343.
• Quasispecies in time-dependent environments;
  C.O. Wilke, R. Forster, and I.S. Novella, Curr. Topics Microbiol. Immun. 299 (2005) 33-50.
• The heavy, the cold, and the slow;
  C.O. Wilke, Heridity 95 (2005) 115.
• Avida: Evolution experiments with self-replicating computer programs;
  C. Ofria and C.O. Wilke, in Artificial Life Models in Software, A. Adamatzky and M. Komosinski, eds., Springer Verlag (2005) 3-36.
• Exploring the evolution of ecosystems with digital organisms;
  C.O. Wilke and S.S. Chow, in Ecological Networks: Linking Structure to Dynamics in Food Webs. M. Pascual and J.A. Donne, eds., Oxford University Press (2005), pp. 271-286.
• On the conservative nature of intragenic recombination;
  D.A. Drummond, J.J. Silberg, M.M. Meyer, C.O. Wilke, and F.H. Arnold, Proc. Natl. Acad. Sci. USA 102 (2005) 5380-5385.
• Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins;
  D.A. Drummond, B.I. Iverson, G. Georgiou, and F.H. Arnold, J. Mol. Biol. 350 (2005) 806-816.
• Thermodynamic prediction of protein neutrality;
  J.D. Bloom, J.J. Silberg, C.O. Wilke, D.A. Drummond, C. Adami, and F.H. Arnold, Proc. Natl. Acad. Sci. USA 102 (2005) 606-611

2004

• Molecular clock in neutral protein evolution
  C.O. Wilke, BMC Genetics 5 (2004) 25
• Supplementary Materials Need The Right Format;
  C.O. Wilke, Nature 430 (2004) 291.
• Evolution of Robust Developmental Neural Networks;
  A.N. Hampton and C. Adami, Proc. Artificial Life IX, Boston, MA, Sep 12-15, 2004. J. Pollack, M.A. Bedau, P. Husbands, T. Ikegami, and R. Watson, eds., pp. 438-443.
• Co-infection Weakens Selection Against Epistatic Mutations in RNA Viruses;
  R. Froissart, C.O. Wilke, R. Montville, S.K. Remold, L. Chao, and P.E. Turner, Genetics 168 (2004)
• The Speed of Adaptation in Large Asexual Populations;
  C.O. Wilke, Genetics 167 (2004) 2045-2053
• Evolutionary Rate Depends on Number of Protein-Protein Interactions Independently of Gene Expression Level: Response;
  J.D. Bloom and C. Adami. BMC Evol. Biol. 4 (2004) 14.
• Adaptive Radiation from Resource Competition in Digital Organisms;
  S.S. Chow, C.O. Wilke, C. Ofria, R.E. Lenski, C. Adami. Science 305 (2004) 84-86
• Density-dependent Selection in Vesicular Stomatitis Virus;
  I.S. Novella, D.D. Reissig, and C.O. Wilke J. Virology 78 (2004) 5799-5804
  
• Replication at Periodically Changing Multiplicity of Infection Promotes Stable Coexistence of Competing Viral Populations;
  C.O. Wilke, D.D. Reissig, and I.S. Novella, Evolution 58 (2004) 900-905.
• Stability and the Evolvability of Function in a Model Protein;
  J.D. Bloom, C.O. Wilke, F.H. Arnold, and C. Adami, Biophysical Journal 86 (2004) 2758-2764.
• Experiments in Digital Evolution (Editors' Introduction);
  C. Adami and C.O. Wilke, Artif. Life 10 (2004) 117-122.
• Digital Evolution in Time-Dependent Fitness Landscapes;
  Y. Li and C.O. Wilke, Artif. Life 10 (2004) 123-134.
• Bifurcation into Functional Niches in Adaptation;
  J.S. White and C. Adami, Artif. Life 10 (2004) 135-144.
• Evolution of Resource Competition Between Mutually Dependent Digital Organisms;
  T.J. Johnson and C.O. Wilke, Artif. Life 10 (2004) 145-156.
• Using Avida to Test the Effects of Natural Selection on Phylogenetic Reconstruction Methods;
  G.I. Hagstrom, D.H. Hang, C. Ofria, and E. Torng, Artif. Life 10 (2004) 157-166.
• Evolution of Robustness in Digital Organisms;
  J.A. Edlund and C. Adami, Artif. Life 10 (2004) 167-179.
• Influence of Chance, History, and Adaptation on Digital Evolution;
  D.A. Wagenaar and C. Adami, Artif. Life 10 (2004) 181-190.
• Avida: A Software Platform for Research in Computational Evolutionary Biology;
  C. Ofria and C.O. Wilke, Artif. Life 10 (2004) 191-229.
• Information Theory in Molecular Biology;
  C. Adami, Physics of Life Reviews 1 (2004) 3-22.
  
• Modeling Stochastic Clonal Interference;
  P.R.A. Campos, C. Adami, and C.O. Wilke, in Modeling in Molecular Biology (Springer Series in Natural Computing, 2004) G. Ciobanu and G. Rozenberg, eds., pp. 21-39.
  

2003

• Principal component analysis and neural networks for detection of amino acid biosignatures;
  E.D. Dorn, G.D. McDonald, M.C. Storrie-Lombardi, and K.H. Nealson, Icarus 166 (2004), 403-409.
• Apparent Dependence of Protein Evolutionary Rate on Number of Interactions is Linked to Biases in Protein-Protein Interaction Data Sets;
  J.D. Bloom and C. Adami, BMC Evol Biol. 3 (2003) 21.
  
• Does the Red Queen Reign in the Kingdom of Digital Organisms?;
  C.O. Wilke, Lect. Notes Artif. Intell. 2801 (2003) 405-414.
  
• Phenotypic Mixing and Hiding May Contribute to Memory in Viral Quasispecies;
  C.O. Wilke and I.S. Novella, BMC Microbiology 3 (2003) 11.
  
• The Evolutionary Origin of Complex Features;
  R.E. Lenski, C. Ofria, R.T. Pennock, and C. Adami, Nature 423 (2003) 139-145.
  
• Selective Pressures on Genomes in Molecular Evolution;
  C. Ofria, C. Adami, T.C. Collier, J. Theor. Biol. 222 (2003) 477-483.
• Sequence Complexity in Darwinian Evolution;
  C. Adami, Complexity (Wiley) 8 (2002) 49-56.
• Probability of Fixation of an Advantageous Mutant in a Viral Quasispecies;
  C. O. Wilke, Genetics 163 (2003) 467-474.
• Viral Evolution Under the Pressure of an Adaptive Immune System--Optimal Mutation Rate for Viral Escape;
  C. Kamp, C.O. Wilke, C. Adami, S. Bornholdt, Complexity (Wiley) 8 (2002) 28-33.
• Compensatory Mutations Cause Excess of Antagonistic Epistasis in RNA Secondary Structure Folding;
  C.O. Wilke, R.E. Lenski, C. Adami, BMC Evol. Biol. 3 (2003) 3
  
• Small-World Effects in the Majority-Vote Model;
  P.R.A. Campos, V.M. de Oliveira, and F.G. Brady Moreira, Physical Review E 67 (2003) 026104
  
• Evolution of Mutational Robustness;
  C.O. Wilke and C. Adami, Mutation Research 522 (2003) 3-11
  

2002

• What is Complexity?;
  C. Adami, BioEssays 24 (2002) 1085-1094.
  
• The Biology of Digital Organisms;
  C.O. Wilke and C. Adami, Trends in Ecology and Evolution 17 (2002) 528-5 32.
  
• The Genealogical Process on a Correlated Fitness Landscape;
  C. O. Wilke, P. R. A. Campos, and J. F. Fontanari, J. exp. Zool., Mol. Dev. Evolution 294 (2002) 274-284.
• Design of Evolvable Computer Languages;
  C. Ofria, C. Adami, and T.C. Collier, IEEE Trans. Evol. Comp. 6 (2002) 420-424.
• Critical and Near-Critical Branching Processes;
  C. Adami and J. Chu, Physical Review E 66 (2002) 011907
  
• Ab Initio Modeling of Ecosystems with Artificial Life;
  C. Adami, Natural Resource Modeling 15 (2002) 133-146.
• Simulations of Evolution;
  C. Adami, in M. Pagel, S. Frank, C. Godfray, B. K. Hall, K. Hawkes, D. M. Hillis, A. Kodric-Brown, R. E. Lenski, and A. Pomiankowski, eds. Encyclopedia of Evolution, (Oxford University Press, 2002) p. 1064-1066.
  
• Maternal Effects in Molecular Evolution;
  C. O. Wilke, Phys. Rev. Lett. 88 (2002) 078101.
• Optimal Adaptive Performance and Delocalization in NK Fitness Landscapes;
  P. R. A. Campos, C. Adami, and C. O. Wilke, Physica A 304 (2002 ) 177-188.
  

2001

• Selection for Fitness vs. Selection for Robustness in RNA Secondary Structure Folding;
  C.O. Wilke, Evolution 55 (2001) 2412-2420.
  
• Evolution of Digital Organisms at High Mutation Rate Leads To Survial of the Flattest;
  C.O. Wilke, J.L. Wang, C. Ofria, R.E. Lenski, and C. Adami, Nature 412 (2001) 331-333.
  
• Interaction Between Directional Epistasis and Average Mutational Effects;
  C.O. Wilke and C. Adami, Proc. Roy. Soc. London. Ser. B 268 (2001) 1469-1474.
• Adaptive Evolution on Neutral Networks;
  C.O. Wilke, Bulletin of Mathematical Biology 63 (2001) 715-730.
• Molecular Evolution in Dynamic Fitness Landscapes;
  C.O. Wilke, C. Ronnewinkel, and T. Martinetz, Physics Reports 349 (2001) 395-446
  
• Dynamic Fitness Landscapes: Expansions for Small Mutation Rates;
  C.O. Wilke and C. Ronnewinkel, Physica A 290 (2001) 475-490

1994-2000