Table of contents
    1. 1. Reading
    2. 2. Bibliography

    24 June 2009 - Michael Gribskov

    Reading

    • W. Fontana and P. Schuster, “Continuity in Evolution: On the Nature of Transitions”, Science, 280, 1451-1455 (1998).[PDF]
    • W. Fontana and P. Schuster, “Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping”, J. Theor. Biol., 194, 491-515 (1998) [PDF]
    • Fontana W, Stadler PF, …, Schuster P. "RNA folding and combinatory landscapes", Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1993 Mar; 47(3): 2083-2099 [Online]
    • L.W. ANCEL and W. FONTANA, "Plasticity, Evolvability, and Modularity in RNA", J. Exp. Zoology (Mol Dev Evol) 288:242–283 (2000) [PDF]

    Bibliography

    1. Eigen M. Self organization of matter and the evolution of biological macromolecules. Naturwissenschaften 58: 465–523 (1971).
    2. Fontana W, Stadler PF, Tarazona P, Weinberger ED, Schuster P. RNA folding and combinatory landscapes, Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 47: 2083-2099 (1993) http://prola.aps.org/abstract/PRE/v47/i3/p2083_1
    3. Huynen MA, Hogeweg P. Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes. J Mol Evol. 39: 71-79 (1994)
    4. Schuster P, Fontana W, Stadler PF, Hofacker I. From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures, Proc. Roy. Soc. (London) B, 255: 279-284 (1994).
    5. Gruner W, Giegerich U, Strothmann D, Reidys C, Weber J, et al. Analysis of RNA sequence structure maps by exhaustive enumeration. I. Neutral Networks. Monatshefte fur Chemie 127: 355–374 (1996).
    6. Gruner W, Giegerich U, Strothmann D, Reidys C, Weber J, et al. Analysis of RNA sequence structure maps by exhaustive enumeration. II. Structure of neutral networks and shape space covering. Monatshefte fur Chemie 127: 375–389 (1996).
    7. Huynen MA. Exploring phenotype space through neutral evolution. J Mol Evol. 43: 165-169 (1996).
    8. Huynen MA, Stadler PF, Fontana W Smoothness within ruggedness: the role of neutrality in adaptation. Proc Natl Acad Sci USA 93: 397–401 (1996).
    9. Reidys C, Stadler PF, Schuster P. Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bull Math Biol. 59: 339-97 (1997).
    10. Fontana W, Schuster P. Continuity in Evolution: On the Nature of Transitions, Science, 280, 1451-1455 (1998).
    11. Fontana W, Schuster P. Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping, J. Theor. Biol. 194: 491-515 (1998)
    12. van Nimwegen E, Crutchfield J, Huynen M. Neutral evolution of mutational robustness. Proc Natl Acad Sci USA 17: 9716–9720 (1999).
    13. Ancel L, Fontana W. Plasticity, Modularity and Evolvability in RNA. Journal of Experimental Zoology 288: 242–283 (2000).
    14. Reidys C, Forst CV, Schuster P. Replication and mutation on neutral networks. Bull Math Biol. 63: 57-94 (2001).
    15. Stadler BMR, Stadler P, Wagner GP, Fontana W. The topology of the possible: Formal spaces underlying patterns of evolutionary change. Journal of Theoretical Biology 213: 241–274 (2001).
    16. Fontana W. Modeling ‘evo-devo’ with RNA. Bioessays 24: 1164–1177 (2002).
    17. Cowperthwaite MC, Bull JJ, Meyers LA. Distributions of Beneficial Fitness Effects in RNA. Genetics 170: 1449–1457 (2005).
    18. Wagner A. Robustness, evolvability, and neutrality. FEBS Letters 579:1772–1778 (2005).
    19. Cowperthwaite MC, Bull JJ, Meyers LA. From bad to good: Fitness reversals and the ascent of deleterious mutations. PLoS Computational Biology 2: 1292–1300 (2006).
    20. Wagner A. Robustness and evolvability: a paradox resolved. Proc Biol Sci 275: 91–100 (2008).

     

     


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