All papers are copyrighted by the authors; revised versions that appear in print are copyrighted by the publication in which each appears. Electronic versions may not correspond exactly to the published versions. If you would like to use all or a portion of any paper, please contact the author(s).
- S. Krishnamurthy, E. Smith, D. Krakauer and W. Fontana
Non-equilibrium phase transitions in a cellular signaling chain
submitted (2003)
- [pdf]
- J. Lobo, J. H. Miller and W. Fontana
Neutrality in Technological Landscapes
submitted (2004)
- [pdf]
- J. Arjan G. M. de Visser, J. Hermisson, G. P. Wagner, L. W. Ancel, H. Bagheri, J. L. Blanchard, L. Chao, J. M. Cheverud, S. F. Elena, W. Fontana, G. Gibson, T. F. Hansen, D. Krakauer, R. C. Lewontin, C. Ofria, S. H. Rice, G. von Dassow, A. Wagner, and M. C. Whitlock
Perspective: Evolution and Detection of Genetic Robustness
Evolution, 57(9), 1959-1972 (2003)
- [pdf]
- W. Fontana
Modelling 'Evo-Devo' with RNA
BioEssays, 24, 1164-1177 (2002)
- [pdf]
Contents of the special issue on Modelling complex biological systems - [pdf]
- Nina V. Fedoroff and W. Fontana
Small numbers of big molecules
Science, 297, 1129-1131 (2002)
- (A perspective on genetic noise.)
- [pdf]
- (A perspective on genetic noise.)
- W. Fontana
The topology of the possible
to appear as a chapter in some book...
- (This paper attempts to address a general scientific readership.)
- [pdf] (version 05/19/03)
- (This paper attempts to address a general scientific readership.)
- B. M. R. Stadler, P. F. Stadler, G. Wagner and W. Fontana
The topology of the possible: Formal spaces underlying patterns of evolutionary change
Journal of Theoretical Biology, 213 (2), 241-274 (2001)
[abstract] [pdf]
- L. W. Ancel and W. Fontana
Evolutionary Lock-in and the Origin of Modularity in RNA Structure
in: Modularity: Understanding the Development and Evolution of Complex Natural Systems.- W. Callebaut and D. Rasskin-Gutman (eds.). MIT Press, Cambridge (2002)
[pdf] [US ps.gz] - W. Callebaut and D. Rasskin-Gutman (eds.). MIT Press, Cambridge (2002)
- L. W. Ancel and W. Fontana
Plasticity, Evolvability and Modularity in RNA
Journal of Experimental Zoology (Molecular and Developmental Evolution), 288, 242-283 (2000)
[abstract] [reprint pdf (1MB) 41 pp] [US ps (13MB)] [US ps.gz (3MB) 84 pp] [pdf (2MB) 84 pp]
- [figures only (pdf) (2.1MB)]
- [figures only (pdf) (2.1MB)]
- C. Flamm, W. Fontana, I. L. Hofacker and P. Schuster
RNA Folding at Elementary Step Resolution,
RNA, 6, 325-338 (2000)
[abstract] [pdf]
- P. Schuster and W. Fontana
Chance and Necessity in Evolution: Lessons from RNA,
Physica D:Nonlinear Phenomena, 133, 427-452 (1999)
(Special Issue on "Predictability: Quantifying Uncertainty in Models of Complex Phenomena")
[abstract] [pdf]
- S. Wuchty, W. Fontana, I. L. Hofacker and P. Schuster
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures,
Biopolymers, 49, 145-165 (1999)
[abstract] [pdf]
- W. Fontana and P. Schuster
Continuity in Evolution: On the Nature of Transitions,
Science, 280, 1451-1455 (1998)
[abstract] [pdf]
color figure 1 [US ps.gz] [A4 ps.gz]. See also additional material on the web.
- W. Fontana and P. Schuster
Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping,
J. Theor. Biol., 194, 491-515 (1998)
[abstract] [pdf]
- W. Fontana and Leo W. Buss
The barrier of objects: From dynamical systems to bounded organizations,
in: Boundaries and Barriers, J. Casti and A. Karlqvist (eds.), pp. 56-116, Addison-Wesley, 1996
[abstract] [US ps.gz] [pdf]
The tutorial appendices [pdf] on
-calculus (Appendix A), type theory (Appendix B) and proof-theory (Appendix C) can also be obtained with the main text as IIASA WP-96-027 [pdf] or as paper 41 from the Yale Center for Computational Ecology.
- M. Huynen, P. F. Stadler and W. Fontana
Smoothness within Ruggedness: The role of neutrality in adaptation,
Proc. Natl. Acad. Sci. USA, 93, 397-401 (1996)
[abstract] [pdf]
- W. Fontana
Molekulare Semantik - Evolution zwischen Variation und Konstruktion,
in: Evolution: Entwicklung und Organisation in der Natur,
V. Braitenberg and I. Hosp (eds.), rororo - science 1 9706 5, 69-106 (1994)
[A4 ps.gz]
- reprinted in Spanish: "Orígenes de la vida. En el centenario de Aleksandr Ivanovich Oparin.", F. Morán, J. Peretó, and Á. Moreno (eds.), pp. 269-302, Editorial Complutense, 1995.
- W. Fontana, G. Wagner and L. W. Buss
Beyond Digital Naturalism,
Artificial Life, 1/2, 211-227 (1994)
[abstract] [US ps.gz] [A4 ps.gz]
- reprinted in: "Artificial Life: an Overview", Chris Langton (editor), pp. 211-227, MIT Press, Cambridge, MA, 1995.
- I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker and P. Schuster
Fast Folding and Comparison of RNA Secondary Structures,
Chemical Monthly, 125, 167-188 (1994)
[abstract] [A4 ps.gz]
- W. Fontana and L. W. Buss
'The Arrival of the Fittest': Toward a Theory of Biological Organization
Bull. Math. Biol., 56, 1-64 (1994)
[abstract] [US ps.gz] [A4 ps.gz]
- P. Schuster, W. Fontana, P. F. Stadler and I. Hofacker
From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures
Proc. Roy. Soc. (London) B, 255, 279-284 (1994)
[abstract] [pdf]
- M. Tacker, W. Fontana, P. F. Stadler and P. Schuster
Statistics of RNA Melting Kinetics
European Journal of Biophysics, 23, 29-38, (1994)
[abstract] [US ps.gz]
- W. Fontana and L. W. Buss
What would be conserved if `the tape were played twice'?
Proc. Natl. Acad. Sci. USA, 91, 757-761 (1994)
[abstract] [pdf] [US ps.gz] [A4 ps.gz]
- reprinted in: "Complexity: Metaphors, Models, and Reality", George A. Cowan, David Pines, and David Meltzer (eds.), pp. 223-244, Addison-Wesley, Reading, MA, 1994.
- W. Fontana, D. A. M. Konings, P. F. Stadler, and P. Schuster
Statistics of RNA Secondary Structures
Biopolymers, 33, 1389-1404 (1993)
[abstract]
- W. Fontana, P. F. Stadler, E. Bauer, T. Griesmacher, I. L. Hofacker, M. Tacker, P. Tarazona, E. D. Weinberger and P. Schuster
RNA Folding and Combinatory Landscapes
Phys. Rev. E, 47, 2083-2099 (1993)
[abstract] [pdf] [US ps.gz]
- P. F. Stadler, W. Fontana and J. H. Miller
Random Catalytic Reaction Networks
Physica D, 63, 378-392 (1993)
[abstract] [US ps.gz] [A4 ps.gz]
- W. Fontana
Algorithmic Chemistry
in: Artificial Life II, C.G.Langton et al. (eds.), pp. 159-209, Addison-Wesley, 1991
[pdf]
- R. J. Bagley, J. D. Farmer and W. Fontana
Evolution of a Metabolism
in: Artificial Life II, C.G.Langton et al. (eds.), pp. 141-158, Addison-Wesley, 1991
- W. Fontana
Functional Self-Organization in Complex Systems
in: 1990 Lectures in Complex Systems, SFI Studies in the Sciences of Complexity, Lecture Notes Vol. III, L.Nadel and D.Stein (eds.), pp. 407-426, Addison-Wesley, 1991
- reprinted in: "Pattern Formation in the Physical and Biological Sciences", H. F. Nijhout, L. Nadel, and D. Stein (eds.), pp. 43-63, Addison-Wesley, Reading, MA, 1997.
- W. Fontana, T. Griesmacher, W. Schnabl, P. F. Stadler and P. Schuster
Statistics of Landscapes Based on Free Energy, Replication and Degradation Rate Constants of RNA Secondary Structures
Chemical Monthly, 122, 795-819 (1991)
- W. Fontana, W. Schnabl and P. Schuster
Physical Aspects of Evolutionary Optimization and Adaptation
Phys. Rev. A, 40, 3301-3321 (1989)
[pdf] [errata (pdf)]
- W. Fontana and P. Schuster
A Computer Model of Evolutionary Optimization
Biophysical Chemistry, 26, 123-147 (1987)
Book Reviews
- W. Fontana
"The Theory of Evolution and Dynamical Systems" by J. Hofbauer and K. Sigmund
Mathematical Biosciences, 96, 135-137 (1989)
Critique and Commentary
- W. Fontana
"Novelty in Evolution"
- Green Paper for "Bioevolutionary Concepts for NASA (BEACON)", 2001
[pdf] - Green Paper for "Bioevolutionary Concepts for NASA (BEACON)", 2001
- W. Fontana
"Keine Information ohne Evolution"
Ethik- und Sozialwissenschaften, 9, 198-200 (1998)
[A4 ps.gz]
- W. Fontana and S. Ballati
"Complexity - An Essay"
Complexity, 4, 14-16 (1999)
[postscript]
Theses
- W. Fontana
A Computer Model of Evolutionary Optimization
PhD Thesis (in German), University of Vienna, Austria (1987)
- W. Fontana
Molecular Replication and Random Selection. On a Simple Stochastic Model of Non-Darwinian Behavior
Master Thesis (in German), University of Vienna, Austria (1984)
Public Domain Software Packages
- I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker and P. Schuster
Vienna RNA package (maintained)
- W. Fontana, L. W. Buss and H. Freund
AlChemy - a package for the study of abstract organizations (not maintained)
Unpublished
- W. Fontana
Mammals, Florence and Chemistry: Chance and Necessity in Organizational Change (1998)
[postscript]
- Dorothea Heiss-Czedik and Walter Fontana
Evolution of lambda-expressions through Genetic Programming
[abstract] [pdf] [US ps.gz] [A4 ps.gz]
- P.Schuster, W.Fontana, P.F.Stadler and I.L.Hofacker
Biopolymer folding: When the details don't matter
[US ps.gz] [A4 ps.gz]