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S. E. Hulme, S. S. Shevkoplyas, A. P. McGuigan, J. Apfeld, W. Fontana, G. M. Whitesides, Lifespan-on-a-Chip: microfluidic chambers for performing lifelong observation of C. elegans Lab on a Chip, in press (2009) |
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V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine, Rule-based Modelling and Model Perturbation Transactions on Computational Systems Biology, 11:116-137 (2009) [pdf] |
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V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine, Investigation of a biological repair scheme Membrane Computing, Lecture Notes in Computer Science, 539:1-12 (2009) [pdf] |
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J. Feret, V. Danos, J. Krivine, R. Harmer and W. Fontana, Internal coarse-graining of molecular systems Proc. Natl. Acad. Sci. USA, 106, 6453-6458 (2009) [main | supplement | combined] doi:10.1073/pnas.0809908106 |
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V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine Rule-based modeling, symmetries, refinements Formal Methods in Systems Biology 2008, Lecture Notes in Bioinformatics, 5054:103-122 (2008) [pdf] |
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V. M. Savage, E. J. Deeds and W. Fontana Sizing up allometric scaling theory PLoS Comp. Bio., 4(9): e1000171 (2008) [main | supplement | combined] doi:10.1371/journal.pcbi.1000171 |
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S. E. Hulme, S. S. Shevkoplyas, J. Apfeld, W. Fontana, and G. M. Whitesides A Microfabricated Array of Clamps for Immobilizing and Imaging C. elegans Lab on a Chip, 7, 1515-1523 (2007) [pdf] |
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V. Danos, J. Feret, W. Fontana, R. Harmer and J. Krivine Rule-Based Modeling of Cellular Signaling Concurrency Theory 2007, Lecture Notes in Computer Science, 4703:17-41 (2007) [pdf] |
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S. Krishnamurthy, E. Smith, D. Krakauer and W. Fontana The stochastic behavior of a molecular switching circuit with feedback Biology Direct, 2:13 (31 May 2007). [pdf] |
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V. Danos, J. Feret, W. Fontana and J. Krivine Abstract interpretation of cellular signalling networks Verification, Model Checking, and Abstract Interpretation (VMCAI) 2008, Lecture Notes in Computer Science, 4905:83–97 (2008) [pdf] |
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V. Danos, J. Feret, W. Fontana and J. Krivine Scalable simulation of cellular signalling networks APLAS 2007, Lecture Notes in Computer Science, 4807:139–157 (2007) [pdf] |
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W.Fontana [Perspective:] Pulling Strings Science, 314, 1552-1553 (2006) [pdf] |
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W.S.Hlavacek, J.R.Faeder, M.L.Blinov, R.G.Posner, M.Hucka and W.Fontana Rules for Modeling Signal-Transduction Systems Science STKE, Vol. 2006, Issue 344, pp. re6, 18 July 2006 [pdf] [DOI: 10.1126/stke.3442006re6] |
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W.Fontana The Topology of the Possible in: “Understanding Change: Models, Methodologies and Metaphors.” A.Wimmer and R.Kössler (editors), Palgrave Macmillan (2005). [pdf] |
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L.W.Ancel-Myers and W.Fontana Evolutionary Lock-in and the Origin of Modularity in RNA Structure, in "Modularity –Understanding the Development and Evolution of Natural Complex Systems", W.Callebaut and D.Rasskin-Gutman (editors) MIT Press, Cambridge, MA (2005). [pdf scan] [pdf preprint] |
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W.Fontana, J.Karkanias, L.G.Meredith, and M.Radestock Lab-to-lab connectivity and semantics in the life sciences Position Paper for the W3C workshop on “Semantic Web for Life Sciences”, 27-28 October 2004, Cambridge, MA. Published online (2004) [pdf] |
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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] |
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W.Fontana Modelling ‘Evo-Devo’ with RNA BioEssays, 24, 1164–1177 (2002) [pdf] |
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N.V.Fedoroff and W.Fontana Small numbers of big molecules Science, 297, 1129–1131 (2002) [pdf] |
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B.M.R.Stadler, P.F.Stadler, G.Wagner and W.Fontana The topology of the possible: Formal spaces underlying patterns of evolutionary change J. theor. Biol., 213(2), 241-274 (2001) [pdf] |
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L.W.Ancel and W.Fontana Plasticity, Evolvability and Modularity in RNA, J. Exp. Zool. (Mol. Dev. Evol.), 288, 242–283 (2000) [pdf] |
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C.Flamm, W.Fontana, I.Hofacker and P.Schuster RNA Folding at Elementary Step Resolution, RNA, 6, 325-338 (2000) [pdf] |
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P.Schuster and W.Fontana Chance and Necessity in Evolution: Lessons from RNA, Physica D: Nonlinear Phenomena, 133, 427-452 (1999) [pdf] |
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S.Wuchty, W.Fontana, I.Hofacker and P.Schuster Complete Suboptimal Folding of RNA and the Stability of Secondary Structures, Biopolymers, 49, 145–165 (1999) [pdf] |
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W.Fontana and S.Ballati Complexity: An Essay Complexity, 4, 14–16 (1999) [pdf] |
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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] |
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W.Fontana and P.Schuster Continuity in Evolution: On the Nature of Transitions, Science, 280, 1451–1455 (1998) [pdf] |
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W.Fontana Keine Information ohne Evolution Ethik-und Sozialwissenschaften, 9, 198–200 (1998) [pdf] [pdf] |
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W.Fontana and L.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) [pdf] Tutorial appendices on lambda-calculus (Appendix A), type theory (Appendix B) and proof-theory (Appendix C) [pdf]. A brief summary has appeared as: |
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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) [pdf] |
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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) [pdf]
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W.Fontana, G.Wagner and L.W.Buss Beyond Digital Naturalism, Artificial Life, 1/2, 211–227 (1994) [pdf]
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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) [pdf] [pdf] [Vienna RNA package] |
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W.Fontana and L.W.Buss ‘The Arrival of the Fittest’: Toward a Theory of Biological Organization Bull. Math. Biol., 56, 1–64 (1994) [pdf] |
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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) [pdf] |
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M.Tacker, W.Fontana, P.F.Stadler and P.Schuster Statistics of RNA Melting Kinetics European Journal of Biophysics, 23, 29–38, (1994) [pdf] |
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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) [pdf]
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W.Fontana, D.A.M.Konings, P.F.Stadler, and P.Schuster Statistics of RNA Secondary Structures Biopolymers, 33, 1389–1404 (1993) [pdf] |
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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) [pdf] |
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P.F.Stadler, W.Fontana and J.H.Miller Random Catalytic Reaction Networks Physica D, 63, 378–392 (1993) [pdf][pdf] |
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W.Fontana Algorithmic Chemistry in: "Artificial Life II", C.G.Langton et al. (eds.), pp. 159–209, Addison-Wesley (1991) [pdf] |
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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) [pdf] |
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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) [pdf]
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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) [pdf] |
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W.Fontana, W.Schnabl and P.Schuster Physical Aspects of Evolutionary Optimization and Adaptation Phys.Rev.A, 40, 3301–3321 (1989) [pdf] [erratum] |
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W.Fontana and P.Schuster A Computer Model of Evolutionary Optimization Biophysical Chemistry, 26, 123–147 (1987) [pdf] |
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M.D.Laubichler, G.B.Mueller, W.Fontana
and G.P.Wagner Sacrificing Dialogue for Politics? Science, 309, 1324 (2005) [pdf] |
