W. Fontana

Publications
Influence

Fast folding and comparison of RNA secondary structures

I. Hofacker, W. Fontana, P. Stadler, L. S. Bonhoeffer, M. Tacker, P. Schuster
Chemistry, Computer Science
1 February 1994

An efficient heuristic for the inverse folding problem of RNA is introduced. Expand

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Smoothness within ruggedness: the role of neutrality in adaptation.

M. Huynen, P. Stadler, W. Fontana
Biology, Medicine
Proceedings of the National Academy of Sciences…
9 January 1996

RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks, evolving populations split into subpopulations,… Expand

Rule-Based Modelling of Cellular Signalling

V. Danos, J. Feret, W. Fontana, R. Harmer, J. Krivine
Computer Science
CONCUR
3 September 2007

Rule-based modeling tames combinatorial explosion by decontextualizing reactions between molecular species into rules defined on patterns. Expand

Scalable Simulation of Cellular Signaling Networks

V. Danos, J. Feret, W. Fontana, J. Krivine
Computer Science
APLAS
29 November 2007

We present in this paper a radically different method which does not attempt to count species without sampling down the number of potential generated species. Expand

Sizing Up Allometric Scaling Theory

V. Savage, Eric J. Deeds, W. Fontana
Mathematics, Computer Science
PLoS Comput. Biol.
1 September 2008

We show that the WBE model only holds in the limit of infinite network size (body mass) and that the actual exponent predicted by the model depends on the sizes of the organisms. Expand

Rules for Modeling Signal-Transduction Systems

W. S. Hlavacek, J. Faeder, M. Blinov, R. Posner, M. Hucka, W. Fontana
Computer Science, Medicine
Science's STKE
18 July 2006

Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Expand

What would be conserved if "the tape were played twice"?

W. Fontana, L. Buss
Medicine, Mathematics
Proceedings of the National Academy of Sciences…
18 January 1994

We develop an abstract chemistry, implemented in a lambda-calculus-based modeling platform, and argue that the following features are generic to this particular abstraction of chemistry; hence, they… Expand

Internal coarse-graining of molecular systems

J. Feret, V. Danos, J. Krivine, R. Harmer, W. Fontana
Mathematics, Medicine
Proceedings of the National Academy of Sciences
1 April 2009

We present a formal (and automated) method for constructing a coarse-grained and self-consistent dynamical system aimed at molecular patterns that are distinguishable by the dynamics of the original system as posited by the rules. Expand

Modelling 'evo-devo' with RNA.

W. Fontana
Biology, Medicine
BioEssays : news and reviews in molecular…
1 December 2002

The folding of RNA sequences into secondary structures is a simple yet biophysically grounded model of a genotype-phenotype map. Its computational and mathematical analysis has uncovered a… Expand

Abstract Interpretation of Cellular Signalling Networks

V. Danos, J. Feret, W. Fontana, J. Krivine
Computer Science
VMCAI
7 January 2008

We propose in this paper a method to enumerate a superset of the reachable complexes that a κ rule set can generate. Expand

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