• Publications
  • Influence
Fast folding and comparison of RNA secondary structures
TLDR
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.
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
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Rule-Based Modelling of Cellular Signalling
TLDR
Rule-based modeling tames combinatorial explosion by decontextualizing reactions between molecular species into rules defined on patterns. Expand
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Scalable Simulation of Cellular Signaling Networks
TLDR
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
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Sizing Up Allometric Scaling Theory
TLDR
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
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Rules for Modeling Signal-Transduction Systems
TLDR
Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Expand
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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, theyExpand
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Internal coarse-graining of molecular systems
TLDR
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
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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 aExpand
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Abstract Interpretation of Cellular Signalling Networks
TLDR
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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