Robustness is the invariance of phenotypes in the face of perturbation. The robustness of
phenotypes appears at various levels of biological organization, including gene expression, …

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

… Fontana and Schuster construct shape space by defining a relation of accessibility between
two shapes, a and b, in terms of the adjacency of their corresponding neutral networks in …

Computer codes for computation and comparison of RNA secondary structures, the Vienna
RNA paCKage, are presented, that are based on dynamic programming algorithms and aim …

… in folding algorithms, as well as to the distance measure between structures used in the
sds (essentially the same sdss were obtained with a now superseded parameter set (Fontana …

RNA folding from sequences into secondary structures is a simple yet powerful, biophysically
grounded model of a genotype–phenotype map in which concepts like plasticity, …

An algorithm is presented for generating rigorously all suboptimal secondary structures
between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast …

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

The formal structure of evolutionary theory is based upon the dynamics of alleles, individuals
and populations. As such, the theory must assume the prior existence of these entities. This …

To distinguish continuous from discontinuous evolutionary change, a relation of nearness
between phenotypes is needed. Such a relation is based on the probability of one phenotype …