We consider the general problem of constructing a physical map of genome by welding islands of overlapping clones. Both distribution of clone length and nonuniform probability of overlap detection are taken into account, the latter restricted to the Markov case in which only the location of the...

n Gene Perturbations in Fewer than n2 Easy Steps <p> [gzipped postscript] [postscript] [pdf] <p> Andreas Wagner <p>I present an algorithm to reconstruct direct regulatory interactions in gene networks from the effects of genetic perturbations on gene activity. Genomic technology has made feasible...</p></p></p>

We propose an explanation of cooperation among unrelated members of a social group, in which providing group benefits evolves because it constitutes an honest signal of the member's quality as a mate, coalition partner or competitor, and therefore results in advantageous alliances for those...

We show that the way in which the Shannon entropy of sequences produced by an information source converges to the source's entropy rate can be used to monitor how an intelligent agent builds and effectively uses a predictive model of its environment. We introduce natural measures of the...

Many properties of organisms show great robustness against mutations. Whether this robustness is an evolved property or intrinsic to genetic systems is by and large unknown. An evolutionary origin of robustness would require a rethinking of key concepts in the field of molecular evolution, such...

The population dynamics of macromolecules that reproduce by means of template-directed ligation of two fragments are shown to be represented by a replicator equation with a special non-linear response function. This result is obtained through detailed consideration of the mechanism of ligation...

Recently, it has been shown that the power spectrum of extinction intensity during the Phanerozoic takes a power-law form, which, it is suggested, may indicate the presence of critical phenomena in the dynamics underlying the extinction process. In this paper we reproduce these results using the...

Fitness landscapes have proven to be a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. A fitness landscape is a mapping from a configuration space into the real numbers. The configuration space is equipped with some notion of...

Optimization of systems with many conflicting constraints arises in numerous settings. Common optimization procedures seek to improve performance of the system as a whole. We show that coevolutionary problem solving, in which a system is partitioned into subsystems each of which selfishly...