I present an algorithm that determines the longest path between every gene pair in an arbitrarily large genetic network from large scale gene perturbation data. As a by-product, the algorithm reconstructs all direct regulatory gene interactions in the network. The algorithm is recursive, and is...

We analyze the structure of a large metabolic network, that of the energy and biosynthesis metabolism of Escherichia coli. This network is a paradigmatic case for the large genetic and metabolic networks that functional genomics efforts are beginning to elucidate. To analyze the structure of...

Sheltered from deleterious mutations, genes with overlapping or partially redundant functions may be important sources of novel gene functions. While most partially redundant genes originated in gene duplications, it is much less clear why genes with overlapping functions have been retained, in...

The structure and evolution of the protein interaction network of the yeast Saccharomyces cerevisiae is analyzed. The network is viewed as a graph whose nodes correspond to proteins. Two proteins are connected by an edge if they interact. The network resembles a random graph, in that it consists...

During the development of a multicellular organism for a zygote, a large number of epigenetic interactions take place on every level of suborganismal organization. This raises the possibility that the system of epigenetic interactions may compensate or ÒbufferÓ some of the changes that occur...

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...

Resilience of an organism's physiological and developmental processes against mutations can have two principal causes, the first being overlapping gene functions. In this case, loss-of-function mutations in one gene will have little phenotypic effects if one or more other genes with similar...

Redundant gene functions are ubiquitous, and they are a potentially important source of evolutionary innovations on the biochemical level. It is therefore highly desirable to understand the mechanisms governing their evolution. Gene duplication is clearly a prominent mechanism generating...

The neutralist perspective on molecular evolution maintains that the vast majority of mutations effecting gene function are neutral or deleterious. Following a gene duplication where both genes are retained, it predicts that original and duplicate genes diverge at clock-like rates. This...

To delineate the astronomical number of possible interactions of all genes in a genome is a task for which conventional experimental techniques are ill suited. Sorely needed are rapid and inexpensive methods that identify candidates for interacting genes, candidates that can be further...