Many complex systems can be represented and analyzed as networks, and examples that
have benefited from this approach span the natural sciences. For instance, we now know …

Background There is evidence that genes and their protein products are organized into
functional modules according to cellular processes and pathways. Gene co-expression …

Many empirical networks display an inherent tendency to cluster, ie, to form circles of
connected nodes. This feature is typically measured by the clustering coefficient (CC). The …

The recent high level of interest in weighted complex networks gives rise to a need to
develop new measures and to generalize existing ones to take the weights of links into …

Background Network methods are increasingly used to represent the interactions of genes
and/or proteins. Genes or proteins that are directly linked may have a similar biological …

Background Network concepts are increasingly used in biology and genetics. For example,
the clustering coefficient has been used to understand network architecture; the connectivity …

Abstract Systems-oriented genetic approaches that incorporate gene expression and
genotype data are valuable in the quest for genetic regulatory loci underlying complex traits …

Most cancer genes remain functionally uncharacterized in the physiological context of
disease development. High-throughput molecular profiling and interaction studies are …

Background Large-scale sequencing of entire genomes has ushered in a new age in
biology. One of the next grand challenges is to dissect the cellular networks consisting of …

Motivation: The goal of neighborhood analysis is to find a set of genes (the neighborhood)
that is similar to an initial 'seed'set of genes. Neighborhood analysis methods for network …