We describe an algorithm for radial layout of undirected graphs, in which nodes are constrained to the circumferences of a set of concentric circles around the origin. Such constraints frequently occur in the layout of social or policy networks, when structural centrality is mapped to geometric centrality, or when the primary intention of the layout is the display of the vicinity of a distingui...

In the present study the effect of the locally produced genetic adjuvant of ginea pig specific CpG-motif-containing oligodeoxynucleotide (CpG-ODN) in an inactivated FMD virus vaccine was evaluated. Boosting the ginea pigs with FMD vaccine along with CpG-ODN adjuvant produced relatively higher ratio (5-fold) of FMDV-specific IgG2a / IgG1 than those vaccinated in the absence of CpG-ODN. The neutr...

Motif overrepresentation analysis of proximal promoters is a common approach to characterize the regulatory properties of co-expressed sets of genes. Here we show that these approaches perform well on mammalian CpG-depleted promoter sets that regulate expression in terminally differentiated tissues such as liver and heart. In contrast, CpG-rich promoters show very little overrepresentation sign...

Semi-supervised or constrained graph clustering incorporates prior information in order to improve results. Pairwise constraints are often utilized guide the process. This work addresses a problem biological networks where (1) subgraph connectivity strictly required be satisfied and (2) quality is assessed with respect pairwise constraint violations. Existing methods fail fully satisfy constrai...

We calculate explicit formulae for the Shannon entropies of several families of tailored random graph ensembles for which no such formulae were as yet available, in leading orders in the system size. These include bipartite graph ensembles with imposed (and possibly distinct) degree distributions for the two node sets, graph ensembles constrained by specified node neighbourhood distributions, a...

We calculate explicit formulae for the Shannon entropies of several families of tailored random graph ensembles for which no such formulae were as yet available, in leading orders in the system size. These include bipartite graph ensembles with imposed (and possibly distinct) degree distributions for the two node sets, graph ensembles constrained by specified node neighbourhood distributions, a...