WebGraph

[…] uncovering the possible mechanism involved in the development (or evolution) of the graph. As the most famous example, the Barabási-Albert model for the description of the degree distribution of the webgraph, uses the “preferential attachment” principle in the description of the development of the webgraph. In the Barabási-Albert model, roughly, in every step one new vertex appears, and it connec […]

[…] interactions. In order to compare the biological graphs with random graphs, we generated uniform random power-law graphs that are similar in terms of number of nodes and interactions using the Python Webgraph Generator ( http://pywebgraph.sourceforge.net/), which implements the RMAT algorithm []. […]

[…] tive to gene regions was analyzed by CEAS . Top 10% of enriched regions for each ChIP-seq library were selected to identify the overrepresented features using EpiGRAPH (http://epigraph.mpi-inf.mpg.de/WebGRAPH/) . 2214 H1d/H1c common peaks, 1939 H1d unique peaks, 433 H1c unique peaks, 1891 H3K9me3 peaks, 4778 H3K27me3 peaks, and 3446 H3K4me3 peaks were analyzed by EpiGRAPH. […]

[…] EpiGRAPH (http://epigraph.mpi-inf.mpg.de/WebGRAPH/) is an online software to analyze genomic and epigenomic features that are enriched in given DNA fragments (). As described above, we have identified 924 CpG sites correlated to 902 genes th […]

[…] DNA methylation patterns while amplicons with low values do not (but may still exhibit similar average methylation levels across individuals).The EpiGRAPH web service (http://epigraph.mpi-inf.mpg.de/WebGRAPH/) was used to test a large number of genomic attributes for their ability to distinguish between amplicons with high versus low high-resolution improvement. To that end, two lists of amplicon […]