@article {586,
	title = {SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.},
	journal = {Nucleic Acids Res},
	volume = {37},
	year = {2009},
	month = {2009 Jul},
	pages = {W109-14},
	abstract = {<p>Understanding the structure and the dynamics of the complex intercellular network of interactions that contributes to the structure and function of a living cell is one of the main challenges of today{\textquoteright}s biology. SNOW inputs a collection of protein (or gene) identifiers and, by using the interactome as scaffold, draws the connections among them, calculates several relevant network parameters and, as a novelty among the rest of tools of its class, it estimates their statistical significance. The parameters calculated for each node are: connectivity, betweenness and clustering coefficient. It also calculates the number of components, number of bicomponents and articulation points. An interactive network viewer is also available to explore the resulting network. SNOW is available at http://snow.bioinfo.cipf.es.</p>},
	keywords = {Computer Graphics, Data Interpretation, Statistical, Databases, Protein, Humans, Internet, Protein Interaction Mapping, Software},
	issn = {1362-4962},
	doi = {10.1093/nar/gkp402},
	author = {Minguez, Pablo and G{\"o}tz, Stefan and Montaner, David and Al-Shahrour, F{\'a}tima and Dopazo, Joaquin}
}
@article {594,
	title = {High-throughput functional annotation and data mining with the Blast2GO suite.},
	journal = {Nucleic Acids Res},
	volume = {36},
	year = {2008},
	month = {2008 Jun},
	pages = {3420-35},
	abstract = {<p>Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.</p>},
	keywords = {Animals, Computational Biology, Computer Graphics, Databases, Genetic, Expressed Sequence Tags, Genes, Genomics, Sequence Analysis, DNA, Sequence Analysis, Protein, Software, Vocabulary, Controlled},
	issn = {1362-4962},
	doi = {10.1093/nar/gkn176},
	author = {G{\"o}tz, Stefan and Garc{\'\i}a-G{\'o}mez, Juan Miguel and Terol, Javier and Williams, Tim D and Nagaraj, Shivashankar H and Nueda, Maria Jos{\'e} and Robles, Montserrat and Talon, Manuel and Dopazo, Joaquin and Conesa, Ana}
}
