<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Salavert, Francisco</style></author><author><style face="normal" font="default" size="100%">García-Alonso, Luz</style></author><author><style face="normal" font="default" size="100%">Sánchez, Rubén</style></author><author><style face="normal" font="default" size="100%">Alonso, Roberto</style></author><author><style face="normal" font="default" size="100%">Bleda, Marta</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Web-based network analysis and visualization using CellMaps.</style></title><secondary-title><style face="normal" font="default" size="100%">Bioinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioinformatics</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Biochemical Phenomena</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2016</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2016 Oct 01</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">32</style></volume><pages><style face="normal" font="default" size="100%">3041-3</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;&lt;b&gt;UNLABELLED: &lt;/b&gt;: CellMaps is an HTML5 open-source web tool that allows displaying, editing, exploring and analyzing biological networks as well as integrating metadata into them. Computations and analyses are remotely executed in high-end servers, and all the functionalities are available through RESTful web services. CellMaps can easily be integrated in any web page by using an available JavaScript API.&lt;/p&gt;&lt;p&gt;&lt;b&gt;AVAILABILITY AND IMPLEMENTATION: &lt;/b&gt;The application is available at: http://cellmaps.babelomics.org/ and the code can be found in: https://github.com/opencb/cell-maps The client is implemented in JavaScript and the server in C and Java.&lt;/p&gt;&lt;p&gt;&lt;b&gt;CONTACT: &lt;/b&gt;jdopazo@cipf.es&lt;/p&gt;&lt;p&gt;&lt;b&gt;SUPPLEMENTARY INFORMATION: &lt;/b&gt;Supplementary data are available at Bioinformatics online.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">19</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/27296979?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sebastián-Leon, Patricia</style></author><author><style face="normal" font="default" size="100%">Carbonell, José</style></author><author><style face="normal" font="default" size="100%">Salavert, Francisco</style></author><author><style face="normal" font="default" size="100%">Sánchez, Rubén</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Inferring the functional effect of gene expression changes in signaling pathways.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals</style></keyword><keyword><style  face="normal" font="default" size="100%">Humans</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Mice</style></keyword><keyword><style  face="normal" font="default" size="100%">Models, Statistical</style></keyword><keyword><style  face="normal" font="default" size="100%">Receptors, Cell Surface</style></keyword><keyword><style  face="normal" font="default" size="100%">Signal Transduction</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword><keyword><style  face="normal" font="default" size="100%">Transcriptome</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2013</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2013 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">41</style></volume><pages><style face="normal" font="default" size="100%">W213-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few methods aimed to identify the signaling circuits, within a pathway, associated to the biological problem studied exist and none of them provide a convenient graphical web interface. We present PATHiWAYS, a web-based signaling pathway visualization system that infers changes in signaling that affect cell functionality from the measurements of gene expression values in typical expression microarray case-control experiments. A simple probabilistic model of the pathway is used to estimate the probabilities for signal transmission from any receptor to any final effector molecule (taking into account the pathway topology) using for this the individual probabilities of gene product presence/absence inferred from gene expression values. Significant changes in these probabilities allow linking different cell functionalities triggered by the pathway to the biological problem studied. PATHiWAYS is available at: http://pathiways.babelomics.org/. &lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/23748960?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="7.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Sánchez, Rubén</style></author><author><style face="normal" font="default" size="100%">Serra, François</style></author><author><style face="normal" font="default" size="100%">Tárraga, Joaquín</style></author><author><style face="normal" font="default" size="100%">Medina, Ignacio</style></author><author><style face="normal" font="default" size="100%">Carbonell, José</style></author><author><style face="normal" font="default" size="100%">Pulido, Luis</style></author><author><style face="normal" font="default" size="100%">De Maria, Alejandro</style></author><author><style face="normal" font="default" size="100%">Capella-Gutíerrez, Salvador</style></author><author><style face="normal" font="default" size="100%">Huerta-Cepas, Jaime</style></author><author><style face="normal" font="default" size="100%">Gabaldón, Toni</style></author><author><style face="normal" font="default" size="100%">Dopazo, Joaquin</style></author><author><style face="normal" font="default" size="100%">Dopazo, Hernán</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Evolution, Molecular</style></keyword><keyword><style  face="normal" font="default" size="100%">Genomics</style></keyword><keyword><style  face="normal" font="default" size="100%">Internet</style></keyword><keyword><style  face="normal" font="default" size="100%">Phylogeny</style></keyword><keyword><style  face="normal" font="default" size="100%">Sequence Alignment</style></keyword><keyword><style  face="normal" font="default" size="100%">Software</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2011</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2011 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">W470-4</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.&lt;/p&gt;</style></abstract><issue><style face="normal" font="default" size="100%">Web Server issue</style></issue><custom1><style face="normal" font="default" size="100%">https://www.ncbi.nlm.nih.gov/pubmed/21646336?dopt=Abstract</style></custom1></record></records></xml>