<?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%">Wilkinson, M. D.</style></author><author><style face="normal" font="default" size="100%">Senger, M.</style></author><author><style face="normal" font="default" size="100%">Kawas, E.</style></author><author><style face="normal" font="default" size="100%">Bruskiewich, R.</style></author><author><style face="normal" font="default" size="100%">Gouzy, J.</style></author><author><style face="normal" font="default" size="100%">Noirot, C.</style></author><author><style face="normal" font="default" size="100%">Bardou, P.</style></author><author><style face="normal" font="default" size="100%">Ng, A.</style></author><author><style face="normal" font="default" size="100%">Haase, D.</style></author><author><style face="normal" font="default" size="100%">Saiz Ede, A.</style></author><author><style face="normal" font="default" size="100%">Wang, D.</style></author><author><style face="normal" font="default" size="100%">Gibbons, F.</style></author><author><style face="normal" font="default" size="100%">Gordon, P. M.</style></author><author><style face="normal" font="default" size="100%">Sensen, C. W.</style></author><author><style face="normal" font="default" size="100%">Carrasco, J. M.</style></author><author><style face="normal" font="default" size="100%">Fernandez, J. M.</style></author><author><style face="normal" font="default" size="100%">Shen, L.</style></author><author><style face="normal" font="default" size="100%">Links, M.</style></author><author><style face="normal" font="default" size="100%">Ng, M.</style></author><author><style face="normal" font="default" size="100%">Opushneva, N.</style></author><author><style face="normal" font="default" size="100%">Neerincx, P. B.</style></author><author><style face="normal" font="default" size="100%">Leunissen, J. A.</style></author><author><style face="normal" font="default" size="100%">Ernst, R.</style></author><author><style face="normal" font="default" size="100%">Twigger, S.</style></author><author><style face="normal" font="default" size="100%">Usadel, B.</style></author><author><style face="normal" font="default" size="100%">Good, B.</style></author><author><style face="normal" font="default" size="100%">Wong, Y.</style></author><author><style face="normal" font="default" size="100%">Stein, L.</style></author><author><style face="normal" font="default" size="100%">Crosby, W.</style></author><author><style face="normal" font="default" size="100%">Karlsson, J.</style></author><author><style face="normal" font="default" size="100%">Royo, R.</style></author><author><style face="normal" font="default" size="100%">Parraga, I.</style></author><author><style face="normal" font="default" size="100%">Ramirez, S.</style></author><author><style face="normal" font="default" size="100%">Gelpi, J. L.</style></author><author><style face="normal" font="default" size="100%">Trelles, O.</style></author><author><style face="normal" font="default" size="100%">Pisano, D. G.</style></author><author><style face="normal" font="default" size="100%">Jimenez, N.</style></author><author><style face="normal" font="default" size="100%">Kerhornou, A.</style></author><author><style face="normal" font="default" size="100%">Rosset, R.</style></author><author><style face="normal" font="default" size="100%">Zamacola, L.</style></author><author><style face="normal" font="default" size="100%">Tarraga, J.</style></author><author><style face="normal" font="default" size="100%">Huerta-Cepas, J.</style></author><author><style face="normal" font="default" size="100%">Carazo, J. M.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author><author><style face="normal" font="default" size="100%">R. Guigo</style></author><author><style face="normal" font="default" size="100%">Navarro, A.</style></author><author><style face="normal" font="default" size="100%">Orozco, M.</style></author><author><style face="normal" font="default" size="100%">Valencia, A.</style></author><author><style face="normal" font="default" size="100%">Claros, M. G.</style></author><author><style face="normal" font="default" size="100%">Perez, A. J.</style></author><author><style face="normal" font="default" size="100%">Aldana, J.</style></author><author><style face="normal" font="default" size="100%">Rojano, M. M.</style></author><author><style face="normal" font="default" size="100%">Fernandez-Santa Cruz, R.</style></author><author><style face="normal" font="default" size="100%">Navas, I.</style></author><author><style face="normal" font="default" size="100%">Schiltz, G.</style></author><author><style face="normal" font="default" size="100%">Farmer, A.</style></author><author><style face="normal" font="default" size="100%">Gessler, D.</style></author><author><style face="normal" font="default" size="100%">Schoof, H.</style></author><author><style face="normal" font="default" size="100%">Groscurth, A.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Interoperability with Moby 1.0–it’s better than sharing your toothbrush!</style></title><secondary-title><style face="normal" font="default" size="100%">Brief Bioinform</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computational Biology/*methods *Database Management Systems *Databases</style></keyword><keyword><style  face="normal" font="default" size="100%">Factual Information Storage and Retrieval/*methods *Internet *Programming Languages Systems Integration</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2008</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=18238804</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">3</style></number><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">220-31</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">&lt;p&gt;The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry Application Programming Interface and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/.&lt;/p&gt;</style></abstract><notes><style face="normal" font="default" size="100%">&lt;p&gt;BioMoby Consortium Wilkinson, Mark D Senger, Martin Kawas, Edward Bruskiewich, Richard Gouzy, Jerome Noirot, Celine Bardou, Philippe Ng, Ambrose Haase, Dirk Saiz, Enrique de Andres Wang, Dennis Gibbons, Frank Gordon, Paul M K Sensen, Christoph W Carrasco, Jose Manuel Rodriguez Fernandez, Jose M Shen, Lixin Links, Matthew Ng, Michael Opushneva, Nina Neerincx, Pieter B T Leunissen, Jack A M Ernst, Rebecca Twigger, Simon Usadel, Bjorn Good, Benjamin Wong, Yan Stein, Lincoln Crosby, William Karlsson, Johan Royo, Romina Parraga, Ivan Ramirez, Sergio Gelpi, Josep Lluis Trelles, Oswaldo Pisano, David G Jimenez, Natalia Kerhornou, Arnaud Rosset, Roman Zamacola, Leire Tarraga, Joaquin Huerta-Cepas, Jaime Carazo, Jose Maria Dopazo, Joaquin Guigo, Roderic Navarro, Arcadi Orozco, Modesto Valencia, Alfonso Claros, M Gonzalo Perez, Antonio J Aldana, Jose Rojano, M Mar Fernandez-Santa Cruz, Raul Navas, Ismael Schiltz, Gary Farmer, Andrew Gessler, Damian Schoof, Heiko Groscurth, Andreas Research Support, Non-U.S. Gov’t Review England Briefings in bioinformatics Brief Bioinform. 2008 May;9(3):220-31. Epub 2008 Jan 31.&lt;/p&gt;</style></notes></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%">Goni, J. R.</style></author><author><style face="normal" font="default" size="100%">Vaquerizas, J. M.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author><author><style face="normal" font="default" size="100%">Orozco, M.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions</style></title><secondary-title><style face="normal" font="default" size="100%">BMC Genomics</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Animals Base Sequence Computational Biology DNA/chemistry/*genetics/*metabolism Genome</style></keyword><keyword><style  face="normal" font="default" size="100%">Genetic/genetics Regulatory Sequences</style></keyword><keyword><style  face="normal" font="default" size="100%">Human/genetics Humans Mice Nucleic Acid Conformation Nucleotides/genetics Oligonucleotides/chemistry/*genetics/*metabolism Promoter Regions</style></keyword><keyword><style  face="normal" font="default" size="100%">Nucleic Acid/*genetics Transcription Factors/metabolism</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2006</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=16566817</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">7</style></volume><pages><style face="normal" font="default" size="100%">63</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: DNA duplex sequences that can be targets for triplex formation are highly over-represented in the human genome, especially in regulatory regions. RESULTS: Here we studied using bioinformatics tools several properties of triplex target sequences in an attempt to determine those that make these sequences so special in the genome. CONCLUSION: Our results strongly suggest that the unique physical properties of these sequences make them particularly suitable as &quot;separators&quot; between protein-recognition sites in the promoter region.</style></abstract><notes><style face="normal" font="default" size="100%">Goni, Josep Ramon Vaquerizas, Juan Manuel Dopazo, Joaquin Orozco, Modesto Research Support, Non-U.S. Gov’t England BMC genomics BMC Genomics. 2006 Mar 27;7:63.</style></notes></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%">L. Conde</style></author><author><style face="normal" font="default" size="100%">Vaquerizas, J. M.</style></author><author><style face="normal" font="default" size="100%">Ferrer-Costa, C.</style></author><author><style face="normal" font="default" size="100%">de la Cruz, X.</style></author><author><style face="normal" font="default" size="100%">Orozco, M.</style></author><author><style face="normal" font="default" size="100%">Dopazo, J.</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic Acids Res</style></secondary-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">Computer Graphics Genes *Genetic Predisposition to Disease Genotype Internet Phenotype *Polymorphism</style></keyword><keyword><style  face="normal" font="default" size="100%">Single Nucleotide *Software User-Computer Interface</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2005</style></year></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;dopt=Citation&amp;list_uids=15980522</style></url></web-urls></urls><number><style face="normal" font="default" size="100%">Web Server issue</style></number><volume><style face="normal" font="default" size="100%">33</style></volume><pages><style face="normal" font="default" size="100%">W501-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We have developed a web tool, PupasView, for the selection of single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupasView constitutes an interactive environment in which functional information and population frequency data can be used as sequential filters over linkage disequilibrium parameters to obtain a final list of SNPs optimal for genotyping purposes. PupasView is the first resource that integrates phenotypic effects caused by SNPs at both the translational and the transcriptional level. PupasView retrieves SNPs that could affect conserved regions that the cellular machinery uses for the correct processing of genes (intron/exon boundaries or exonic splicing enhancers), predicted transcription factor binding sites and changes in amino acids in the proteins for which a putative pathological effect is calculated. The program uses the mapping of SNPs in the genome provided by Ensembl. PupasView will be of much help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of the identification of the genes responsible for the disease. The PupasView web interface is accessible through http://pupasview.ochoa.fib.es and through http://www.pupasnp.org.</style></abstract><notes><style face="normal" font="default" size="100%">Conde, Lucia Vaquerizas, Juan M Ferrer-Costa, Carles de la Cruz, Xavier Orozco, Modesto Dopazo, Joaquin Research Support, Non-U.S. Gov’t England Nucleic acids research Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W501-5.</style></notes></record></records></xml>