@article {15591357, title = {Highly specific and accurate selection of siRNAs for high-throughput functional assays}, journal = {Bioinformatics}, volume = {21}, number = {8}, year = {2005}, note = {Santoyo, Javier Vaquerizas, Juan M Dopazo, Joaquin Comparative Study Evaluation Studies Research Support, Non-U.S. Gov{\textquoteright}t England Bioinformatics (Oxford, England) Bioinformatics. 2005 Apr 15;21(8):1376-82. Epub 2004 Dec 10.}, pages = {1376-82}, abstract = {MOTIVATION: Small interfering RNA (siRNA) is widely used in functional genomics to silence genes by decreasing their expression to study the resulting phenotypes. The possibility of performing large-scale functional assays by gene silencing accentuates the necessity of a software capable of the high-throughput design of highly specific siRNA. The main objective sought was the design of a large number of siRNAs with appropriate thermodynamic properties and, especially, high specificity. Since all the available procedures require, to some extent, manual processing of the results to guarantee specific results, specificity constitutes to date, the major obstacle to the complete automation of all the steps necessary for the selection of optimal candidate siRNAs. RESULT: Here, we present a program that for the first time completely automates the search for siRNAs. In SiDE, the most complete set of rules for the selection of siRNA candidates (including G+C content, nucleotides at determined positions, thermodynamic properties, propensity to form internal hairpins, etc.) is implemented and moreover, specificity is achieved by a conceptually new method. After selecting possible siRNA candidates with the optimal functional properties, putative unspecific matches, which can cause cross-hybridization, are checked in databases containing a unique entry for each gene. These truly non-redundant databases are constructed from the genome annotations (Ensembl). Also intron/exon boundaries, presence of polymorphisms (single nucleotide polymorphisms) specificity for either gene or transcript, and other features can be selected to be considered in the design of siRNAs. AVAILABILITY: The program is available as a web server at http://side.bioinfo.cnio.es. The program was written under the GPL license. CONTACT: jdopazo@cnio.es.}, keywords = {*Algorithms Base Sequence *Gene Silencing Molecular Sequence Data RNA, RNA/*methods *Software *User-Computer Interface, Small Interfering/*genetics Sequence Alignment/*methods Sequence Analysis}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=15591357}, author = {J. Santoyo and Vaquerizas, J. M. and Dopazo, J.} } @article {15262789, title = {Phylogenomics and the number of characters required for obtaining an accurate phylogeny of eukaryote model species}, journal = {Bioinformatics}, volume = {20 Suppl 1}, year = {2004}, note = {

Dopazo, Hernan Santoyo, Javier Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Bioinformatics (Oxford, England) Bioinformatics. 2004 Aug 4;20 Suppl 1:i116-21.

}, pages = {i116-21}, abstract = {

MOTIVATION: Through the most extensive phylogenomic analysis carried out to date, complete genomes of 11 eukaryotic species have been examined in order to find the homologous of more than 25,000 amino acid sequences. These sequences correspond to the exons of more than 3000 genes and were used as presence/absence characters to test one of the most controversial hypotheses concerning animal evolution, namely the Ecdysozoa hypothesis. Distance, maximum parsimony and Bayesian methods of phylogenetic reconstruction were used to test the hypothesis. RESULTS: The reliability of the ecdysozoa, grouping arthropods and nematodes in a single clade was unequivocally rejected in all the consensus trees. The Coelomata clade, grouping arthropods and chordates, was supported by the highest statistical confidence in all the reconstructions. The study of the dependence of the genomes{\textquoteright} tree accuracy on the number of exons used, demonstrated that an unexpectedly larger number of characters are necessary to obtain robust phylogenies. Previous studies supporting ecdysozoa, could not guarantee an accurate phylogeny because the number of characters used was clearly below the minimum required.

}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=15262789}, author = {H. Dopazo and J. Santoyo and Dopazo, J.} } @article {15215388, title = {PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level}, journal = {Nucleic Acids Res}, volume = {32}, number = {Web Server issue}, year = {2004}, note = {Conde, Lucia Vaquerizas, Juan M Santoyo, Javier Al-Shahrour, Fatima Ruiz-Llorente, Sergio Robledo, Mercedes Dopazo, Joaquin England Nucleic acids research Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W242-8.}, pages = {W242-8}, abstract = {We have developed a web tool, PupaSNP Finder (PupaSNP for short), for high-throughput searching for single nucleotide polymorphisms (SNPs) with potential phenotypic effect. PupaSNP takes as its input lists of genes (or generates them from chromosomal coordinates) and retrieves SNPs that could affect the 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 (TFBS) and changes in amino acids in the proteins. The program uses the mapping of SNPs in the genome provided by Ensembl. Additionally, user-defined SNPs (not yet mapped in the genome) can be easily provided to the program. Also, additional functional information from Gene Ontology, OMIM and homologies in other model organisms is provided. In contrast to other programs already available, which focus only on SNPs with possible effect in the protein, PupaSNP includes SNPs with possible transcriptional effect. PupaSNP will be of significant help in studies of multifactorial disorders, where the use of functional SNPs will increase the sensitivity of identification of the genes responsible for the disease. The PupaSNP web interface is accessible through http://pupasnp.bioinfo.cnio.es.}, keywords = {Amino Acid Substitution Binding Sites Humans Internet Phenotype *Polymorphism, Genetic, Single Nucleotide RNA Splicing *Software Transcription Factors/metabolism *Transcription}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=15215388}, author = {L. Conde and Vaquerizas, J. M. and J. Santoyo and Fatima Al-Shahrour and Ruiz-Llorente, S. and M. Robledo and Dopazo, J.} } @article {12824345, title = {GEPAS: A web-based resource for microarray gene expression data analysis}, journal = {Nucleic Acids Res}, volume = {31}, number = {13}, year = {2003}, note = {

Herrero, Javier Al-Shahrour, Fatima Diaz-Uriarte, Ramon Mateos, Alvaro Vaquerizas, Juan M Santoyo, Javier Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2003 Jul 1;31(13):3461-7.

}, pages = {3461-7}, abstract = {

We present a web-based pipeline for microarray gene expression profile analysis, GEPAS, which stands for Gene Expression Profile Analysis Suite (http://gepas.bioinfo.cnio.es). GEPAS is composed of different interconnected modules which include tools for data pre-processing, two-conditions comparison, unsupervised and supervised clustering (which include some of the most popular methods as well as home made algorithms) and several tests for differential gene expression among different classes, continuous variables or survival analysis. A multiple purpose tool for data mining, based on Gene Ontology, is also linked to the tools, which constitutes a very convenient way of analysing clustering results. On-line tutorials are available from our main web server (http://bioinfo.cnio.es).

}, keywords = {gepas, microarray data analysis}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=12824345}, author = {Herrero, J. and Fatima Al-Shahrour and Diaz-Uriarte, R. and A. Mateos and Vaquerizas, J. M. and J. Santoyo and Dopazo, J.} } @inbook {492, title = {Using Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes}, booktitle = {Neural Networks for Signal Processing XIII}, year = {2003}, pages = {43-52}, publisher = {IEEE Press}, organization = {IEEE Press}, address = {New York, USA}, keywords = {babelomics}, author = {Fatima Al-Shahrour and Herrero, J. and A. Mateos and J. Santoyo and D{\'\i}az-Uriarte, R and Dopazo, J.} }