Spanish National Bioinformatics Institute INB

Madrid, Spain

Spanish National Bioinformatics Institute INB

Madrid, Spain
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Rodriguez-Nieto S.,Lhospitalet Of Llobregat | Canada A.,Bioinformatics Unit | Pros E.,Lhospitalet Of Llobregat | Pinto A.I.,Lhospitalet Of Llobregat | And 6 more authors.
Human Mutation | Year: 2011

The tumor suppressor gene, SMARCA4 (or BRG1), which encodes the ATPase component of the chromatin remodeling complex SWI/SNF, is commonly inactivated by mutations and deletions in lung cancer cell lines. However, SMARCA4 alterations appear to be rare in lung primary tumors. Ultra-deep sequencing technologies provide a promising alternative to achieve a sensitivity superior to that of current sequencing strategies. Here we used ultra-deep pyrosequencing to screen for mutations over the entire SMARCA4 coding region in 12 lung tumors without detectable BRG1 protein. While automatic-fluorescence-based sequencing detected one somatic mutation (p.K586X), the pyrosequencing revealed additional variants, thus increasing the sensitivity. One of the variants, which affected a consensus splice site, was confirmed by individual cloning of PCR products, ruling out the possibility of PCR or pyrosequencing artifacts. This mutation, confirmed to be somatic, was present at a frequency of ten percent, suggesting normal cell contamination in the tumor. Our analysis also allowed us to determine the sensitivity and to identify some limitations of the technology. In conclusion, in addition to cell lines, SMARCA4 is biallelically inactivated in a significant proportion of lung primary tumors, thereby constituting one of the most important genes contributing to the development of this type of cancer. © 2010 Wiley-Liss, Inc.


Rodriguez J.M.,Spanish National Bioinformatics Institute INB | Maietta P.,Spanish National Cancer Research Center | Ezkurdia I.,Spanish National Cancer Research Center | Pietrelli A.,Spanish National Bioinformatics Institute INB | And 8 more authors.
Nucleic Acids Research | Year: 2013

Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform. © The Author(s) 2012.


Lees J.G.,University College London | Heriche J.-K.,Cell Biology Biophysics Unit | Morilla I.,Paris-Sorbonne University | Fernandez J.M.,Spanish National Bioinformatics Institute INB | And 7 more authors.
Bioinformatics | Year: 2015

Motivation: Most biological processes remain only partially characterized with many components still to be identified. Given that a whole genome can usually not be tested in a functional assay, identifying the genes most likely to be of interest is of critical importance to avoid wasting resources. Results: Given a set of known functionally related genes and using a state-of-the-art approach to data integration and mining, our Functional Lists (FUN-L) method provides a ranked list of candidate genes for testing. Validation of predictions from FUN-L with independent RNAi screens confirms that FUN-L-produced lists are enriched in genes with the expected phenotypes. In this article, we describe a website front end to FUN-L. © The Author 2015. Published by Oxford University Press.


Rubio-Camarillo M.,Structural Computational Biology Group | Gomez-Lopez G.,Bioinformatics Unit UBio | Fernandez J.M.,Spanish National Bioinformatics Institute INB | Valencia A.,Structural Computational Biology Group | And 2 more authors.
Bioinformatics | Year: 2013

Motivation: RUbioSeq has been developed to facilitate the primary and secondary analysis of re-sequencing projects by providing an integrated software suite of parallelized pipelines to detect exome variants (single-nucleotide variants and copy number variations) and to perform bisulfite-seq analyses automatically. RUbioSeq's variant analysis results have been already validated and published. © The Author 2013.


Rodriguez J.M.,Spanish National Bioinformatics Institute INB | Carro A.,Bioinformatics Unit | Valencia A.,Spanish National Bioinformatics Institute INB | Tress M.L.,Spanish National Cancer Research Center
Nucleic acids research | Year: 2015

This paper introduces the APPRIS WebServer (http://appris.bioinfo.cnio.es) and WebServices (http://apprisws.bioinfo.cnio.es). Both the web servers and the web services are based around the APPRIS Database, a database that presently houses annotations of splice isoforms for five different vertebrate genomes. The APPRIS WebServer and WebServices provide access to the computational methods implemented in the APPRIS Database, while the APPRIS WebServices also allows retrieval of the annotations. The APPRIS WebServer and WebServices annotate splice isoforms with protein structural and functional features, and with data from cross-species alignments. In addition they can use the annotations of structure, function and conservation to select a single reference isoform for each protein-coding gene (the principal protein isoform). APPRIS principal isoforms have been shown to agree overwhelmingly with the main protein isoform detected in proteomics experiments. The APPRIS WebServer allows for the annotation of splice isoforms for individual genes, and provides a range of visual representations and tools to allow researchers to identify the likely effect of splicing events. The APPRIS WebServices permit users to generate annotations automatically in high throughput mode and to interrogate the annotations in the APPRIS Database. The APPRIS WebServices have been implemented using REST architecture to be flexible, modular and automatic. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.


PubMed | Spanish National Bioinformatics Institute INB, Bioinformatics Unit and Spanish National Cancer Research Center
Type: Journal Article | Journal: Nucleic acids research | Year: 2015

This paper introduces the APPRIS WebServer (http://appris.bioinfo.cnio.es) and WebServices (http://apprisws.bioinfo.cnio.es). Both the web servers and the web services are based around the APPRIS Database, a database that presently houses annotations of splice isoforms for five different vertebrate genomes. The APPRIS WebServer and WebServices provide access to the computational methods implemented in the APPRIS Database, while the APPRIS WebServices also allows retrieval of the annotations. The APPRIS WebServer and WebServices annotate splice isoforms with protein structural and functional features, and with data from cross-species alignments. In addition they can use the annotations of structure, function and conservation to select a single reference isoform for each protein-coding gene (the principal protein isoform). APPRIS principal isoforms have been shown to agree overwhelmingly with the main protein isoform detected in proteomics experiments. The APPRIS WebServer allows for the annotation of splice isoforms for individual genes, and provides a range of visual representations and tools to allow researchers to identify the likely effect of splicing events. The APPRIS WebServices permit users to generate annotations automatically in high throughput mode and to interrogate the annotations in the APPRIS Database. The APPRIS WebServices have been implemented using REST architecture to be flexible, modular and automatic.


Fernandez J.M.,Spanish National Bioinformatics Institute INB | Hoffmann R.,Sloan Kettering Cancer Center | Valencia A.,Spanish National Bioinformatics Institute INB
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2012

iHOP provides fast, accurate, comprehensive, and up-to-date summary information on thousands of biological molecules by automatically extracting key sentences from millions of PubMed documents. iHOP web services are providing public programmatic access to all this information since their publication in 2007. This manuscript describes recent improvements on the iHOP web services family and some of the scenarios in which the web services have been applied. © 2012 Springer-Verlag.


Fernandez J.M.,Spanish National Bioinformatics Institute INB | Valencia A.,Spanish National Bioinformatics Institute INB
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2012

The Spanish National Bioinformatics Institute (Instituto Nacional de Bioinformática in Spanish, or short INB) is an academic service institution founded in 2003 by the mayor research groups in Spain at that time. The INB serves in the coordination, integration and development of Spanish Bioinformatics Resources in projects in the areas of genomics, proteomics and translational medicine. Its mission is to consolidate Bioinformatics as a scientific discipline, providing technical support in Bioinformatics to laboratories, institutions and companies throughout the territory. The JBI2010 conference featured two sessions, "INB Technicians internal session" and "Bioinformatic Software Developments in Spain and beyond", that introduced the state of the art of bioinformatic software developments at the INB and its role at the national and international level. This paper gives a summary of those sessions and presents an overview of the activities and contributions of the INB to the field of bioinformatics. © 2012 Springer-Verlag.


PubMed | Spanish National Bioinformatics Institute INB
Type: Journal Article | Journal: Nucleic acids research | Year: 2012

Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform.


PubMed | University of Vigo, Spanish National Bioinformatics Institute INB and Bioinformatics Unit UBio
Type: | Journal: Computer methods and programs in biomedicine | Year: 2016

To facilitate routine analysis and to improve the reproducibility of the results, next-generation sequencing (NGS) analysis requires intuitive, efficient and integrated data processing pipelines.We have selected well-established software to construct a suite of automated and parallelized workflows to analyse NGS data for DNA-seq (single-nucleotide variants (SNVs) and indels), CNA-seq, bisulfite-seq and ChIP-seq experiments.Here, we present RUbioSeq+, an updated and extended version of RUbioSeq, a multiplatform application that incorporates a suite of automated and parallelized workflows to analyse NGS data. This new version includes: (i) an interactive graphical user interface (GUI) that facilitates its use by both biomedical researchers and bioinformaticians, (ii) a new pipeline for ChIP-seq experiments, (iii) pair-wise comparisons (case-control analyses) for DNA-seq experiments, (iv) and improvements in the parallelized and multithreaded execution options. Results generated by our software have been experimentally validated and accepted for publication.RUbioSeq+ is free and open to all users at http://rubioseq.bioinfo.cnio.es/.

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