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Rodriguez-Nieto S.,Genes and Cancer Group | Canada A.,Bioinformatics Unit | Pros E.,Genes and Cancer Group | Pinto A.I.,Genes and Cancer Group | 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. Source

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. Source

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. Source

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. Source

Pettifer S.,University of Manchester | Ison J.,European Bioinformatics Institute | Kalas M.,Computational Biology Unit | Kalas M.,University of Bergen | And 26 more authors.
Nucleic Acids Research | Year: 2010

The EMBRACE (European Model for Bioinformatics Research and Community Education) web service collection is the culmination of a 5-year project that set out to investigate issues involved in developing and deploying web services for use in the life sciences. The project concluded that in order for web services to achieve widespread adoption, standards must be defined for the choice of web service technology, for semantically annotating both service function and the data exchanged, and a mechanism for discovering services must be provided. Building on this, the project developed: EDAM, an ontology for describing life science web services; BioXSD, a schema for exchanging data between services; and a centralized registry (http://www.embraceregistry.net) that collects together around 1000 services developed by the consortium partners. This article presents the current status of the collection and its associated recommendations and standards definitions. © The Author(s) 2010. Published by Oxford University Press. Source

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