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High Performance Computing

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Studying at Cambridge

 

Publications

2015
2014
2013
2012
  • Bleda M, Tarraga J, De Maria A, Salavert F, Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I.   CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res. 40(Web Server issue):W609-14.
  • García-Alonso L, Alonso R, Vidal E, Amadoz A, de María A, Minguez P, Medina I, Dopazo J.  Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res.
  • Fernández RM, Bleda M, Núñez-Torres R, Medina I, Luzón-Toro B, García-Alonso L, Torroglosa A, Marbà M, Enguix-Riego M V, Montaner D et al.  Four new loci associations discovered by pathway-based and network analyses of the genome-wide variability profile of Hirschsprung's disease. Orphanet J Rare Dis. 7:103.
  • Bleda M, Medina I, Alonso R, De Maria A, Salavert F, Dopazo J.  Inferring the regulatory network behind a gene expression experiment. Nucleic Acids Res. 40(Web Server issue):W168-72.
  • Carbonell J, Alloza E, Arce P, Borrego S, Santoyo J, Ruiz-Ferrer M, Medina I, Jimenez-Almazan J, Mendez-Vidal C, Gonzalez-Del Pozo M et al.  A map of human microRNA variation uncovers unexpectedly high levels of variability. Genome Med. 4(8):62.
  • Lorente–Galdos B, Medina I, Morcillo–Suarez C, Heredia T, Carreño–Torres Á, Sangrós R, Alegre J, Pita G, Vellalta G, Malats N et al.  Select Your SNPs (SYSNPs): a web tool for automatic and massive selection of SNPs. International Journal of Data Mining and Bioinformatics. 6(3/2012):334.
  • Torres J S, Espert I B, Dominguez A T, Hernendez V, Medina I, Terraga J, Dopazo J.  Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB). 9(4)
  • Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J.   VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Res. 40(Web Server issue):W54-8.
  • Heyn H, Vidal E, Sayols S, Sanchez-Mut JV, Moran S, Medina I, Sandoval J, Simó-Riudalbas L, Szczesna K, Huertas D et al.  Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient. Epigenetics. 7(6):542-50.

 

2011
  • Sánchez R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutíerrez S, Huerta-Cepas J, Gabaldón T et al.  Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res. 39(Web Server issue):W470-4.
2010
  • Medina I, Carbonell J, Pulido L, Madeira SC, Goetz S, Conesa A, Tárraga J, Pascual-Montano A, Nogales-Cadenas R, Santoyo J et al.   Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 38(Web Server issue):W210-3.
  • Németh A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Péterfia B, Solovei I, Cremer T, Dopazo J, Längst G.   Initial genomics of the human nucleolus. PLoS Genet. 6(3):e1000889.
  • Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu T-M, Goodsaid FM, Pusztai L et al.   The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnol. 28(8):827-38.
  • Nueda M J, Carbonell J, Medina I, Dopazo J, Conesa A.   Serial Expression Analysis: a web tool for the analysis of serial gene expression data. Nucleic Acids Res. 38(Web Server issue):W239-45.
2009
  • Medina I, Montaner D, Bonifaci N, Pujana M A, Carbonell J, Tarraga J, Al-Shahrour F, Dopazo J.   Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res. 37(Web Server issue):W340-4.
2008
  • Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.   Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res. 36(Web Server issue):W341-6.
  • Bonifaci N, Berenguer A, Díez J, Reina O, Medina I, Dopazo J, Moreno V, Pujana M A.   Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes. BMC Med Genomics. 1:62.
  • Tárraga J, Medina I, Carbonell J, Huerta-Cepas J, Minguez P, Alloza E, Al-Shahrour F, Vegas-Azcárate S, Goetz S, Escobar P et al..  2008.  GEPAS, a web-based tool for microarray data analysis and interpretation.. Nucleic Acids Res. 36(Web Server issue):W308-14.
  • Reumers J, Conde L, Medina I, Maurer-Stroh S, Van Durme J, Dopazo J, Rousseau F, Schymkowitz J.  2008.  Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.. Nucleic Acids Res. 36(Database issue):D825-9.
  • Saar K, Beck A, Bihoreau M-T, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P et al..  2008.  SNP and haplotype mapping for genetic analysis in the rat.. Nat Genet. 40(5):560-6.
2007
  • Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J.  2007.  FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.. Nucleic Acids Res. 35(Web Server issue):W91-6.
  • Conde L, Montaner D, Burguet-Castell J, Tárraga J, Medina I, Al-Shahrour F, Dopazo J.  2007.  ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling.. Nucleic Acids Res. 35(Web Server issue):W81-5.
  • Tárraga J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.  2007.  Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.. Nucleic Acids Res. 35(Web Server issue):W38-42.
  • Medina I, Montaner D, Tárraga J, Dopazo J.  2007.  Prophet, a web-based tool for class prediction using microarray data.. Bioinformatics. 23(3):390-1.

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