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2011

Alloza E, Al-Shahrour F, Cigudosa JC, Dopazo J. "A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression." BMC Medical Genomics. 2011;4:37. Abstract

2010

Shi W, Bessarabova M, Dosymbekov D, et al. "Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes." Pharmacogenomics J.. 2010;10(4):310-23. Abstract

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2009

Jantus Lewintre E, Reinoso Martin C, Montaner D, et al. "Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups." Leuk Lymphoma. 2009;50:68-79. Abstract

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Nobre LS, Al-Shahrour F, Dopazo J, Saraiva LM. "Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli." Microbiology. 2009;155:813-24. Abstract

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Dopazo J. "Formulating and testing hypotheses in functional genomics." Artif Intell Med. 2009;45:97-107. Abstract

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Montaner D, Minguez P, Al-Shahrour F, Dopazo J. "Gene set internal coherence in the context of functional profiling." BMC Genomics. 2009;10:197.

Minguez P, Dopazo J. "Protein Interactions for Functional Genomics ." In: Li X-L, Ng S-K, eds. Biological Data Mining in Protein Interaction Networks. Hershey, USA: Idea Group Inc (IGI); 2009:.

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2008

Al-Shahrour F, Carbonell J, Minguez P, et al. "Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments." Nucleic Acids Res. 2008;36:W341-6. Abstract

Bonifaci N, Berenguer A, Diez J, et al. "Biological processes, properties and molecular wiring diagrams of candidate low-penetrance breast cancer susceptibility genes." BMC Med Genomics. 2008;1:62. Abstract

Valls J, Grau M, Sole X, et al. "CLEAR-test: combining inference for differential expression and variability in microarray data analysis." J Biomed Inform. 2008;41:33-45. Abstract

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Horcajadas JA, Minguez P, Dopazo J, et al. "Controlled ovarian stimulation induces a functional genomic delay of the endometrium with potential clinical implications." J Clin Endocrinol Metab. 2008;93:4500-10. Abstract

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Conesa A, Bro R, Garcia-Garcia F, et al. "Direct functional assessment of the composite phenotype through multivariate projection strategies." Genomics. 2008;92:373-83. Abstract

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Dopazo J, Al-Shahrour F. "Expression and Microarrays.". In: Methods in Molecular Biology. Vol. 453. NJ,: Humana Press; 2008:.

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Tarraga J, Medina I, Carbonell J, et al. "GEPAS, a web-based tool for microarray data analysis and interpretation." Nucleic Acids Res. 2008;36:W308-14. Abstract

Gotz S, Garcia-Gomez JM, Terol J, et al. "High-throughput functional annotation and data mining with the Blast2GO suite." Nucleic Acids Res. 2008;36:3420-35. Abstract

Wilkinson MD, Senger M, Kawas E, et al. "Interoperability with Moby 1.0–it's better than sharing your toothbrush!" Brief Bioinform. 2008;9:220-31. Abstract

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Reumers J, Conde L, Medina I, et al. "Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases." Nucleic Acids Res. 2008;36:D825-9. Abstract

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Montero-Conde C, Martin-Campos JM, Lerma E, et al. "Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information." Oncogene. 2008;27:1554-61. Abstract

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Saar K, Beck A, Bihoreau MT, et al. "SNP and haplotype mapping for genetic analysis in the rat." Nat Genet. 2008;40:560-6. Abstract

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Huerta-Cepas J, Bueno A, Dopazo J, Gabaldon T. "PhylomeDB: a database for genome-wide collections of gene phylogenies." Nucleic Acids Res. 2008;36:D491-6. Abstract

Capriotti E, Arbiza L, Casadio R, Dopazo J, Dopazo H, Marti-Renom MA. "Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans." Hum Mutat. 2008;29:198-204. Abstract

2007

Dopazo J. "Clustering - Class discovery in the post-genomic era.". In: Fundamentals of data mining in genomics and proteomics. New York, USA: Springer-Verlag, W. Dubitzky, M. Granzow and D.P. Berrar ; 2007.

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Robledo M, González-Neira A, Dopazo J. "f single nucleotide polymorphism arrays: Design, tools and applications.". In: Microarray Technology Through Applications. New York, USA: Taylor & Francis, F. Falciani ; 2007.