BioInfo bibliography

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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  Download: PDF (2.27 MB)
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  Download: PDF (401.81 KB)
Dopazo J. "Formulating and testing hypotheses in functional genomics." Artif Intell Med. 2009;45:97-107. Abstract  Download: PDF (319.6 KB)
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:. Download: PDF (216.1 KB)
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  Download: PDF (7.23 MB)
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  Download: PDF (821.14 KB)
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  Download: PDF (1.38 MB)
Dopazo J, Al-Shahrour F. "Expression and Microarrays.". In: Methods in Molecular Biology. Vol. 453. NJ,: Humana Press; 2008:. Download: PDF (2.52 MB)
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  Download: PDF (155.91 KB)
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  Download: PDF (1.83 MB)
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  Download: PDF (267.4 KB)
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  Download: PDF (332.29 KB)
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. Download: PDF (267.98 KB)
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.
Al-Shahrour F, Minguez P, Tarraga J, et al. "FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments." Nucleic Acids Res. 2007;35:W91-6. Abstract
Al-Shahrour F, Arbiza L, Dopazo H, et al. "From genes to functional classes in the study of biological systems." BMC Bioinformatics. 2007;8:114. Abstract
Dopazo J, Al-Shahrour F. "Functional annotation of microarray experiments.". In: Microarray Technology Through Applications. New York, USA: Taylor & Francis, F. Falciani; 2007.
Conde L, Montaner D, Burguet-Castell J, Tarraga J, Al-Shahrour F, Dopazo J. "Functional profiling and gene expression analysis of chromosomal copy number alterations." Bioinformation. 2007;1:432-5. Abstract