babelomics

Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling.

Medina I, Carbonell J, Pulido L, et al. "Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling." Nucleic acids research. 2010.

Functional genomics and networks: new approaches in the extraction of complex gene modules.

Minguez P, Dopazo J. "Functional genomics and networks: new approaches in the extraction of complex gene modules." Expert Rev Proteomics. 2010;7(1):55-63.

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

Medina I, Montaner D, Bonifaci N, et al. "Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies." Nucl. Acids Res.. 2009;37:W340-344.

Functional assessment of time course microarray data.

Nueda M J, Sebastián P, Tarazona S, et al. "Functional assessment of time course microarray data." BMC Bioinformatics. 2009;10 Suppl 6:S9.

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

Al-Shahrour F, Minguez P, Tarraga J, et al. "BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments." Nucleic Acids Res. 2006;34:W472-6.

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Al-Shahrour F, Diaz-Uriarte R, Dopazo J. "FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes." Bioinformatics. 2004;20:578-80.

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments

Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. "BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments." Nucleic Acids Res. 2005;33:W460-4.

Functional interpretation of microarray experiments

Dopazo J. "Functional interpretation of microarray experiments." OMICS. 2006;10:398-410.

Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information

Al-Shahrour F, Diaz-Uriarte R, Dopazo J. "Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information." Bioinformatics. 2005;21:2988-93.

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. "Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research." Bioinformatics. 2005;21:3674-6.

Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis

Aparicio G, Gotz S, Conesa A, et al. "Blast2GO goes grid: developing a grid-enabled prototype for functional genomics analysis." Stud Health Technol Inform. 2006;120:194-204.

Ontology-driven approaches to analyzing data in functional genomics

Azuaje F, Al-Shahrour F, Dopazo J. "Ontology-driven approaches to analyzing data in functional genomics." Methods Mol Biol. 2006;316:67-86.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments

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.

From genes to functional classes in the study of biological systems

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.

Functional profiling of microarray experiments using text-mining derived bioentities

Minguez P, Al-Shahrour F, Montaner D, Dopazo J. "Functional profiling of microarray experiments using text-mining derived bioentities." Bioinformatics. 2007;23:3098-9.

Functional profiling and gene expression analysis of chromosomal copy number alterations

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.

A function-centric approach to the biological interpretation of microarray time-series

Minguez P, Al-Shahrour F, Dopazo J. "A function-centric approach to the biological interpretation of microarray time-series." Genome Inform. 2006;17:57-66.

Prophet, a web-based tool for class prediction using microarray data

Medina I, Montaner D, Tarraga J, Dopazo J. "Prophet, a web-based tool for class prediction using microarray data." Bioinformatics. 2007;23:390-1.

Formulating and testing hypotheses in functional genomics

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

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

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.

Using Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes

Al-Shahrour F, Herrero J, Mateos A, Santoyo J, Díaz-Uriarte R, Dopazo J. "Using Gene Ontology on genome-scale studies to find significant associations of biologically relevant terms to group of genes.". In: Neural Networks for Signal Processing XIII. New York, USA: IEEE Press; 2003:.

Data analysis and visualisation in genomics and proteomics

Azuaje F, Dopazo J. "Data analysis and visualisation in genomics and proteomics." Wiley, F. Azuaje and J. Dopazo; 2005.

Microarray Technology in Agricultural Research

Conesa A, Forment J, Gadea J, van Dijk J. "Microarray Technology in Agricultural Research.". In: Microarray Technology Through Applications. F. Falciani. Publisher: Taylor and Francis Group; 2007:.
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