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2005
Forment J, Gadea J, Huerta L, et al. Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol. 2005;57:375-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15830128.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15840702.
Vaquerizas JM, Conde L, Yankilevich P, et al. GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res. 2005;33:W616-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15980548.
Azuaje F, Dopazo J. Integrative Data Analysis and Visualization: Introduction to Critical Problems, Goals and Challenges. In: Data analysis and visualisation in genomics and proteomics. Data analysis and visualisation in genomics and proteomics. Wiley, F. Azuaje and J. Dopazo; 2005:3-9.
Al-Shahrour F, Dopazo J. Ontologies and functional genomics. In: Data analysis and visualisation in genomics and proteomics. Data analysis and visualisation in genomics and proteomics. Wiley, F. Azuaje and J. Dopazo; 2005:99-102.
Palacios J, Honrado E, Osorio A, et al. Phenotypic characterization of BRCA1 and BRCA2 tumors based in a tissue microarray study with 37 immunohistochemical markers. Breast Cancer Res Treat. 2005;90:5-14. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15770521.
Alvarez S, Diaz-Uriarte R, Osorio A, et al. A predictor based on the somatic genomic changes of the BRCA1/BRCA2 breast cancer tumors identifies the non-BRCA1/BRCA2 tumors with BRCA1 promoter hypermethylation. Clin Cancer Res. 2005;11:1146-53. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15709182.
Antón J, Peña A, Valens M, et al. Salinibacter ruber: genomics and biogeography. In: Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya.Vol 9. Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya. Dordrecht, Netherlands: Nina Gunde-Cimerman, Ana Plemenitas, and Aharon Oren. Kluwer Academic Publishers; 2005:257-266.
Antón J, Peña A, Valens M, et al. Salinibacter ruber: genomics and biogeography. In: Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya.Vol 9. Adaptation to life in high salt concentrations in Archaea, Bacteria and Eukarya. Dordrecht, Netherlands: Nina Gunde-Cimerman, Ana Plemenitas, and Aharon Oren. Kluwer Academic Publishers; 2005:257-266.
2006
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. Available at: http://nar.oxfordjournals.org/content/34/suppl_2/W472.long.
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. Available at: http://nar.oxfordjournals.org/content/34/suppl_2/W472.long.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16823138.
Dopazo J, Aloy P. Discovery and hypothesis generation through bioinformatics. Genome Biol. 2006;7:307. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16522224.
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.
Largo C, Alvarez S, Saez B, et al. Identification of overexpressed genes in frequently gained/amplified chromosome regions in multiple myeloma. Haematologica. 2006;91:184-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16461302.
Montaner D, Tarraga J, Huerta-Cepas J, et al. Next station in microarray data analysis: GEPAS. Nucleic Acids Res. 2006;34:W486-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16845056.
Montaner D, Tarraga J, Huerta-Cepas J, et al. Next station in microarray data analysis: GEPAS. Nucleic Acids Res. 2006;34:W486-91. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16845056.
Azuaje F, Al-Shahrour F, Dopazo J. Ontology-driven approaches to analyzing data in functional genomics. Methods Mol Biol. 2006;316:67-86. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16671401.
Azuaje F, Al-Shahrour F, Dopazo J. Ontology-driven approaches to analyzing data in functional genomics. Methods Mol Biol. 2006;316:67-86. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16671401.
Arbiza L, Dopazo J, Dopazo H. Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol. 2006;2:e38. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16683019.
Conde L, Vaquerizas JM, Dopazo H, et al. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. 2006;34:W621-5. Available at: http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W621.
Arbiza L, Duchi S, Montaner D, et al. Selective pressures at a codon-level predict deleterious mutations in human disease genes. J Mol Biol. 2006;358:1390-404. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16584746.
2007
Terol J, Conesa A, Colmenero JM, et al. Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics. 2007;8:31. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17254327.
Terol J, Conesa A, Colmenero JM, et al. Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics. 2007;8:31. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17254327.
Terol J, Conesa A, Colmenero JM, et al. Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance. BMC Genomics. 2007;8:31. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17254327.