Publications

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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.
Marti-Renom MA, Rossi A, Al-Shahrour F, et al. The AnnoLite and AnnoLyze programs for comparative annotation of protein structures. BMC Bioinformatics. 2007;8 Suppl 4:S4. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17570147.
Ruiz-Llorente S, Montero-Conde C, Milne RL, et al. Association study of 69 genes in the ret pathway identifies low-penetrance loci in sporadic medullary thyroid carcinoma. Cancer Res. 2007;67:9561-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17909067.
Aragues R, Sali A, Bonet J, Marti-Renom MA, Oliva B. Characterization of protein hubs by inferring interacting motifs from protein interactions. PLoS Comput Biol. 2007;3:1761-71. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17941705.
Marti-Renom MA, Pieper U, Madhusudhan MS, et al. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007;35(Web Server issue):W393-7. doi:10.1093/nar/gkm236.
Marti-Renom MA, Pieper U, Madhusudhan MS, et al. DBAli tools: mining the protein structure space. Nucleic Acids Res. 2007;35:W393-7. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478513.
Nueda MJ, Conesa A, Westerhuis JA, et al. Discovering gene expression patterns in time course microarray experiments by ANOVA-SCA. Bioinformatics. 2007;23:1792-800. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17519250.
Hernández P, Huerta-Cepas J, Montaner D, et al. Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics. 2007;8:185. doi:10.1186/1471-2164-8-185.
Hernandez P, Huerta-Cepas J, Montaner D, et al. Evidence for systems-level molecular mechanisms of tumorigenesis. BMC Genomics. 2007;8:185. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17584915.
Al-Shahrour F, Minguez P, Tárraga 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(Web Server issue):W91-6. doi:10.1093/nar/gkm260.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17478504.
Gabaldón T, Huynen MA. From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism. PLoS Comput Biol. 2007;3:e219. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17983265.
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. doi:10.1186/1471-2105-8-114.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17407596.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17597935.
Conde L, Montaner D, Burguet-Castell J, Tárraga J, Al-Shahrour F, Dopazo J. Functional profiling and gene expression analysis of chromosomal copy number alterations. Bioinformation. 2007;1(10):432-5. doi:10.6026/97320630001432.
Minguez P, Al-Shahrour F, Montaner D, Dopazo J. Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics. 2007;23(22):3098-9. doi:10.1093/bioinformatics/btm445.
Minguez P, Al-Shahrour F, Montaner D, Dopazo J. Functional profiling of microarray experiments using text-mining derived bioentities. Bioinformatics. 2007;23:3098-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17855415.
Huerta-Cepas J, Dopazo H, Dopazo J, Gabaldón T. The human phylome. Genome Biol. 2007;8:R109. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17567924.
Rico D, Vaquerizas JM, Dopazo H, Bosca L. Identification of conserved domains in the promoter regions of nitric oxide synthase 2: implications for the species-specific transcription and evolutionary differences. BMC Genomics. 2007;8:271. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17686182.
Conde L, Montaner D, Burguet-Castell J, et al. ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res. 2007;35:W81-5. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17468499.
Conde L, Montaner D, Burguet-Castell J, et al. ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res. 2007;35(Web Server issue):W81-5. doi:10.1093/nar/gkm257.
Schluter A, Fourcade S, Domenech-Estevez E, et al. PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. Nucleic Acids Res. 2007;35:D815-22. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17135190.
Tarraga J, Medina I, Arbiza L, et al. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res. 2007;35:W38-42. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17452346.