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2008
Dopazo J, Al-Shahrour F. Expression and microarrays. Methods Mol Biol. 2008;453:245-55. doi:10.1007/978-1-60327-429-6_12.
Tárraga J, Medina I, Carbonell J, et al. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 2008;36(Web Server issue):W308-14. doi:10.1093/nar/gkn303.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18508806.
Götz S, García-Gómez JMiguel, Terol J, et al. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 2008;36(10):3420-35. doi:10.1093/nar/gkn176.
Wilkinson MD, Senger M, Kawas E, et al. Interoperability with Moby 1.0--it's better than sharing your toothbrush!. Brief Bioinform. 2008;9(3):220-31. doi:10.1093/bib/bbn003.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18238804.
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. Available at: http://nar.oxfordjournals.org/cgi/content/full/36/suppl_1/D825.
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(Database issue):D825-9. doi:10.1093/nar/gkm979.
Botton A, Galla G, Conesa A, Bachem C, Ramina A, Barcaccia G. Large-scale Gene Ontology analysis of plant transcriptome-derived sequences retrieved by AFLP technology. BMC Genomics. 2008;9:347. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18652646.
Montero-Conde C, Martín-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(11):1554-61. doi:10.1038/sj.onc.1210792.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17873908.
Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 2008;36(Database issue):D491-6. doi:10.1093/nar/gkm899.
Huerta-Cepas J, Bueno A, Dopazo J, Gabaldón T. PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 2008;36:D491-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17962297.
Espadaler J, Eswar N, Querol E, et al. Prediction of enzyme function by combining sequence similarity and protein interactions. BMC Bioinformatics. 2008;9:249. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18505562.
Capriotti E, Marti-Renom MA. RNA structure alignment by a unit-vector approach. Bioinformatics. 2008;24:i112-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18689811.
Dopazo H. Selective Constraints and Human Disease Genes: Evolutionary and Bioinformatic Approaches. In: Encyclopedia of Life Science. Encyclopedia of Life Science. UK: John Wiley & Sons, Ltd.; 2008. doi:10.1002/9780470015902.a0020762.
Dopazo H. Selective Constraints on Human Disease Mutations and Polymorphisms. In: Handbook of Human Molecular Evolution. Handbook of Human Molecular Evolution. UK: Hildegard Kehrer-Sawatzki & David N. Cooper. John Wiley & Sons, Ltd; 2008. Available at: http://eu.wiley.com/WileyCDA/WileyTitle/productCd-0470517468,descCd-description.html.
Saar K, Beck A, Bihoreau MT, et al. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet. 2008;40:560-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18443594.
Saar K, Beck A, Bihoreau M-T, et al. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet. 2008;40(5):560-6. doi:10.1038/ng.124.
Agudo M, Perez-Marin MC, Lonngren U, et al. Time course profiling of the retinal transcriptome after optic nerve transection and optic nerve crush. Mol Vis. 2008;14:1050-63. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18552980.
Hoogerwerf WA, Sinha M, Conesa A, et al. Transcriptional profiling of mRNA expression in the mouse distal colon. Gastroenterology. 2008;135:2019-29. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18848557.
Stierum R, Conesa A, Heijne W, et al. Transcriptome analysis provides new insights into liver changes induced in the rat upon dietary administration of the food additives butylated hydroxytoluene, curcumin, propyl gallate and thiabendazole. Food Chem Toxicol. 2008;46:2616-28. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18539377.
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(1):198-204. doi:10.1002/humu.20628.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17935148.
2009
Madhusudhan MS, Webb BM, Marti-Renom MA, Eswar N, Sali A. Alignment of multiple protein structures based on sequence and structure features. Protein engineering, design & selection : PEDS. 2009;22:569-74.