Publications

Export 372 results:
Author Title Type [ Year(Asc)]
2009
Pieper U, Eswar N, Webb BM, et al. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009;37:D347-54. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18948282.
Jones AR, Lister AL, Hermida L, et al. Modeling and managing experimental data using FuGE. OMICS. 2009;13:239-51.
Fornes O, Aragues R, Espadaler J, Marti-Renom MA, Sali A, Oliva B. ModLink+: Improving fold recognition by using protein-protein interactions. Bioinformatics. 2009. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19357100.
van Heerden JH, Conesa A, Stein DJ, Montaner D, Russell V, Illing N. Parallel changes in gene expression in peripheral blood mononuclear cells and the brain after maternal separation in the mouse. BMC Res Notes. 2009;2:195.
Reiss JO, Burke AC, Archer C, et al. Pere Alberch: Originator of EvoDevo. Biological Theory. 2009;3:351-353.
Minguez P, Dopazo J. Protein Interactions for Functional Genomics. In: Li X-L, Ng S-K, eds. Biological Data Mining in Protein Interaction Networks. Biological Data Mining in Protein Interaction Networks. Hershey, USA: Idea Group Inc (IGI); 2009:223-238. Available at: http://books.google.es/books?id=pNyCy5GsqtkC.
Capriotti E, Marti-Renom MA. SARA: a server for function annotation of RNA structures. Nucl. Acids Res. 2009:gkp433. doi:10.1093/nar/gkp433.
Martin-Coello J, Dopazo H, Arbiza L, Ausio J, Roldan ER, Gomendio M. Sexual selection drives weak positive selection in protamine genes and high promoter divergence, enhancing sperm competitiveness. Proc Biol Sci. 2009. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19364735.
Minguez P, Gotz S, Montaner D, Al-Shahrour F, Dopazo J. SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucl. Acids Res. 2009;37:W109-114. doi:10.1093/nar/gkp402.
Birmingham A, Selfors LM, Forster T, et al. Statistical methods for analysis of high-throughput RNA interference screens. Nature Methods. 2009;6:569 - 575. Available at: http://dx.doi.org/10.1038/nmeth.1351.
Marti-Renom MA, Capriotti E, Shindyalov I, Bourne P. Structural Comparison and Alignment. In: Structural Bioinformatics. 2ndnd ed. Structural Bioinformatics. New Jersey. USA: Wiley-Blackwell; 2009. Available at: http://www.amazon.com/gp/product/0470181052/.
2008
Capriotti E, Marti-Renom MA. Assessment of protein structure predictions. In: Computational Structural Biology. Computational Structural Biology. New Jersey, USA: World Scientific Publishing Company; 2008. Available at: http://www.amazon.com/dp/9812778772/.
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. Available at: http://nar.oxfordjournals.org/content/36/suppl_2/W341.long.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19094230.
Conesa A, Gotz S. Blast2GO: A Comprehensive Suite for Functional Analysis in Plant Genomics. Int J Plant Genomics. 2008;2008:619832. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18483572.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17597009.
Gabaldón T. Comparative genomics-based prediction of protein function. In: Methods in Molecular Biology.Vol 439. Methods in Molecular Biology. M. Starkey and R. Elaswarapu, Humana press; 2008. Available at: http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-188-8_26.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18697870.
Gabaldón T, Gil R, Peretó J, Latorre A, Moya A. The core of a minimal gene set: insights from natural reduced genomes. In: Protocells: Bridging nonliving and living matter. Protocells: Bridging nonliving and living matter. USA: The MIT Press; 2008:347-366.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18652888.
Panjkovich A, Melo F, Marti-Renom MA. Evolutionary potentials: structure specific knowledge-based potentials exploiting the evolutionary record of sequence homologs. Genome Biol. 2008;9:R68. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18397517.
Dopazo J, Al-Shahrour F. Expression and Microarrays. In: Methods in Molecular Biology.Vol 453. Methods in Molecular Biology. NJ,: Humana Press; 2008:245-255. doi:10.1007/978-1-60327-429-6_12.
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.
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. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18445632.
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.