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Gabald\'f3n 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.\par \par Gabald\'f3n T, Gil R, Peret\'f3 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.\par \par Huerta-Cepas J, Bueno A, Dopazo J, Gabald\'f3n 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.\par \par Gabald\'f3n 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.\par \par Huerta-Cepas J, Dopazo H, Dopazo J, Gabald\'f3n 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.\par \par 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.\par \par 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.\par \par Gabald\'f3n T, Huynen MA. Reconstruction of ancestral proteomes. In:  Ancestral Sequence Reconstruction. Ancestral Sequence Reconstruction. Oxford: D. Liberles; 2007. Available at: http://www.us.oup.com/us/catalog/general/subject/LifeSciences/EvolutionaryBiology/?view=usa&ci=9780199299188.\par \par Gabald\'f3n T, Peret\'f3 J, Montero F, Gil R, Latorre A, Moya A. Structural analyses of a hypothetical minimal metabolism. Philos Trans R Soc Lond B Biol Sci. 2007;362:1751-62. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17510022.\par \par Gabald\'f3n T. Computational approaches for the prediction of protein function in the mitochondrion. Am J Physiol Cell Physiol. 2006;291:C1121-8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16870830.\par \par Gabald\'f3n T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA. Origin and evolution of the peroxisomal proteome. Biol Direct. 2006;1:8. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16556314.\par \par Boxma B, de Graaf RM, van der Staay GW, et al. An anaerobic mitochondrion that produces hydrogen. Nature. 2005;434:74-9. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15744302.\par \par Huynen MA, Spronk CA, Gabald\'f3n T, Snel B. Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin. FEBS Lett. 2005;579:591-6. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15670813.\par \par Gabald\'f3n T. Evolution of proteins and proteomes: a phylogenetics approach. Evol Bioinform Online. 2005;1:51-61. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19325853.\par \par Gabald\'f3n T, Huynen MA. Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. Bioinformatics. 2005;21 Suppl 2:ii144-50. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16204094.\par \par Gabald\'f3n T, Rainey D, Huynen MA. Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I). J Mol Biol. 2005;348:857-70. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15843018.\par \par Huynen MA, Gabald\'f3n T, Snel B. Variation and evolution of biomolecular systems: searching for functional relevance. FEBS Lett. 2005;579:1839-45. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15763561.\par \par Vella F, Mietchen D, Gabald\'f3n T. Perceptions about postdocs. EMBO Rep. 2004;5:1104. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15577920.\par \par Gabald\'f3n T, Huynen MA. Prediction of protein function and pathways in the genome era. Cell Mol Life Sci. 2004;61:930-44. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15095013.\par \par Gabald\'f3n T, Huynen MA. Shaping the mitochondrial proteome. Biochim Biophys Acta. 2004;1659:212-20. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15576054.\par \par Gabald\'f3n T, Huynen MA. Reconstruction of the proto-mitochondrial metabolism. Science. 2003;301:609. Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12893934.\par \par }