Publications

Info about publications

2010

Gabaldón, T, Capella-Gutiérrez S.  2010.  Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes.. Gene. Abstract
Pubmed
Huerta-Cepas, J, Marcet-Houben M, Pignatelli M, Moya A, Gabaldón T.  2010.  The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes.. Insect Mol. Biol.. 19 Suppl 2:13–21. Abstract
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Huerta_Cepas_IMB_2010.pdf
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Gómez-Baldó, L, Schmidt S, Maxwell CA., Bonifaci N, Gabaldón T, Vidalain PO., Senapedis W, Kletke A, Rosing M, Barnekow A et al..  2010.  TACC3-TSC2 maintains nuclear envelope structure and controls cell division.. Cell cycle . 9 Abstract
Pubmed
Díez, J, Walter D, Muñoz-Pinedo C, Gabaldón T.  2010.  DeathBase: a database on structure, evolution and function of proteins involved in apoptosis and other forms of cell death.. Cell Death Differ.. 17:735–736.
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Diez_DeathBase_CDD_2010.pdf
 Pubmed
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Diez_DeathBase_CDD_2010.pdf
Gerardo, NM., Altincicek B, Anselme C, Atamian H, Barribeau SM., de Vos M, Duncan E, Evans JD., Gabaldón T, Ghanim M et al..  2010.  Immunity and other defenses in pea aphids, Acyrthosiphon pisum.. Genome biology. 11:R21. Abstract
Pubmed
Peña, A, Teeling H, Huerta-Cepas J, Santos F, Yarza P, Brito-Echeverría J, Lucio M, Schmitt-Kopplin P, Meseguer I, Schenowitz C et al..  2010.  Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains.. The ISME journal. Abstract
Pubmed
Ahmadinejad, N, Dagan T, Gruenheit N, Martin W, Gabaldón T.  2010.  Evolution of spliceosomal introns following endosymbiotic gene transfer.. BMC evolutionary biology. 10:57. Abstract
Pubmed
Consortium, T I A G.  2010.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
Pubmed
Milinkovitch, MC., Helaers R, Depiereux E, Tzika AC., Gabaldon T.  2010.  2X genomes - depth does matter.. Genome biology. 11:R16. Abstract
Pubmed
Gabaldón, T.  2010.  Peroxisome diversity and evolution.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 365:765–773. Abstract
Pubmed
Mihailovich, M, Militti C, Gabaldón T, Gebauer F.  2010.  Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression.. BioEssays. 32:109–118. Abstract
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Mihailovich_et_al_BioEssays_2009_coldShok.pdf
 Pubmed
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Mihailovich_et_al_BioEssays_2009_coldShok.pdf
Huerta-Cepas, J, Dopazo J, Gabaldón T.  2010.  ETE: a python Environment for Tree Exploration.. BMC bioinformatics. 11:24. Abstract
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Huerta_cepas_et_al_2010_ETE.pdf
 Pubmed
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Huerta_cepas_et_al_2010_ETE.pdf

2009

Marcet-Houben, M, Marceddu G, Gabaldón T.  2009.  Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence.. BMC Evol. Biol.. 9:295. Abstract
Pubmed
Gabaldón, T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer EL, Lewis S.  2009.  Joining forces in the quest for orthologs. Genome Biol.. 10:403.
Pubmed
Marcet-Houben, M, Gabaldón T.  2009.  Acquisition of prokaryotic genes by fungal genomes. Trends Genet..
Pubmed
Schlüter, A, Real-Chicharro A, Gabaldón T, Sánchez-Jiménez F, Pujol A.  2009.  PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. Nucleic Acids Res..
Pubmed
Marcet-Houben, M, Gabaldón T.  2009.  The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome.. PLoS ONE. 4:e4357. Abstract
Pubmed
Gil-Borlado, MC., González-Hoyuela M, Blázquez A, García-Silva MT., Gabaldón T, Manzanares J, Vara J, Martín MA., Seneca S, Arenas J et al..  2009.  Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency.. Mitochondrion. 9:299–305. Abstract
Pubmed
Capella-Gutiérrez, S, Silla-Martínez JM., Gabaldón T.  2009.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.. Bioinformatics. 25:1972–1973. Abstract
Pubmed

2008

Gabaldón, T.  2008.  Large-scale assignment of orthology: back to phylogenetics? Genome Biol.. 9:235. Abstract
Pubmed
Huerta-Cepas, J, Bueno A, Dopazo J, Gabaldón T.  2008.  PhylomeDB: a database for genome-wide collections of gene phylogenies.. Nucleic Acids Res.. 36:D491–D496. Abstract
Pubmed

2007

Gabaldón, T, Peretó J, Montero F, Gil R, Latorre A, Moya A.  2007.  Structural analyses of a hypothetical minimal metabolism.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 362:1751–1762. Abstract
Pubmed
Schlüter, A, Fourcade S, Domènech-Estévez E, Gabaldón T, Huerta-Cepas J, Berthommier G, Ripp R, Wanders RJ., Poch O, Pujol A.  2007.  PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.. Nucleic Acids Res.. 35:D815–D822. Abstract
Pubmed
Huerta-Cepas, J, Dopazo H, Dopazo J, Gabaldón T.  2007.  The human phylome.. Genome Biol.. 8:R109. Abstract
Pubmed
Tárraga, J, Medina I, Arbiza L, Huerta-Cepas J, Gabaldón T, Dopazo J, Dopazo H.  2007.  Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res.. 35:38–42.
Pubmed

2006

Gabaldón, T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA..  2006.  Origin and evolution of the peroxisomal proteome.. Biol. Direct. 1:8. Abstract
Pubmed

2005

Gabaldón, T, Huynen MA..  2005.  Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.. Bioinformatics. 21 Suppl 2:ii144–ii150. Abstract
Pubmed
Gabaldón, T, Rainey D, Huynen MA..  2005.  Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).. J. Mol. Biol.. 348:857–870. Abstract
Pubmed
Boxma, B, de Graaf RM., van der Staay GW., van Alen TA., Ricard G, Gabaldón T, van Hoek AH., Moon-van der Staay SY., Koopman WJ., van Hellemond JJ. et al..  2005.  An anaerobic mitochondrion that produces hydrogen.. Nature. 434:74–79. Abstract
Pubmed

2004

Vella, F, Mietchen D, Gabaldón T.  2004.  Perceptions about postdocs. EMBO Rep.. 5:1104.
Pubmed

2003

Gabaldón, T, Huynen MA..  2003.  Reconstruction of the proto-mitochondrial metabolism.. Science. 301:609.
Pubmed
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