Publications

Info about publications

2011

Silva, LL., Marcet-Houben M, Zerlotini A, Gabaldón T, Oliveira G, Nahum LA..  2011.  Evolutionary histories of expanded peptidase families in Schistosoma mansoni.. Mem. Inst. Oswaldo Cruz. 106:864–877. Abstract
application/pdf iconLopezSilva_Schistosoma_Peptidases_MIOC_2011.pdf
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application/pdf iconLopezSilva_Schistosoma_Peptidases_MIOC_2011.pdf
Neurohr, G, Naegeli A, Titos I, Theler D, Greber B, Díez J, Gabaldón T, Mendoza M, Barral Y.  2011.  A midzone-based ruler adjusts chromosome compaction to anaphase spindle length.. Science. 332:465–468. Abstract
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Huerta-Cepas, J, Dopazo J, Huynen MA., Gabaldón T.  2011.  Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.. Briefings in bioinformatics. Abstract
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Vellozo, AF., Véron AS., Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE., Gabaldón T et al..  2011.  CycADS: an annotation database system to ease the development and update of BioCyc databases.. Database (Oxford). 2011:bar008. Abstract
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Sánchez, R, Serra F, Tárraga J, Medina I, Carbonell J, Pulido L, de María A, Capella-Gutiérrez S, Huerta-Cepas J, Gabaldón T et al..  2011.  Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.. Nucleic Acids Res.. 39 Suppl 2:W470–W474. Abstract
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Huerta-Cepas, J, Gabaldón T.  2011.  Assigning duplication events to relative temporal scales in genome-wide studies.. Bioinformatics. 27:38–45. Abstract
application/pdf iconHuerta-cepas_Gabaldon_Bioinformatics_2010.pdf
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application/pdf iconHuerta-cepas_Gabaldon_Bioinformatics_2010.pdf
Huerta-Cepas, J, Capella-Gutiérrez S, Pryszcz LP., Denisov I, Kormes D, Marcet-Houben M, Gabaldón T.  2011.  PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.. Nucleic Acids Res.. 39:D556–D560. Abstract
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Pryszcz, LP., Huerta-Cepas J, Gabaldón T.  2011.  MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.. Nucleic Acids Res.. 39:e32. Abstract
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Marcet-Houben, M, Gabaldón T.  2011.  TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.. Nucleic acids research. Abstract
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Roetzer, A, Klopf E, Gratz N, Marcet-Houben M, Hiller E, Rupp S, Gabaldón T, Kovarik P, Schüller C.  2011.  Regulation of Candida glabrata oxidative stress resistance is adapted to host environment.. FEBS Lett.. 585:319–327. Abstract
Pubmed

2010

Benítez-Páez, A, Villarroya M, Douthwaite S, Gabaldón T, Armengod ME..  2010.  YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNALeu isoacceptors.. RNA (New York, N.Y.). Abstract
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Roetzer, A, Gabaldón T, Schüller C.  2010.  From Saccharomyces cerevisiae to Candida glabrata in a few easy steps: important adaptations for an opportunistic pathogen.. FEMS microbiology letters. Abstract
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Gil Borlado, MC., Moreno Lastres D, Gonzalez Hoyuela M, Moran M, Blazquez A, Pello R, Marin Buera L, Gabaldón T, Garcia Peñas JJ., Martín MA. et al..  2010.  Impact of the mitochondrial genetic background in complex III deficiency.. PLoS ONE. 5 Abstract
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Lingner, T, Muhlhausen S, Gabaldón T, Notredame C, Meinicke P.  2010.  Predicting phenotypic traits of prokaryotes from protein domain frequencies.. BMC bioinformatics. 11:481. Abstract
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Gabaldón, T, Capella-Gutiérrez S.  2010.  Lack of phylogenetic support for a supposed actinobacterial origin of peroxisomes.. Gene. Abstract
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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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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
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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.
application/pdf iconDiez_DeathBase_CDD_2010.pdf
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application/pdf iconDiez_DeathBase_CDD_2010.pdf
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
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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
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Consortium, T I A G.  2010.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
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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
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Milinkovitch, MC., Helaers R, Depiereux E, Tzika AC., Gabaldon T.  2010.  2X genomes - depth does matter.. Genome biology. 11:R16. Abstract
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Gabaldón, T.  2010.  Peroxisome diversity and evolution.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 365:765–773. Abstract
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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
application/pdf iconMihailovich_et_al_BioEssays_2009_coldShok.pdf
 Pubmed
application/pdf iconMihailovich_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
application/pdf iconHuerta_cepas_et_al_2010_ETE.pdf
 Pubmed
application/pdf iconHuerta_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
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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.
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Marcet-Houben, M, Gabaldón T.  2009.  Acquisition of prokaryotic genes by fungal genomes. Trends Genet..
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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..
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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
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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
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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

2008

Gabaldón, T.  2008.  Large-scale assignment of orthology: back to phylogenetics? Genome Biol.. 9:235. Abstract
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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
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2007

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
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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
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Huerta-Cepas, J, Dopazo H, Dopazo J, Gabaldón T.  2007.  The human phylome.. Genome Biol.. 8:R109. Abstract
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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.
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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
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2005

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
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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
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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
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2004

Vella, F, Mietchen D, Gabaldón T.  2004.  Perceptions about postdocs. EMBO Rep.. 5:1104.
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2003

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