Publications
Info about publications
2012
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2012. Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus.. BMC Genomics. 13:646. Abstract
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2012. The genome of wine yeast Dekkera bruxellensis provides a tool to explore its food-related properties.. Int. J. Food Microbiol.. 157:202–209. Abstract
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2012. The genome of melon (Cucumis melo L.).. Proc. Natl. Acad. Sci. U.S.A.. 109:11872–11877. Abstract
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2012. Mitochondrial genome variability within the Candida parapsilosis species complex.. Mitochondrion. 12:514–519. Abstract
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2012. Selection of marker genes using whole-genome DNA polymorphism analysis.. Evol. Bioinform. Online. 8:161–169. Abstract
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2012. Toward community standards in the quest for orthologs.. Bioinformatics (Oxford, England). 28:900–904. Abstract
2011
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2011. Evolutionary histories of expanded peptidase families in Schistosoma mansoni.. Mem. Inst. Oswaldo Cruz. 106:864–877. Abstract
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2011. CycADS: an annotation database system to ease the development and update of BioCyc databases.. Database (Oxford). 2011:bar008. Abstract
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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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2011. A midzone-based ruler adjusts chromosome compaction to anaphase spindle length.. Science. 332:465–468. Abstract
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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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2011. Assigning duplication events to relative temporal scales in genome-wide studies.. Bioinformatics. 27:38–45. Abstract
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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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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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2011. TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees.. Nucleic acids research. Abstract
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2011. Regulation of Candida glabrata oxidative stress resistance is adapted to host environment.. FEBS Lett.. 585:319–327. Abstract
2010
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2010. Impact of the mitochondrial genetic background in complex III deficiency.. PLoS ONE. 5 Abstract
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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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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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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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2010. TACC3-TSC2 maintains nuclear envelope structure and controls cell division.. Cell cycle . 9 Abstract
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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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2010. Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS biology. 8:e1000313. Abstract
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2010. Immunity and other defenses in pea aphids, Acyrthosiphon pisum.. Genome biology. 11:R21. Abstract
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2010. Evolution of spliceosomal introns following endosymbiotic gene transfer.. BMC evolutionary biology. 10:57. Abstract
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2010. Peroxisome diversity and evolution.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 365:765–773. Abstract
2009
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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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2009. PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. Nucleic Acids Res..
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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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2009. Pathogenic mutations in the 5' untranslated region of BCS1L mRNA in mitochondrial complex III deficiency.. Mitochondrion. 9:299–305. Abstract
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2009. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.. Bioinformatics. 25:1972–1973. Abstract
2008
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2008. Large-scale assignment of orthology: back to phylogenetics? Genome Biol.. 9:235. Abstract
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2008. PhylomeDB: a database for genome-wide collections of gene phylogenies.. Nucleic Acids Res.. 36:D491–D496. Abstract
2007
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2007. Structural analyses of a hypothetical minimal metabolism.. Philos. Trans. R. Soc. Lond., B, Biol. Sci.. 362:1751–1762. Abstract
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2007. PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.. Nucleic Acids Res.. 35:D815–D822. Abstract
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2007. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res.. 35:38–42.
2006
2005
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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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2005. Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I).. J. Mol. Biol.. 348:857–870. Abstract
2004
2003
