Affiliation: Center for Genomic Regulation
- Comparative genomics of emerging pathogens in the Candida glabrata cladeToni Gabaldón
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG and UPF, Doctor Aiguader, 88, Barcelona, 08003, Spain
BMC Genomics 14:623. 2013..bracarensis. To gain insight into the genomic changes underlying the emergence of virulence, we sequenced the genomes of these two, and three other non-pathogenic Nakaseomyces, and compared them to other sequenced yeasts...
- Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrusMarina Marcet-Houben
Centre for Genomic Regulation, Barcelona, Spain
BMC Genomics 13:646. 2012..digitatum strains that differ in their antifungal resistance traits have been sequenced and compared with those of 28 other Pezizomycotina...
- Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergenceMarina Marcet-Houben
Comparative Genomics, Centre for Genomics Regulation, 08003 Barcelona, Spain
BMC Evol Biol 9:295. 2009..To identify the main mechanisms behind the evolution of respiratory pathways, we conducted a phylogenomics survey of oxidative phosphorylation components in the genomes of sixty fungal species...
- PhylomeDB v4: zooming into the plurality of evolutionary histories of a genomeJaime Huerta-Cepas
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader, 88 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain and Institució Catalana de Recerca i Estudis Avançats ICREA, Pg Lluis Companys 23, 08010 Barcelona, Spain
Nucleic Acids Res 42:D897-902. 2014....
- TreeKO: a duplication-aware algorithm for the comparison of phylogenetic treesMarina Marcet-Houben
Centre for Genomic Regulation, UPF, Doctor Aiguader 88, 08003 Barcelona, Spain
Nucleic Acids Res 39:e66. 2011..In addition treeKO, implements the possibility of computing phylome support values, and reconciliation-based measures such as the number of inferred duplication and loss events...
- Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungiSalvador Capella-Gutierrez
Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG and UPF, Doctor Aiguader, 88, 08003 Barcelona, Spain
BMC Biol 10:47. 2012..Due to the presence of accelerated evolutionary rates, phylogenetic analyses involving microsporidia are prone to methodological artifacts, such as long-branch attraction, especially when taxon sampling is limited...
- Acquisition of prokaryotic genes by fungal genomesMarina Marcet-Houben
Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Doctor Aiguader, 88 08003 Barcelona, Spain
Trends Genet 26:5-8. 2010..Transferred genes included bacterial arsenite reductase, catalase, different racemases and peptidoglycan metabolism enzymes. Our results suggest an important role for HGT in fungal evolution...
- PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictionsJaime Huerta-Cepas
Bioinformatics and Genomics Programme, Centre de Regulacio Genomica, 08003 Barcelona, Spain
Nucleic Acids Res 39:D556-60. 2011..Finally, PhylomeDB is currently being used by several genome sequencing projects that couple the genome annotation process with the reconstruction of the corresponding phylome, a strategy that provides relevant evolutionary insights...