Toni Gabaldón

Summary

Affiliation: Center for Genomic Regulation
Country: Spain

Publications

  1. doi request reprint Functional and evolutionary implications of gene orthology
    Toni Gabaldón
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation and Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
    Nat Rev Genet 14:360-6. 2013
  2. pmc Immunity and other defenses in pea aphids, Acyrthosiphon pisum
    Nicole M Gerardo
    Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E, Clifton Road NE, Atlanta, GA 30322, USA
    Genome Biol 11:R21. 2010
  3. pmc Evolution of spliceosomal introns following endosymbiotic gene transfer
    Nahal Ahmadinejad
    Institut für Botanik III, Heinrich Heine Universitat Dusseldorf, Dusseldorf, Germany
    BMC Evol Biol 10:57. 2010
  4. pmc Large-scale assignment of orthology: back to phylogenetics?
    Toni Gabaldón
    Bioinformatics and Genomics Program, Center for Genomic Regulation, Doctor Aiguader 88, Barcelona, Spain
    Genome Biol 9:235. 2008
  5. pmc Peroxisome diversity and evolution
    Toni Gabaldón
    Centre for Genomic Regulation CRG, Dr Aiguader, 88 08003 Barcelona, Spain
    Philos Trans R Soc Lond B Biol Sci 365:765-73. 2010
  6. pmc PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome
    Agatha Schluter
    Neurometabolic Disease Lab, Institut de Neuropatologia de Bellvitge, Gran Via n 199, 08907 L Hospitalet de Llobregat, Barcelona, Spain
    Nucleic Acids Res 38:D800-5. 2010
  7. pmc MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
    Leszek P Pryszcz
    Bioinformatics and Genomics Programme, Centre de Regulacio Genomica CRG, Universitat Pompeu Fabra, Dr Aiguader, 88 08003, Barcelona, Spain
    Nucleic Acids Res 39:e32. 2011
  8. pmc PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
    Jaime Huerta-Cepas
    Bioinformatics and Genomics Programme, Centre de Regulacio Genomica, 08003 Barcelona, Spain
    Nucleic Acids Res 39:D556-60. 2011
  9. doi request reprint Assigning duplication events to relative temporal scales in genome-wide studies
    Jaime Huerta-Cepas
    Centre for Genomic Regulation CRG, Barcelona, Spain
    Bioinformatics 27:38-45. 2011
  10. pmc ETE: a python Environment for Tree Exploration
    Jaime Huerta-Cepas
    Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
    BMC Bioinformatics 11:24. 2010

Collaborators

Detail Information

Publications28

  1. doi request reprint Functional and evolutionary implications of gene orthology
    Toni Gabaldón
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation and Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
    Nat Rev Genet 14:360-6. 2013
    ..Here we discuss the complexity of the evolution of gene-phenotype relationships and assess the validity of the key implications of orthology and paralogy relationships as general statistical trends and guiding principles...
  2. pmc Immunity and other defenses in pea aphids, Acyrthosiphon pisum
    Nicole M Gerardo
    Department of Biology, Emory University, O Wayne Rollins Research Center, 1510 E, Clifton Road NE, Atlanta, GA 30322, USA
    Genome Biol 11:R21. 2010
    ....
  3. pmc Evolution of spliceosomal introns following endosymbiotic gene transfer
    Nahal Ahmadinejad
    Institut für Botanik III, Heinrich Heine Universitat Dusseldorf, Dusseldorf, Germany
    BMC Evol Biol 10:57. 2010
    ..We circumvent this problem by using genes originated by endosymbiotic gene transfer, in which an intron-less structure at the time of the transfer can be assumed...
  4. pmc Large-scale assignment of orthology: back to phylogenetics?
    Toni Gabaldón
    Bioinformatics and Genomics Program, Center for Genomic Regulation, Doctor Aiguader 88, Barcelona, Spain
    Genome Biol 9:235. 2008
    ..Recently, automated phylogeny-based orthology prediction has emerged as a feasible alternative for genome-wide studies...
  5. pmc Peroxisome diversity and evolution
    Toni Gabaldón
    Centre for Genomic Regulation CRG, Dr Aiguader, 88 08003 Barcelona, Spain
    Philos Trans R Soc Lond B Biol Sci 365:765-73. 2010
    ..Here, I review recent advances in our understanding of peroxisome diversity and evolution, with a special emphasis on peroxisomes in microbial eukaryotes...
  6. pmc PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome
    Agatha Schluter
    Neurometabolic Disease Lab, Institut de Neuropatologia de Bellvitge, Gran Via n 199, 08907 L Hospitalet de Llobregat, Barcelona, Spain
    Nucleic Acids Res 38:D800-5. 2010
    ..0 is a freely available, highly interactive functional genomics platform that offers an extensive view on the peroxisomal metabolome across lineages, thus facilitating comparative genomics and systems analysis of the organelle...
  7. pmc MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
    Leszek P Pryszcz
    Bioinformatics and Genomics Programme, Centre de Regulacio Genomica CRG, Universitat Pompeu Fabra, Dr Aiguader, 88 08003, Barcelona, Spain
    Nucleic Acids Res 39:e32. 2011
    ..A webserver has been developed to easily access these data (http://orthology.phylomedb.org), which provides users with a global repository of phylogeny-based orthology and paralogy predictions...
  8. pmc PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
    Jaime 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...
  9. doi request reprint Assigning duplication events to relative temporal scales in genome-wide studies
    Jaime Huerta-Cepas
    Centre for Genomic Regulation CRG, Barcelona, Spain
    Bioinformatics 27:38-45. 2011
    ..However, both measures have never been compared in a common framework...
  10. pmc ETE: a python Environment for Tree Exploration
    Jaime Huerta-Cepas
    Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, Barcelona, Spain
    BMC Bioinformatics 11:24. 2010
    ..Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale...
  11. pmc TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees
    Marina 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...
  12. pmc trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
    Salvador Capella-Gutierrez
    Comparative Genomics Group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 88 08003 Barcelona, Spain
    Bioinformatics 25:1972-3. 2009
    ..Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized...
  13. doi request reprint PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
    Jaime 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
    ....
  14. pmc Comparative transcriptomics of early dipteran development
    Eva Jimenez-Guri
    EMBL CRG Research Unit in Systems Biology, Centre de Regulacio Genomica CRG, and Universitat Pompeu Fabra UPF, Barcelona, Spain
    BMC Genomics 14:123. 2013
    ..In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo)...
  15. doi request reprint Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication
    Jaime Huerta-Cepas
    Centre for Genomic Regulation, Barcelona, Spain
    Brief Bioinform 12:442-8. 2011
    ..Our results show that gene duplication leads to increased levels of tissue specificity and that this tends to occur promptly after the duplication event...
  16. pmc Measuring guide-tree dependency of inferred gaps in progressive aligners
    Salvador Capella-Gutierrez
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Doctor Aiguader 88 and Universitat Pompeu Fabra, Barcelona, Spain
    Bioinformatics 29:1011-7. 2013
    ..It has been found that patterns of inferred gaps in alignments contain information towards the true phylogeny, but it is as yet unknown whether gaps are simply reflecting information that was already present in the guide-tree...
  17. pmc Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi
    Salvador 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...
  18. pmc Phylogenomics of the oxidative phosphorylation in fungi reveals extensive gene duplication followed by functional divergence
    Marina 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...
  19. doi request reprint The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)
    Juliane C Dohm
    1 Max Planck Institute for Molecular Genetics, Ihnestraße 63 73, 14195 Berlin, Germany 2 Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain 3 Universitat Pompeu Fabra UPF, C Dr Aiguader 88, 08003 Barcelona, Spain 4
    Nature 505:546-9. 2014
    ..The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology...
  20. pmc Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus
    Marina 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...
  21. doi request reprint A midzone-based ruler adjusts chromosome compaction to anaphase spindle length
    Gabriel Neurohr
    Centre for Genomic Regulation CRG, Barcelona, Spain
    Science 332:465-8. 2011
    ..Thus, the anaphase spindle may function as a ruler to adapt the condensation of chromatids, promoting their segregation regardless of chromosome or spindle length...
  22. pmc PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease
    Agatha Schluter
    Centre de Genètica Mèdica i Molecular, Institut d Investigació Biomèdica de Bellvitge Institut de Recerca Oncològica IDIBELL IRO Hospital Duran i Reynals, Granvia km 2, 7 08907 Hospitalet de Llobregat, Barcelona, Spain
    Nucleic Acids Res 35:D815-22. 2007
    ..PeroxisomeDB should contribute to the systematic characterization of the peroxisomal proteome and facilitate system biology approaches on the organelle...
  23. ncbi request reprint TACC3-TSC2 maintains nuclear envelope structure and controls cell division
    Laia Gómez-Baldó
    Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Barcelona, Spain
    Cell Cycle 9:1143-55. 2010
    ....
  24. pmc Unexpected genomic variability in clinical and environmental strains of the pathogenic yeast Candida parapsilosis
    Leszek P Pryszcz
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Barcelona, Spain
    Genome Biol Evol 5:2382-92. 2013
    ..Furthermore, we report the first evidence for the existence of recombination in this species. Altogether, our results shed new light onto the dynamics of genome evolution in C. parapsilosis...
  25. doi request reprint Acquisition of prokaryotic genes by fungal genomes
    Marina 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...
  26. doi request reprint eggNOG v4.0: nested orthology inference across 3686 organisms
    Sean Powell
    European Molecular Biology Laboratory, Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany, University of Zurich and Swiss Institute of Bioinformatics, Institute of Molecular Life Sciences, Winterthurerstrasse 190, 8057 Zurich, Switzerland, Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109 5234, USA, Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, C Dr Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain, CUBE Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3FG, UK, Biotechnology Center, TU Dresden, 01062 Dresden, Germany, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Atlanta
    Nucleic Acids Res 42:D231-9. 2014
    ..Users can access the complete database of orthologous groups via a web interface, as well as through bulk download. ..
  27. pmc Comparative genomics of emerging pathogens in the Candida glabrata clade
    Toni 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...
  28. doi request reprint Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression
    Marija Mihailovich
    Gene Regulation Programme, Centre de Regulació Genòmica CRG UPF, Barcelona, Spain
    Bioessays 32:109-18. 2010
    ..This review summarizes the current knowledge on eukaryotic CSD/S1 domain-containing proteins with a special emphasis on UNR (upstream of N-ras), a member of this family with multiple copies of the CSD...