Toni Gabaldón

Summary

Affiliation: Center for Genomic Regulation
Country: Spain

Publications

  1. 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
  2. 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
  3. 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
  4. pmc A metabolic scenario for the evolutionary origin of peroxisomes from the endomembranous system
    Toni Gabaldón
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader, 88, 08003, Barcelona, Spain
    Cell Mol Life Sci 71:2373-6. 2014
  5. 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
  6. 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
  7. pmc The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome
    Marina Marcet-Houben
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    PLoS ONE 4:e4357. 2009
  8. pmc Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates
    Hirzahida Mohd-Padil
    School of Biosciences and Biotechnology, Faculty of Science Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
    Mol Biol Evol 30:894-905. 2013
  9. 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
  10. 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

Detail Information

Publications42

  1. 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...
  2. 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...
  3. 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...
  4. pmc A metabolic scenario for the evolutionary origin of peroxisomes from the endomembranous system
    Toni Gabaldón
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader, 88, 08003, Barcelona, Spain
    Cell Mol Life Sci 71:2373-6. 2014
    ..A novel model for the evolutionary origin of peroxisomes and related organelles from within the endoplasmic reticulum is proposed. ..
  5. 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...
  6. 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...
  7. pmc The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome
    Marina Marcet-Houben
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    PLoS ONE 4:e4357. 2009
    ..Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies...
  8. pmc Phylogenetic analyses uncover a novel clade of transferrin in nonmammalian vertebrates
    Hirzahida Mohd-Padil
    School of Biosciences and Biotechnology, Faculty of Science Technology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
    Mol Biol Evol 30:894-905. 2013
    ..Altogether, our results provide novel insights on the evolution of iron-binding proteins in the various vertebrate groups...
  9. 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...
  10. 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
    ....
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. pmc The human phylome
    Jaime Huerta-Cepas
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Autopista del Saler, 46013 Valencia, Spain
    Genome Biol 8:R109. 2007
    ..The use of phylomes also requires the development of new methods that help us to interpret them...
  16. pmc Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
    Ruben Sanchez
    Evolutionary Genomics Lab, Bioinformatics and Genomics Department, Centro de Investigacion Principe Felipe, Autopista del Saler, 16 3, 46013 Valencia, Spain
    Nucleic Acids Res 39:W470-4. 2011
    ..Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing...
  17. pmc 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
    ....
  18. pmc Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics
    Joaquin Tarraga
    Bioinformatics Department, Centro de Investigacion Principe Felipe, INB, CIPF, Valencia 46013, Spain
    Nucleic Acids Res 35:W38-42. 2007
    ..The Phylemon web server is available at http://phylemon.bioinfo.cipf.es...
  19. pmc PhylomeDB: a database for genome-wide collections of gene phylogenies
    Jaime Huerta-Cepas
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Avda Autopista del Saler, 13 Valencia 46013, Spain
    Nucleic Acids Res 36:D491-6. 2008
    ..PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.es...
  20. pmc 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. ..
  21. 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...
  22. 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)...
  23. 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...
  24. 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...
  25. doi request reprint Comparative genomics-based prediction of protein function
    Toni Gabaldón
    Bioinformatics Department, CIPF, Valencia, Spain
    Methods Mol Biol 439:387-401. 2008
    ..Such comparative genomics-based techniques are increasingly being used in the process of genome annotation and in the development of testable working hypothesis...
  26. 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...
  27. 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...
  28. pmc A phylogenomics approach for selecting robust sets of phylogenetic markers
    Salvador Capella-Gutierrez
    Bioinformatics and Genomics Programme Centre for Genomic Regulation CRG and UPF Doctor Aiguader, 88 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF 08003 Barcelona, Spain, University of Kaiserslautern, Molecular Phylogenetics, Postfach 3049, 67653 Kaiserslautern, Germany and Institució Catalana de Recerca i Estudis Avançats ICREA, Pg Lluis Companys 23, 08010 Barcelona, Spain
    Nucleic Acids Res 42:e54. 2014
    ..This approach paves the way for the informed selection of phylogenetic markers in the effort of reconstructing the tree of life. ..
  29. pmc Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies
    Leszek P Pryszcz
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Barcelona, Spain
    Genome Biol Evol 6:1069-78. 2014
    ....
  30. 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...
  31. 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...
  32. 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...
  33. 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...
  34. 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...
  35. 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...
  36. 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
    ....
  37. pmc Structural analyses of a hypothetical minimal metabolism
    Toni Gabaldón
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Avda Autopista del Saler, 16 46013 Valencia, Spain
    Philos Trans R Soc Lond B Biol Sci 362:1751-62. 2007
    ..The implications that these results have on the origins of metabolic complexity and the theoretical design of an artificial minimal cell are discussed...
  38. pmc YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors
    Alfonso Benítez-Páez
    Laboratorio de Genetica Molecular, Centro de Investigacion Principe Felipe, 46012 Valencia, Spain
    RNA 16:2131-43. 2010
    ..YibK is one of the last remaining E. coli tRNA modification enzymes to be identified and is now renamed TrmL...
  39. pmc High variability of mitochondrial gene order among fungi
    Gabriela Aguileta
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Barcelona, Spain
    Genome Biol Evol 6:451-65. 2014
    ..e., most likely nonhomologous and intrachromosomal), accumulated repeats, especially at intergenic regions, and to a lesser extent, mobile element dynamics. ..
  40. 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...
  41. ncbi 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...