Toni Gabaldón

Summary

Country: Spain

Publications

  1. 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
  2. pmc Evolution of proteins and proteomes: a phylogenetics approach
    Toni Gabaldón
    Bioinformatics Department, Centro de Investigacion Principe Felipe
    Evol Bioinform Online 1:51-61. 2007
  3. pmc Origin and evolution of the peroxisomal proteome
    Toni Gabaldón
    CMBI, Center for Molecular and Biomolecular Informatics, NCMLS, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Biol Direct 1:8. 2006
  4. pmc From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism
    Toni Gabaldón
    Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
    PLoS Comput Biol 3:e219. 2007
  5. ncbi Computational approaches for the prediction of protein function in the mitochondrion
    Toni Gabaldón
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Am J Physiol Cell Physiol 291:C1121-8. 2006
  6. 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
  7. 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
  8. ncbi Reconstruction of the proto-mitochondrial metabolism
    Toni Gabaldón
    Nijmegen Center for Molecular Life Sciences, CMBI, Toernooiveld 1, 6525 ED Nijmegen, Netherlands
    Science 301:609. 2003
  9. ncbi Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I)
    Toni Gabaldón
    Center for Molecular and Biomolecular Informatics and Nijmegen Center for Molecular Life Sciences, University Medical Center St Radboud, Toernoooiveld 1, 6525 ED Nijmegen, The Netherlands
    J Mol Biol 348:857-70. 2005
  10. ncbi An anaerobic mitochondrion that produces hydrogen
    Brigitte Boxma
    Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands
    Nature 434:74-9. 2005

Detail Information

Publications22

  1. 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...
  2. pmc Evolution of proteins and proteomes: a phylogenetics approach
    Toni Gabaldón
    Bioinformatics Department, Centro de Investigacion Principe Felipe
    Evol Bioinform Online 1:51-61. 2007
    ..Here I survey recent progress in the elucidation of mechanisms of protein and proteome evolution in which phylogenetics has played a determinant role...
  3. pmc Origin and evolution of the peroxisomal proteome
    Toni Gabaldón
    CMBI, Center for Molecular and Biomolecular Informatics, NCMLS, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Biol Direct 1:8. 2006
    ..We therefore conducted large-scale phylogenetic analyses of the yeast and rat peroxisomal proteomes...
  4. pmc From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism
    Toni Gabaldón
    Nijmegen Center for Molecular Life Sciences, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Nijmegen, The Netherlands
    PLoS Comput Biol 3:e219. 2007
    ..Altogether, the results indicate that the eukaryotic host has hijacked the proto-mitochondrion, taking control of its protein synthesis and metabolism...
  5. ncbi Computational approaches for the prediction of protein function in the mitochondrion
    Toni Gabaldón
    Bioinformatics Department, Centro de Investigacion Principe Felipe, Valencia, Spain
    Am J Physiol Cell Physiol 291:C1121-8. 2006
    ....
  6. 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
    ....
  7. 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...
  8. ncbi Reconstruction of the proto-mitochondrial metabolism
    Toni Gabaldón
    Nijmegen Center for Molecular Life Sciences, CMBI, Toernooiveld 1, 6525 ED Nijmegen, Netherlands
    Science 301:609. 2003
  9. ncbi Tracing the evolution of a large protein complex in the eukaryotes, NADH:ubiquinone oxidoreductase (Complex I)
    Toni Gabaldón
    Center for Molecular and Biomolecular Informatics and Nijmegen Center for Molecular Life Sciences, University Medical Center St Radboud, Toernoooiveld 1, 6525 ED Nijmegen, The Netherlands
    J Mol Biol 348:857-70. 2005
    ..This evolutionary scenario is in contrast to that for Complex I in the prokaryotes, for which the combination of several separate, and previously independently functioning modules into a single complex has been proposed...
  10. ncbi An anaerobic mitochondrion that produces hydrogen
    Brigitte Boxma
    Department of Evolutionary Microbiology, Faculty of Science, Radboud University Nijmegen, Toernooiveld 1, NL 6525 ED Nijmegen, The Netherlands
    Nature 434:74-9. 2005
    ..ovalis organelle as a missing link between mitochondria and hydrogenosomes...
  11. 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...
  12. 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. ..
  13. 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...
  14. ncbi Combining data from genomes, Y2H and 3D structure indicates that BolA is a reductase interacting with a glutaredoxin
    Martijn A Huynen
    CMBI, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Toernooiveld 1, 6525ED Nijmegen, The Netherlands
    FEBS Lett 579:591-6. 2005
    ..We propose that BolA uses the mono-thiol glutaredoxin as the source for these...
  15. ncbi Variation and evolution of biomolecular systems: searching for functional relevance
    Martijn A Huynen
    Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, P O Box 9010, 6500 GL Nijmegen, The Netherlands
    FEBS Lett 579:1839-45. 2005
    ..Mapping the inter-species variation of complex biomolecular systems on a phylogenetic species tree allows one to reconstruct their evolution...
  16. doi 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...
  17. ncbi Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes
    Toni Gabaldón
    Center for Molecular and Biomolecular Informatics and Nijmegen Center for Molecular Life Sciences, Radboud University of Nijmegen Medical Center, Nijmegen, The Netherlands
    Bioinformatics 21:ii144-50. 2005
    ..Proteins functioning in the same biochemical pathway tend to have a similar history of gene loss events, and we use this property to predict functional interactions among proteins in our set...
  18. ncbi Shaping the mitochondrial proteome
    Toni Gabaldón
    NCMLS, Nijmegen Center for Molecular Life Sciences, P O CMBI, Center for Molecular and Biomolecular Informatics, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
    Biochim Biophys Acta 1659:212-20. 2004
    ..Here we review recent advances in the fields of comparative genomics and proteomics that are throwing light on the origin and evolution of the mitochondrial proteome...
  19. 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. ..
  20. 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...
  21. 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...
  22. 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...