Toni Gabaldón

Summary

Country: Spain

Publications

  1. ncbi 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. ncbi 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
  3. 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
  4. ncbi 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
  5. ncbi 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
  6. ncbi 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
  7. 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
  8. ncbi Comparative genomics-based prediction of protein function
    Toni Gabaldón
    Bioinformatics Department, CIPF, Valencia, Spain
    Methods Mol Biol 439:387-401. 2008
  9. 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
  10. 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

Collaborators

Detail Information

Publications13

  1. ncbi 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. ncbi 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...
  3. 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
    ....
  4. ncbi 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...
  5. ncbi 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...
  6. ncbi 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...
  7. 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...
  8. ncbi 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...
  9. 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...
  10. 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...
  11. ncbi 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...
  12. ncbi 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...
  13. ncbi 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...