Jaime Huerta-Cepas

Summary

Affiliation: Center for Genomic Regulation
Country: Spain

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. pmc Evidence for systems-level molecular mechanisms of tumorigenesis
    Pilar Hernandez
    Bioinformatics and Biostatistics Unit, and Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L Hospitalet, Barcelona, Spain
    BMC Genomics 8:185. 2007
  10. 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

Collaborators

Detail Information

Publications10

  1. 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...
  2. 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
    ....
  3. 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. ..
  4. 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...
  5. 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)...
  6. 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...
  7. 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...
  8. 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...
  9. pmc Evidence for systems-level molecular mechanisms of tumorigenesis
    Pilar Hernandez
    Bioinformatics and Biostatistics Unit, and Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, L Hospitalet, Barcelona, Spain
    BMC Genomics 8:185. 2007
    ..Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth...
  10. 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...