R Guigo

Summary

Affiliation: Hospital del Mar
Country: Spain

Publications

  1. pmc Mutation patterns of amino acid tandem repeats in the human proteome
    Loris Mularoni
    Research Unit on Biomedical Informatics, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Barcelona 08003, Spain
    Genome Biol 7:R33. 2006
  2. pmc Gene finding in the chicken genome
    Eduardo Eyras
    Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 6:131. 2005
  3. pmc Multiple non-collinear TF-map alignments of promoter regions
    Enrique Blanco
    Grup d Algorísmica i Genètica, Departament de Llenguatges i Sistemes Informatics, Universitat Politecnica de Catalunya, c Jordi Girona, 1 3, Barcelona, Catalonia, Spain
    BMC Bioinformatics 8:138. 2007
  4. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
  5. ncbi request reprint Assembling genes from predicted exons in linear time with dynamic programming
    R Guigo
    Institut Municipal d Investigacio Medica, Departament d Estadística, Universitat de Barcelona, Spain
    J Comput Biol 5:681-702. 1998
  6. ncbi request reprint EGASP: collaboration through competition to find human genes
    Roderic Guigo
    Municipal Institute of Medical Research and Center for Genomic Regulation, University Pompeu Fabra, C Dr Aiguader 80, 08003 Barcelona, Catalonia, Spain
    Nat Methods 2:575-7. 2005
  7. ncbi request reprint BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations
    Arnaud Kerhornou
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica and Universitat Pompeu Fabra, Pg Maritim de la Barceloneta, 08003 Barcelona, Catalonia, Spain
    Bioinformatics 23:1831-3. 2007
  8. pmc A general definition and nomenclature for alternative splicing events
    Michael Sammeth
    Centre de Regulacio Genomica, Barcelona, Spain
    PLoS Comput Biol 4:e1000147. 2008
  9. pmc Comparative gene prediction in human and mouse
    Genis Parra
    Grup de Recerca en Informàtica Biomèdica Institut Municipal d Investigació Medica Universitat Pompeu Fabra Centre de Regulació Genòmica 08003 Barcelona, Catalonia, Spain
    Genome Res 13:108-17. 2003
  10. ncbi request reprint Computational gene identification: an open problem
    R Guigo
    Departament d Informàtica Mèdica, Institut Municipal d Investigacio Medica IMIM, Barcelona, Spain
    Comput Chem 21:215-22. 1997

Collaborators

Detail Information

Publications32

  1. pmc Mutation patterns of amino acid tandem repeats in the human proteome
    Loris Mularoni
    Research Unit on Biomedical Informatics, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Barcelona 08003, Spain
    Genome Biol 7:R33. 2006
    ..To gain further insight into the mutational mechanisms that operate in this type of sequence, we have analyzed a large number of mutation variants derived from human expressed sequence tags (ESTs)...
  2. pmc Gene finding in the chicken genome
    Eduardo Eyras
    Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain
    BMC Bioinformatics 6:131. 2005
    ..We used the chicken sequence to test comparative and homology-based gene-finding methods followed by experimental validation as an effective genome annotation method...
  3. pmc Multiple non-collinear TF-map alignments of promoter regions
    Enrique Blanco
    Grup d Algorísmica i Genètica, Departament de Llenguatges i Sistemes Informatics, Universitat Politecnica de Catalunya, c Jordi Girona, 1 3, Barcelona, Catalonia, Spain
    BMC Bioinformatics 8:138. 2007
    ....
  4. pmc EGASP: the human ENCODE Genome Annotation Assessment Project
    Roderic Guigo
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
    Genome Biol 7:S2.1-31. 2006
    ..These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment...
  5. ncbi request reprint Assembling genes from predicted exons in linear time with dynamic programming
    R Guigo
    Institut Municipal d Investigacio Medica, Departament d Estadística, Universitat de Barcelona, Spain
    J Comput Biol 5:681-702. 1998
    ..In particular it allows for multiple-gene two-strand predictions and for considering gene features other than coding exons (such as promoter elements) in valid gene structures...
  6. ncbi request reprint EGASP: collaboration through competition to find human genes
    Roderic Guigo
    Municipal Institute of Medical Research and Center for Genomic Regulation, University Pompeu Fabra, C Dr Aiguader 80, 08003 Barcelona, Catalonia, Spain
    Nat Methods 2:575-7. 2005
    ..To contribute strategies to reduce this uncertainty, several groups working on computational gene prediction met recently at the Welcome Trust Sanger Institute with the goal to test and compare predictive methods of genome annotation...
  7. ncbi request reprint BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurations
    Arnaud Kerhornou
    Centre de Regulacio Genomica, Institut Municipal d Investigació Mèdica and Universitat Pompeu Fabra, Pg Maritim de la Barceloneta, 08003 Barcelona, Catalonia, Spain
    Bioinformatics 23:1831-3. 2007
    ..All the steps of this protocol have been developed as web services that are compliant with BioMoby specifications...
  8. pmc A general definition and nomenclature for alternative splicing events
    Michael Sammeth
    Centre de Regulacio Genomica, Barcelona, Spain
    PLoS Comput Biol 4:e1000147. 2008
    ..The AStalavista system therefore provides a general framework to conduct specific studies investigating the occurrence, impact, and regulation of AS...
  9. pmc Comparative gene prediction in human and mouse
    Genis Parra
    Grup de Recerca en Informàtica Biomèdica Institut Municipal d Investigació Medica Universitat Pompeu Fabra Centre de Regulació Genòmica 08003 Barcelona, Catalonia, Spain
    Genome Res 13:108-17. 2003
    ..Our results suggest that another few thousand human and mouse genes currently not in ENSEMBL are worth verifying experimentally...
  10. ncbi request reprint Computational gene identification: an open problem
    R Guigo
    Departament d Informàtica Mèdica, Institut Municipal d Investigacio Medica IMIM, Barcelona, Spain
    Comput Chem 21:215-22. 1997
    ....
  11. ncbi request reprint gff2ps: visualizing genomic annotations
    J F Abril
    Grup de Recerca en Informàtica Mèdica, Institut Municipal d Investigacio Medica IMIM, Universitat Pompeu Fabra UPF, c Dr Aiguader, 80 08003 Barcelona, Spain
    Bioinformatics 16:743-4. 2000
    ..While it can be used in a very simple way, it also allows for a great degree of customization through a number of options and/or customization files...
  12. ncbi request reprint Splice site identification by idlBNs
    Robert Castelo
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Centre de Regulacio Genomica, Psg Marítim 37 49, Barcelona, Spain
    Bioinformatics 20:i69-76. 2004
    ..We apply the method to the identification of splice sites, and further evaluate its effect within the context of exon and gene prediction...
  13. pmc Transcription factor map alignment of promoter regions
    Enrique Blanco
    Research Group in Biomedical Informatics, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    PLoS Comput Biol 2:e49. 2006
    ....
  14. pmc ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
    Enrique Blanco
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra Centre de Regulació Genòmica C Doctor Aiguader 80, 08003 Barcelona, Spain
    Nucleic Acids Res 34:D63-7. 2006
    ..0 of ABS includes a customizable generator of artificial datasets based on the known sites contained in the collection and an evaluation tool to aid during the training and the assessment of motif-finding programs...
  15. ncbi request reprint Using geneid to identify genes
    Enrique Blanco
    Centre de Regulacio Genomica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Barcelona, Spain
    Curr Protoc Bioinformatics . 2007
    ..Geneid software is in the public domain, and it is undergoing constant development. It is easy to install and use. Exhaustive benchmark evaluations show that geneid compares favorably with other existing gene finding tools...
  16. ncbi request reprint gff2aplot: Plotting sequence comparisons
    Josep F Abril
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra Centre de Regulació Genòmica, Passeig Marítim de la Barceloneta 37 49, 08003 Barcelona, Catalonia, Spain
    Bioinformatics 19:2477-9. 2003
    ..Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis...
  17. pmc Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genes
    Robert Castelo
    Research Unit on Biomedical Informatics, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Centre de Regulació Genòmica E08003 Barcelona, Spain
    Nucleic Acids Res 33:1935-9. 2005
    ..This highlights the importance of developing methods that could provide a reliable estimate of the number of these two types of genes...
  18. pmc Comparative analysis of amino acid repeats in rodents and humans
    M Mar Albà
    Grup de Recerca en Informàtica Biomèdica, Departament de Ciencies Experimentals i de la Salut, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, 08003 Barcelona, Spain
    Genome Res 14:549-54. 2004
    ..We propose that the different GC content isochore structure in rodents and humans may result in an increased amino acid repeat prevalence in the human lineage...
  19. pmc Efficient targeted transcript discovery via array-based normalization of RACE libraries
    Sarah Djebali
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
    Nat Methods 5:629-35. 2008
    ....
  20. pmc An assessment of gene prediction accuracy in large DNA sequences
    R Guigo
    Grup de Recerca en Informàtica Mèdica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, E 08003 Barcelona, Spain
    Genome Res 10:1631-42. 2000
    ....
  21. pmc Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions
    France Denoeud
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
    Genome Res 17:746-59. 2007
    ....
  22. pmc SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements
    Charles E Chapple
    Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra and Parc de Recerca Biomedica de Barcelona, Carrer del Doctor Aiguader 88, 08003, Barcelona, Catalonia, Spain
    Bioinformatics 25:674-5. 2009
    ..We have used SECISaln to improve our knowledge of SECIS secondary structure and to discover novel, conserved nucleotide positions and we believe it will be a useful tool for the selenoprotein and RNA scientific communities...
  23. doi request reprint Nucleosome positioning as a determinant of exon recognition
    Hagen Tilgner
    Center for Genomic Regulation, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain
    Nat Struct Mol Biol 16:996-1001. 2009
    ..Our analysis provides a framework that contributes to the understanding of splicing on the basis of chromatin architecture...
  24. ncbi request reprint Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition
    Jose Maria Izquierdo
    Centre de Regulacio Genomica, Passeig Maritim 37 49, 08003 Barcelona, Spain
    Mol Cell 19:475-84. 2005
    ..We propose that TIA-1 and PTB regulate Fas splicing and possibly Fas-mediated apoptosis by targeting molecular events that lead to exon definition...
  25. pmc Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distribution
    Sergi Castellano
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Dr Aiguader 80, 08003 Barcelona, Catalonia, Spain
    EMBO Rep 5:71-7. 2004
    ..Our data indicate a scattered evolutionary distribution of selenoproteins in eukaryotes, and suggest that, contrary to the picture emerging from data available so far, other taxa-specific selenoproteins probably exist...
  26. pmc In silico identification of novel selenoproteins in the Drosophila melanogaster genome
    S Castellano
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, Dr Aiguader 80, 08003 Barcelona, Spain
    EMBO Rep 2:697-702. 2001
    ..One of them belongs to a known family of selenoproteins, and we have tested experimentally two other predictions with positive results. Finally, we have characterized the expression pattern of these two novel selenoprotein genes...
  27. pmc Conserved chromosomal clustering of genes governed by chromatin regulators in Drosophila
    Enrique Blanco
    Departament de Genètica and Institut de Biomedicina de la Universitat de Barcelona, Universitat de Barcelona, Barcelona, Catalonia, Spain
    Genome Biol 9:R134. 2008
    ..They bind to specific regions of DNA and direct the post-translational modifications of histones, playing a role in the dynamics of chromatin structure...
  28. pmc Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogaster
    Sergi Beltran
    Departament de Genetica, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
    Proc Natl Acad Sci U S A 100:3293-8. 2003
    ..This work represents the first microarray analysis, to our knowledge, of a trithorax-group gene...
  29. ncbi request reprint Unweaving the meanings of messenger RNA sequences
    Roderic Guigo
    Centre de Regulacio Genomica, Passeig Maritim 37 49, 08003 Barcelona, Spain
    Mol Cell 23:150-1. 2006
    ..Goren et al. (2006) and Wang et al. (2006) explore the diversity of these signals and the rules by which they function...
  30. pmc Comparison of splice sites in mammals and chicken
    Josep F Abril
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigacio Medica, Universitat Pompeu Fabra, and Programa de Bioinformàtica i Genòmica, Centre de Regulacio Genomica, C Dr Aiguader 80, E 08003 Barcelona, Catalonia, Spain
    Genome Res 15:111-9. 2005
    ..Switching between GT-AG and the noncanonical GC-AG U2 subtypes, on the contrary, does not appear to be unusual; in particular, T to C mutations appear to be relatively well tolerated in GT-AG introns with very strong donor sites...
  31. doi request reprint A combinatorial code for CPE-mediated translational control
    Maria Piqué
    Centre for Genomic Regulation CRG, UPF, c Dr Aiguader, 88, 08003 Barcelona, Spain
    Cell 132:434-48. 2008
    ....
  32. pmc Tandem chimerism as a means to increase protein complexity in the human genome
    Genis Parra
    Grup de Recerca en Informàtica Biomèdica, Institut Municipal d Investigació Mèdica Universitat Pompeu Fabra, and Programa de Bioinformàtica i Genòmica, Centre de Regulacio Genomica, E08003 Barcelona, Catalonia, Spain
    Genome Res 16:37-44. 2006
    ....