Research Topics
| R GuigoSummaryAffiliation: Hospital del Mar Country: Spain Publications
| Collaborators
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Detail Information
Publications
Mutation patterns of amino acid tandem repeats in the human proteomeLoris Mularoni
Research Unit on Biomedical Informatics, , Universitat Pompeu Fabra, Barcelona 08003, Spain
Genome Biol 7:R33. 2006..We show that the mutational dynamics of different amino acid repeat types are very diverse. We provide a list of loci with highly variable repeat structures, some of which may be potentially involved in disease...- Gene finding in the chicken genomeEduardo 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... - Multiple non-collinear TF-map alignments of promoter regionsEnrique 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.... - EGASP: the human ENCODE Genome Annotation Assessment ProjectRoderic 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... 
Assembling genes from predicted exons in linear time with dynamic programmingR 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...- EGASP: collaboration through competition to find human genesRoderic 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... - BioMoby web services to support clustering of co-regulated genes based on similarity of promoter configurationsArnaud 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..AVAILABILITY: {http://genome.imim.es/cgi-bin/moby/GeneClustering_DataSubmission.cgi}. SUPPLEMENTARY INFORMATION: Supplementary data are available at {http://genome.imim.es/webservices/}.. - A general definition and nomenclature for alternative splicing eventsMichael 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... - Comparative gene prediction in human and mouseGenis 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... - Computational gene identification: an open problemR Guigo
Departament d Informàtica Mèdica, Institut Municipal d Investigacio Medica IMIM, Barcelona, Spain
Comput Chem 21:215-22. 1997.... - gff2ps: visualizing genomic annotationsJ 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... - Splice site identification by idlBNsRobert 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... - Transcription factor map alignment of promoter regionsEnrique Blanco
Research Group in Biomedical Informatics, , Barcelona, Catalonia, Spain
PLoS Comput Biol 2:e49. 2006.... - ABS: a database of Annotated regulatory Binding Sites from orthologous promotersEnrique 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... - Using geneid to identify genesEnrique 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... - gff2aplot: Plotting sequence comparisonsJosep 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... - Comparative gene finding in chicken indicates that we are closing in on the set of multi-exonic widely expressed human genesRobert 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... - Comparative analysis of amino acid repeats in rodents and humansM 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... - Efficient targeted transcript discovery via array-based normalization of RACE librariesSarah 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.... - An assessment of gene prediction accuracy in large DNA sequencesR 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.... - Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regionsFrance 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.... - SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elementsCharles 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..AVAILABILITY: SECISaln is freely available as a web-based tool at http://genome.crg.es/software/secisaln/... 
Nucleosome positioning as a determinant of exon recognitionHagen 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...- Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definitionJose 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... - Reconsidering the evolution of eukaryotic selenoproteins: a novel nonmammalian family with scattered phylogenetic distributionSergi 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... - In silico identification of novel selenoproteins in the Drosophila melanogaster genomeS 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... - Conserved chromosomal clustering of genes governed by chromatin regulators in DrosophilaEnrique 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... - Transcriptional network controlled by the trithorax-group gene ash2 in Drosophila melanogasterSergi Beltran
, 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... - Unweaving the meanings of messenger RNA sequencesRoderic 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... - Comparison of splice sites in mammals and chickenJosep F Abril
, , Universitat Pompeu Fabra, , , 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... - A combinatorial code for CPE-mediated translational controlMaria Piqué
Centre for Genomic Regulation CRG, UPF, c Dr Aiguader, 88, 08003 Barcelona, Spain
Cell 132:434-48. 2008.... - Tandem chimerism as a means to increase protein complexity in the human genomeGenis 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....