Roderic Guigo

Summary

Publications

  1. pmc Grape RNA-Seq analysis pipeline environment
    David G Knowles
    Bioinformatics and genomics group, Centre for Genomic Regulation CRG and Universitat Pompeu Fabra UPF, Dr Aiguader 88, 08003 Barcelona, Spain
    Bioinformatics 29:614-21. 2013
  2. 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
  3. pmc The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    Thomas Derrien
    Bioinformatics and Genomics, Centre for Genomic Regulation and UPF, 08003 Barcelona, Catalonia, Spain
    Genome Res 22:1775-89. 2012
  4. 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
  5. 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
  6. pmc The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
    Rory Johnson
    Centre for Genomic Regulation CRG, 08003 Barcelona, Spain Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain Institut Hospital del Mar d Investigacions Mèdiques IMIM, 08003 Barcelona, Spain
    RNA 20:959-76. 2014
  7. pmc Intron-centric estimation of alternative splicing from RNA-seq data
    Dmitri D Pervouchine
    Centre de Regulacio Genomica, 08003 Barcelona, Spain
    Bioinformatics 29:273-4. 2013
  8. pmc Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
    Marco Mariotti
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, 08003 Barcelona, Catalonia, Spain Universitat Pompeu Fabra UPF, 08003 Barcelona, Catalonia, Spain Institut Hospital del Mar d Investigacions Mèdiques IMIM, 08003 Barcelona, Catalonia, Spain Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 25:1256-67. 2015
  9. pmc SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
    Frederic Romagne
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany, Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain and Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 42:D437-43. 2014
  10. pmc SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins
    Marco Mariotti
    Division of Genetics, Department of Medicine, Brigham and Womens Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, 02115, Boston, MA, USA and Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra UPF, 08003, Barcelona, Spain
    Nucleic Acids Res 41:e149. 2013

Collaborators

Detail Information

Publications22

  1. pmc Grape RNA-Seq analysis pipeline environment
    David G Knowles
    Bioinformatics and genomics group, Centre for Genomic Regulation CRG and Universitat Pompeu Fabra UPF, Dr Aiguader 88, 08003 Barcelona, Spain
    Bioinformatics 29:614-21. 2013
    ....
  2. 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
    ....
  3. pmc The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    Thomas Derrien
    Bioinformatics and Genomics, Centre for Genomic Regulation and UPF, 08003 Barcelona, Catalonia, Spain
    Genome Res 22:1775-89. 2012
    ..Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs...
  4. 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...
  5. 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...
  6. pmc The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs
    Rory Johnson
    Centre for Genomic Regulation CRG, 08003 Barcelona, Spain Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain Institut Hospital del Mar d Investigacions Mèdiques IMIM, 08003 Barcelona, Spain
    RNA 20:959-76. 2014
    ..The RIDL hypothesis has the potential to explain how functional evolution can keep pace with the rapid gene evolution observed in lncRNA. More practically, TE maps may in the future be used to predict lncRNA function. ..
  7. pmc Intron-centric estimation of alternative splicing from RNA-seq data
    Dmitri D Pervouchine
    Centre de Regulacio Genomica, 08003 Barcelona, Spain
    Bioinformatics 29:273-4. 2013
    ..However, the majority of human splicing events are more complex than single-exon skipping...
  8. pmc Evolution of selenophosphate synthetases: emergence and relocation of function through independent duplications and recurrent subfunctionalization
    Marco Mariotti
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, 08003 Barcelona, Catalonia, Spain Universitat Pompeu Fabra UPF, 08003 Barcelona, Catalonia, Spain Institut Hospital del Mar d Investigacions Mèdiques IMIM, 08003 Barcelona, Catalonia, Spain Division of Genetics, Department of Medicine, Brigham and Women s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
    Genome Res 25:1256-67. 2015
    ....
  9. pmc SelenoDB 2.0: annotation of selenoprotein genes in animals and their genetic diversity in humans
    Frederic Romagne
    Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany, Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader 88, 08003 Barcelona, Spain, Universitat Pompeu Fabra UPF, 08003 Barcelona, Spain and Department of Medicine, Division of Genetics, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Nucleic Acids Res 42:D437-43. 2014
    ..The addition of these datasets into the second release of the database provides a valuable resource for addressing medical and evolutionary questions in selenium biology. ..
  10. pmc SECISearch3 and Seblastian: new tools for prediction of SECIS elements and selenoproteins
    Marco Mariotti
    Division of Genetics, Department of Medicine, Brigham and Womens Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, 02115, Boston, MA, USA and Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, Dr Aiguader 88, 08003 Barcelona, Spain and Universitat Pompeu Fabra UPF, 08003, Barcelona, Spain
    Nucleic Acids Res 41:e149. 2013
    ..An analysis of a representative candidate belonging to the AhpC family shows how the use of Sec in this protein evolved in bacterial and eukaryotic lineages. ..
  11. pmc Unravelling the hidden DNA structural/physical code provides novel insights on promoter location
    Elisa Duran
    Institute for Research in Biomedicine IRB Barcelona, Barcelona 08028, Spain, Joint IRB BSC Research Program on Computational Biology, Barcelona 08028, Spain, Bioinformatics and genomics group, Center for Genomic Regulation and Universitat Pompeu Fabra, Barcelona 08003, Spain, Barcelona Supercomputing Center, Barcelona 08034, Spain and Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona 08028, Spain
    Nucleic Acids Res 41:7220-30. 2013
    ....
  12. pmc Topoisomerase II regulates yeast genes with singular chromatin architectures
    Christoforos Nikolaou
    Molecular Biology Institute of Barcelona, CSIC, 08028 Barcelona, Spain, Department of Biology, University of Crete, 71409 Heraklion, Greece, Department of Genetics and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain, Centre for Genomic Regulation CRG, 08003 Barcelona, Spain and Department of Biochemistry and Molecular Biology and ERI Biotecmed, University of Valencia, 46100 Burjassot, Spain
    Nucleic Acids Res 41:9243-56. 2013
    ..These findings indicate that yeast topo II operates on singular chromatin architectures to activate or repress DNA transcription and that this activity produces functional responses to ensure chromatin stability. ..
  13. pmc Role of six single nucleotide polymorphisms, risk factors in coronary disease, in OLR1 alternative splicing
    J Ramón Tejedor
    Centre de Regulacio Genomica, 08003 Barcelona, Spain Universitat Pompeu Fabra, 08003 Barcelona, Spain
    RNA 21:1187-202. 2015
    ....
  14. 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...
  15. pmc Modelling and simulating generic RNA-Seq experiments with the flux simulator
    Thasso Griebel
    Bioinformatics and Genomics Program, Centre de Regulacio Genomica CRG, 08003 Barcelona, Spain
    Nucleic Acids Res 40:10073-83. 2012
    ..Moreover, our simulations identify hitherto unreported sources of systematic bias from RNA hydrolysis, a fragmentation technique currently employed by most RNA-Seq protocols...
  16. 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...
  17. 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...
  18. 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
    ....
  19. 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
    ....
  20. pmc DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs
    Estel Aparicio-Prat
    Centre for Genomic Regulation CRG, The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003, Barcelona, Spain
    BMC Genomics 16:846. 2015
    ..The key feature of DECKO is its use of a single 165 bp starting oligonucleotide carrying the variable sequences of both gRNAs, making it fully scalable from single-locus studies to complex library cloning...
  21. pmc Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia
    Pedro G Ferreira
    Bioinformatics and Genomics Programme, Centre for Genomic Regulation CRG, 08003 Barcelona, Catalonia, Spain
    Genome Res 24:212-26. 2014
    ..Further analysis shows that B-cell receptor (BCR) activation in the microenvironment of the lymph node may be at the origin of the C1/C2 differences. ..
  22. 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...