Eduardo Eyras

Summary

Affiliation: Hospital del Mar
Country: Spain

Publications

  1. pmc The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution
    Nurit Gal-Mark
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS Genet 5:e1000717. 2009
  2. pmc Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
    Matthias B Wahl
    Institute of Molecular Radiobiology, GSF, Ingolstädter Landstr, 1, D 85764 Neuherberg, Germany
    BMC Genomics 5:98. 2004
  3. 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
  4. doi request reprint Co-evolution of the branch site and SR proteins in eukaryotes
    Mireya Plass
    Computational Genomics Group, Universitat Pompeu Fabra, PRBB, Dr Aiguader 88 E08003, Barcelona, Spain
    Trends Genet 24:590-4. 2008
  5. 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
  6. pmc Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    Schraga H Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 18:88-103. 2008
  7. doi request reprint Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing
    Markus Meyer
    Centre de Regulacio Genomica, Dr Aiguader 88, 08003 Barcelona, Spain
    Mol Cell 43:1033-9. 2011
  8. 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
  9. pmc Differentiated evolutionary rates in alternative exons and the implications for splicing regulation
    Mireya Plass
    Research Unit of Biomedical Informatics, IMIM Pompeu Fabra University, E08003, Barcelona, Spain
    BMC Evol Biol 6:50. 2006
  10. pmc Exon creation and establishment in human genes
    André Corvelo
    Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
    Genome Biol 9:R141. 2008

Detail Information

Publications24

  1. pmc The pivotal roles of TIA proteins in 5' splice-site selection of alu exons and across evolution
    Nurit Gal-Mark
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
    PLoS Genet 5:e1000717. 2009
    ..Overall, these findings expand our understanding of the role of TIA1/TIAR proteins in enhancing recognition of exons, in general, and Alu exons, in particular...
  2. pmc Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell line
    Matthias B Wahl
    Institute of Molecular Radiobiology, GSF, Ingolstädter Landstr, 1, D 85764 Neuherberg, Germany
    BMC Genomics 5:98. 2004
    ..The best currently available chicken transcript catalog is the Ensembl build based on the mappings of a relatively small number of full length cDNAs and ESTs to the genome as well as genome sequence derived in silico gene predictions...
  3. 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...
  4. doi request reprint Co-evolution of the branch site and SR proteins in eukaryotes
    Mireya Plass
    Computational Genomics Group, Universitat Pompeu Fabra, PRBB, Dr Aiguader 88 E08003, Barcelona, Spain
    Trends Genet 24:590-4. 2008
    ..The density of RS repeats in these regions correlates with the conservation of the branch site signal, providing evidence for an ancestral origin of SR proteins and indicating that the SR proteins and the branch site co-evolved...
  5. 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...
  6. pmc Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes
    Schraga H Schwartz
    Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
    Genome Res 18:88-103. 2008
    ....
  7. doi request reprint Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing
    Markus Meyer
    Centre de Regulacio Genomica, Dr Aiguader 88, 08003 Barcelona, Spain
    Mol Cell 43:1033-9. 2011
    ..Thus, our data point to a deeper role for the pre-mRNA in the control of its own fate, and to a simple mechanism for some alternative splicing...
  8. 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...
  9. pmc Differentiated evolutionary rates in alternative exons and the implications for splicing regulation
    Mireya Plass
    Research Unit of Biomedical Informatics, IMIM Pompeu Fabra University, E08003, Barcelona, Spain
    BMC Evol Biol 6:50. 2006
    ..We have used this measure to correlate the changes in the arrangement of ESEs with the divergence of exon and intron sequences...
  10. pmc Exon creation and establishment in human genes
    André Corvelo
    Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
    Genome Biol 9:R141. 2008
    ..Despite many recent studies, it is still unclear which are the splicing regulatory requirements for de novo exonization and how splicing regulation changes throughout an exon's lifespan...
  11. pmc Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data
    Sonja Althammer
    Universitat Pompeu Fabra, E08003 Barcelona, Spain
    Bioinformatics 27:3333-40. 2011
    ..With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing...
  12. pmc Genome-wide association between branch point properties and alternative splicing
    André Corvelo
    Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
    PLoS Comput Biol 6:e1001016. 2010
    ..The reported association between BP features and the splicing outcome suggests that this, so far disregarded but yet crucial, element buries information that can complement current acceptor site models...
  13. pmc Databases and resources for human small non-coding RNAs
    Eneritz Agirre
    Department of Computational Genomics, Universitat Pompeu Fabra, Dr Aiguader 88, E08003 Barcelona, Spain
    Hum Genomics 5:192-9. 2011
    ..Some of the main issues related to the integration and annotation of sRNA datasets are also discussed...
  14. doi request reprint RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation
    Elias G Bechara
    Centre de Regulacio Genomica, Dr Aiguader, 88, 08003 Barcelona, Spain Universitat Pompeu Fabra, Dr Aiguader, 88, 08003 Barcelona, Spain
    Mol Cell 52:720-33. 2013
    ..RBM10 mutations identified in lung cancer cells disrupt NUMB splicing regulation to promote cell growth. Our results reveal a key genetic circuit in the control of cancer cell proliferation...
  15. doi request reprint Methods to study splicing from high-throughput RNA sequencing data
    Gael P Alamancos
    Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain
    Methods Mol Biol 1126:357-97. 2014
    ..We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods. ..
  16. pmc Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    Ewan Birney
    Nature 447:799-816. 2007
    ..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
  17. pmc ESTGenes: alternative splicing from ESTs in Ensembl
    Eduardo Eyras
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Genome Res 14:976-87. 2004
    ..ensembl.org as ESTgenes for the mosquito, Caenorhabditis briggsae, C. elegans, zebrafish, human, mouse, and rat genomes. Here we also report on the results of this method applied to the human and mouse genomes...
  18. pmc The Ensembl automatic gene annotation system
    Val Curwen
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:942-50. 2004
    ..gambiae genome sequence analysis. Here we describe in detail the gene-building system and the algorithms involved. All code and data are freely available from http://www.ensembl.org...
  19. pmc Integrative annotation of 21,037 human genes validated by full-length cDNA clones
    Tadashi Imanishi
    Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
    PLoS Biol 2:e162. 2004
    ..The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology...
  20. ncbi request reprint Genome sequence of the Brown Norway rat yields insights into mammalian evolution
    Richard A Gibbs
    Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA lt http www hgsc bcm tmc edu
    Nature 428:493-521. 2004
    ....
  21. ncbi request reprint Initial sequencing and comparative analysis of the mouse genome
    Robert H Waterston
    Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
    Nature 420:520-62. 2002
    ....
  22. pmc Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21
    Robert Lyle
    Department of Genetic Medicine and Development, University of Geneva Medical School, and University Hospitals, 1211 Geneva, Switzerland
    Genome Res 17:1690-6. 2007
    ..The sequencing of the "heterochromatic" regions of the human genome is likely to reveal many additional functional elements and provide important evolutionary information...
  23. pmc An overview of Ensembl
    Ewan Birney
    EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Res 14:925-8. 2004
    ....