Affiliation: Hospital del Mar
- Evaluation of the chicken transcriptome by SAGE of B cells and the DT40 cell lineMatthias 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...
- 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...
- Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicingMarkus 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...
- 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...
- Differentiated evolutionary rates in alternative exons and the implications for splicing regulationMireya 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...
- 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...
- Pyicos: a versatile toolkit for the analysis of high-throughput sequencing dataSonja 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...
- Databases and resources for human small non-coding RNAsEneritz 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...
- Genome-wide association between branch point properties and alternative splicingAndré 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...
- Exon creation and establishment in human genesAndré 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...
- Co-evolution of the branch site and SR proteins in eukaryotesMireya 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...
- Genome sequence of the Brown Norway rat yields insights into mammalian evolutionRichard 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....
- Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotesSchraga 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....
- Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot projectEwan Birney
Nature 447:799-816. 2007..Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function...
- Integrative annotation of 21,037 human genes validated by full-length cDNA clonesTadashi 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...
- The Ensembl automatic gene annotation systemVal 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...
- ESTGenes: alternative splicing from ESTs in EnsemblEduardo 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...
- Initial sequencing and comparative analysis of the mouse genomeRobert 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....
- Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21Robert 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...
- An overview of EnsemblEwan Birney
EMBL European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Genome Res 14:925-8. 2004....