Browsing Recerca: articles, congressos, llibres by Author "Eyras Jiménez, Eduardo"

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Browsing Recerca: articles, congressos, llibres by Author "Eyras Jiménez, Eduardo"

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  • Castelo, Robert; Reymond, Alexandre; Wyss, Carine; Cámara, Francisco; Parra Farré, Genís; Antonarakis, Stylianos E.; Guigó Serra, Roderic; Eyras Jiménez, Eduardo (Oxford University Press, 2005)
    The recent availability of the chicken genome sequence poses the question of whether there are human protein-coding genes conserved in chicken that are currently not included in the human gene catalog. Here, we show, using ...
  • Meyer, Markus; Plass Pórtulas, Mireya; Pérez Valle, Jorge; Eyras Jiménez, Eduardo; Vilardell, Josep (Elsevier, 2011)
    Poor understanding of the spliceosomal mechanisms to select intronic 3' ends (3'ss) is a major obstacle to deciphering eukaryotic genomes. Here, we discern the rules for global 3'ss selection in yeast. We show that, in ...
  • Plass Pórtulas, Mireya; Eyras Jiménez, Eduardo (BioMed Central, 2006)
    Background: Alternatively spliced exons play an important role in the diversification of gene function in most metazoans and are highly regulated by conserved motifs in exons and introns. Two contradicting properties have ...
  • Shen, Manli; Eyras Jiménez, Eduardo; Wu, Jie; Josiah, Serene; Rederstorff, Mathieu; Zhang, Michael Q; Stamm, Stefan (Oxford University Press, 2011)
    We describe a new method that allows cloning of double-stranded RNAs (dsRNAs) that are generated in RNase protection experiments. We demonstrate that the mouse C/D box snoRNA MBII-85 (SNORD116) is processed into at least ...
  • Guigó Serra, Roderic; Flicek, Paul; Abril Ferrando, Josep Francesc; Reymond, Alexandre; Lagarde, Julien; Denoeud, France; Antonarakis, Stylianos E.; Ashburner, Michael; Bajic, Vladimir B.; Birney, Ewan; Castelo, Robert; Eyras Jiménez, Eduardo; Ucla, Catherine; Gingeras, Thomas R.; Harrow, Jennifer; Hubbard, Tim J.; Lewis, Suzanna E.; Reese, Martin G. (BioMed Central, 2006)
    Background: We present the results of EGASP, a community experiment to assess the state-ofthe- art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major ...
  • Wahl, Matthias B.; Caldwell, Randolph B.; Kierzek, Andrzej M.; Arakawa, Hirosi; Eyras Jiménez, Eduardo; Hubner, Nina; Jung, Christian; Soeldenwagner, Manuel; Cervelli, Manuela; Wang, Yan-Dong; Liebscher, Volkmar; Buerstedde, Jean-Marie (BioMed Central, 2004)
    Background: The understanding of whole genome sequences in higher eukaryotes depends to a large degree on the reliable definition of transcription units including exon/intron structures, translated open reading frames ...
  • Eyras Jiménez, Eduardo; Reymond, Alexandre; Castelo, Robert; Bye, Jacqueline M.; Cámara, Francisco; Flicek, Paul; Huckle, Elizabeth J.; Parra Farré, Genís; Shteynberg, David D.; Wyss, Carine; Rogers, Jane; Antonarakis, Stylianos E.; Birney, Ewan; Guigó Serra, Roderic; Brent, Michael R. (BioMed Central, 2005)
    Background: Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which ...
  • Corvelo, André; Hallegger, Martina; Smith, Christopher WJ; Eyras Jiménez, Eduardo (Public Library of Science (PLoS), 2010)
    The branch point (BP) is one of the three obligatory signals required for pre-mRNA splicing. In mammals, the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task ...
  • Nadal Ribelles, Mariona; Conde Pueyo, Núria; Flores, Oscar; González-Vallinas Rostes, Juan, 1983-; Eyras Jiménez, Eduardo; Nadal Clanchet, Eulàlia de; Posas Garriga, Francesc (BioMed Central, 2012)
    Cells are subjected to dramatic changes of gene expression upon environmental changes. Stress causes a general down-regulation of gene expression together with the induction of a set of stress-responsive genes. The ...
  • Lyle, Robert; Prandini, Paola; Osoegawa, Kazutoyo; Ten Hallers, Boudewijn; Humphray, Sean; Zhu, Baoli; Eyras Jiménez, Eduardo; Castelo, Robert; Bird, Christine P.; Gagos, Sarantos; Scott, Carol; Cox, Antony; Deutsch, Samuel; Ucla, Catherine; Cruts, Marc; Dahoun, Sophie; She, Xinwei; Bena, Frederique; Wang, Sheng-Yue; Van Broeckhoven, Christine; Eichler, Evan E.; Guigó Serra, Roderic; Rogers, Jane; De Jong, Pieter J.; Reymond, Alexandre; Antonarakis, Stylianos E. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    The goals of the human genome project did not include sequencing of the heterochromatic regions. We describe here an initial sequence of 1.1 Mb of the short arm of human chromosome 21 (HSA21p), estimated to be 10% of 21p. ...
  • Fernandez, Noemí; Fernandez Miragall, Olga; Ramajo, Jorge; García Sacristán, Ana; Bellora Pereyra, Nicolás; Eyras Jiménez, Eduardo; Briones, Carlos; Martinez Salas, Encarnación (Oxford University Press, 2011)
    RNA structure plays a fundamental role in internal initiation of translation. Picornavirus internal ribosome entry site (IRES) are long, efficient cis-acting elements that recruit the ribosome to internal mRNA sites. ...
  • Erb, Ionas; González-Vallinas Rostes, Juan, 1983-; Bussotti, Giovanni, 1983-; Blanco, Enrique; Eyras Jiménez, Eduardo; Notredame, Cedric (Oxford University Press, 2012)
    We address the challenge of regulatory sequence alignment with a new method, Pro-Coffee, a multiple aligner specifically designed for homologous promoter regions. Pro-Coffee uses a dinucleotide substitution matrix estimated ...

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