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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  • Agirre Ortiz de Guzmán, Eneritz, 1983-; Bellora Pereyra, Nicolás; Alló, Mariano; Pagès Pinós, Amadís; Bertucci, Paola; Kornblihtt, Alberto R.; Eyras Jiménez, Eduardo (BioMed Central, 2015)
    BACKGROUND: Alternative splicing is primarily controlled by the activity of splicing factors and by the elongation of the RNA polymerase II (RNAPII). Recent experiments have suggested a new complex network of splicing ...
  • Kremsky, Isaac Jacob, 1983-; Bellora Pereyra, Nicolás; Eyras Jiménez, Eduardo (Public Library of Science (PLoS), 2015)
    High-throughput sequencing, and genome-based datasets in general, are often represented as profiles centered at reference points to study the association of protein binding and other signals to particular regulatory ...
  • González-Vallinas Rostes, Juan, 1983-; Pagès Pinós, Amadís; Singh, Babita; Eyras Jiménez, Eduardo (BioMed Central, 2015)
    Background. Transcriptional enhancers are generally known to regulate gene transcription from afar. Their activation involves a series of changes in chromatin marks and recruitment of protein factors. These enhancers may ...
  • Zhang, Runxuan; Calixto, Cristiane P. G.; Tzioutziou, Nikoleta A.; James, Allan B.; Simpson, Craig G.; Guo, Wenbin; Marquez, Yamile; Kalyna, Maria; Patro, Rob; Eyras Jiménez, Eduardo; Barta, Andrea; Nimmo, Hugh G.; Brown, John W. S. (Wiley, 2015)
    RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed ...
  • Castelo Valdueza, 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 ...
  • Agirre Ortiz de Guzmán, Eneritz, 1983-; Eyras Jiménez, Eduardo (BioMed Central, 2011)
    Recent advances in high-throughput sequencing have facilitated the genome-wide studies of small non-coding RNAs (sRNAs). Numerous studies have highlighted the role of various classes of sRNAs at different levels of gene ...
  • Meyer, Markus; Plass Pórtulas, Mireya, 1982-; 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 ...
  • Sebestyén, Endre; Zawisza, Michal; Eyras Jiménez, Eduardo (Oxford University Press, 2015)
    The determination of the alternative splicing isoforms expressed in cancer is fundamental for the development of tumor-specific molecular targets for prognosis and therapy, but it is hindered by the heterogeneity of tumors ...
  • Plass Pórtulas, Mireya, 1982-; 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 ...
  • Gromak, Natalia; Dienstbier, Martin; Macias, Sara; Plass Pórtulas, Mireya, 1982-; Eyras Jiménez, Eduardo; Cáceres, Javier F.; Proudfoot, Nicholas J. (Elsevier, 2013)
    Drosha is the main RNase III-like enzyme involved in the process of microRNA (miRNA) biogenesis in the nucleus. Using whole-genome ChIP-on-chip analysis, we demonstrate that, in addition to miRNA sequences, Drosha specifically ...
  • 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 Valdueza, 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 ...
  • Corvelo, André; Eyras Jiménez, Eduardo (BioMed Central, 2008)
    BACKGROUND: A large proportion of species-specific exons are alternatively spliced. In primates, Alu elements play a crucial role in the process of exon creation but many new exons have appeared through other mechanisms. ...
  • Eyras Jiménez, Eduardo; Lozano, Yolanda (Elsevier, 2000)
    We construct the effective action of certain exotic branes in the Type II theories which are not predicted by their space-time supersymmetry algebras. We analyze in detail the case of the NS-7B brane, S-dual to the D7-brane, ...
  • Eyras Jiménez, Eduardo; Reymond, Alexandre; Castelo Valdueza, 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, 1984-; Conde Pueyo, Núria, 1983-; 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 ...
  • Imanishi, Tadashi; Eyras Jiménez, Eduardo; Sugano, Sumio (Public Library of Science (PLoS), 2004)
    The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. ...
  • Lyle, Robert; Prandini, Paola; Osoegawa, Kazutoyo; Ten Hallers, Boudewijn; Humphray, Sean; Zhu, Baoli; Eyras Jiménez, Eduardo; Castelo Valdueza, 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; Broeckhoven, Christine van; 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. ...

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