Browsing Articles (Departament de Ciències Experimentals i de la Salut) by Subject "RNA"

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Browsing Articles (Departament de Ciències Experimentals i de la Salut) by Subject "RNA"

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  • Guigó Serra, Roderic; Sammeth, Michael; Foissac, Sylvain (Public Library of Science (PLoS), 2008)
    Understanding the molecular mechanisms responsible for the regulation of the transcriptome present in eukaryotic cells is one of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) ...
  • Takeuchi, Akiko; Schmitt, David; Chapple, Charles E.; Babaylova, Elena; Karpova, Galina; Guigó Serra, Roderic; Krol, Alain; Allmang, Christine (Oxford University Press, 2009)
    Selenoproteins contain the amino acid selenocysteine which is encoded by a UGA Sec codon. Recoding UGA Sec requires a complex mechanism, comprising the cis-acting SECIS RNA hairpin in the 3′UTR of selenoprotein mRNAs, and ...
  • Agostini, Federico, 1985-; Zanzoni, Andreas; Klus, Petr; Marchese, Domenica; Cirillo, Davide; Tartaglia, Gian Gaetano (Oxford University Press, 2013)
    SUMMARY: Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences ...
  • 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 ...
  • Djebali, Sarah; Lagarde, Julien; Lacroix, Vincent; Foissac, Sylvain; Ribeca, Paolo; Martin, David; Guigó Serra, Roderic; Gingeras, Thomas R. (Public Library of Science (PLoS), 2012)
    The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast ...
  • Monlong, Jean; Calvo, Miquel; Ferreira, Pedro G.; Guigó Serra, Roderic (Nature Publishing Group, 2014)
    Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype ...
  • Andreu Martínez, David; Freire, Joao Miguel; Veiga, Ana Salomé; Conceiçao, Thaís M.; Kowalczyk, Wioleta; Mohana-Borges, Ronaldo; Santos, Nuno C.; Da Poian, Andrea T.; Castanho, Miguel A.R.B. (Public Library of Science (PLoS), 2014)
    Supercharged proteins are a recently identified class of proteins that have the ability to efficiently deliver functional macromolecules into mammalian cells. They were first developed as bioengineering products, but were ...
  • Pervouchine, Dmitri D.; Knowles, David G.; Guigó Serra, Roderic (Oxford University Press, 2013)
    MOTIVATION: Novel technologies brought in unprecedented amounts of high-throughput sequencing data along with great challenges in their analysis and interpretation. The percent-spliced-in (PSI, ) metric estimates the ...
  • Huffman, Tori; Link, Kathryn; Nardini, John; Poag, Laura; Flores, Kevin; Banks, H.T.; Blasco, Bernat; Jungfleisch, Jennifer, 1986-; Díez Antón, Juana, 1962- (Academic Publications, 2014)
    Positive-strand RNA viruses, such as the brome mosaic virus (BMV) and hepatitis C virus, utilize a replication cycle which involves the recruitment of RNA genomes from the cellular translation machinery to the viral ...
  • Guix, Francesc X.; Wahle, Tina; Vennekens, Kristel; Snellinx, An; Chávez-Gutiérrez, Lucía; Ill-Raga, Gerard, 1982-; Ramos-Fernández, Eva, 1984-; Guardia-Laguarta, Cristina; Lleó, Alberto; Arimon, Muriel; Berezovska, Oksana; Muñoz, Francisco J.; Dotti, Carlos G.; De Strooper, Bart (Wiley-VCH Verlag, 2012)
    Inherited familial Alzheimer's disease (AD) is characterized by small increases in the ratio of Aβ42 versus Aβ40 peptide which is thought to drive the amyloid plaque formation in the brain of these patients. Little is known ...
  • Taskov, Kalin; Chapple, Charles E.; Kryukov, Gregory V.; Castellano Hereza, Sergi; Lobanov, Alexei V.; Korotkov, Konstantin V.; Guigó Serra, Roderic; Gladyshev, Vadim N. (Oxford University Press, 2005)
    Selenocysteine (Sec) is co-translationally inserted into selenoproteins in response to codon UGA with the help of the selenocysteine insertion sequence (SECIS) element. The number of selenoproteins in animals varies, with ...
  • Cirillo, Davide; Agostini, Federico, 1985-; Klus, Petr; Marchese, Domenica; Rodríguez, Silvia; Bolognesi, Benedetta; Tartaglia, Gian Gaetano (Cold Spring Harbor Laboratory Press (CSHL Press), 2013)
    Increasing evidence indicates that RNA plays an active role in a number of neurodegenerative diseases. We recently introduced a theoretical framework, catRAPID, to predict the binding ability of protein and RNA molecules. ...
  • Solé, Carme; Nadal Ribelles, Mariona, 1984-; De Nadal, Eulàlia; Posas Garriga, Francesc (Springer, 2014)
    Eukaryotic cells have developed sophisticated systems to constantly monitor changes in the extracellular environment and to orchestrate a proper cellular response. To maximize survival, cells delay cell-cycle progression ...
  • Zanzoni, Andreas; Marchese, Domenica; Agostini, Federico, 1985-; Bolognesi, Benedetta; Cirillo, Davide; Botta-Orfila, Maria; Livi, Carmen Maria; Rodriguez-Mulero, Silvia; Tartaglia, Gian Gaetano (Oxford University Press, 2013)
    Previous evidence indicates that a number of proteins are able to interact with cognate mRNAs. These autogenous associations represent important regulatory mechanisms that control gene expression at the translational level. ...
  • Paronetto, Maria Paola; Bernardis, Isabella; Volpe, Elisabetta; Bechara, Elias; Sebestyén, Endre; Eyras Jiménez, Eduardo; Valcárcel, J. (Juan) (Elsevier, 2014)
    The Ewing sarcoma protein EWS is an RNA and DNA binding protein implicated in transcription, pre-mRNA splicing, and DNA damage response. Using CLIP-seq, we identified EWS RNA binding sites in exonic regions near 5′ splice ...
  • Johnson, Rory; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)
    Our genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which are likely to have genetic regulatory functions. It has been proposed that lncRNA are organized into combinations of discrete functional ...
  • Meyer, Markus; Vilardell, Josep (Oxford University Press, 2009)
    Removal of introns during pre-mRNA splicing is a critical process in gene expression, and understanding its control at both single-gene and genomic levels is one of the great challenges in Biology. Splicing takes place in ...
  • Agostini, Federico, 1985-; Cirillo, Davide; Bolognesi, Benedetta; Tartaglia, Gian Gaetano (Oxford University Press, 2013)
    The transcriptional silencing of one of the female X-chromosomes is a finely regulated process that requires accumulation in cis of the long non-coding RNA X-inactive-specific transcript (Xist) followed by a series of ...

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