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

Welcome to the UPF Digital Repository

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

Sort by: Order: Results:

  • 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) ...
  • 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 ...
  • 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 ...
  • Lloréns Rico, Verónica; Serrano Pubull, Luis, 1982-; Lluch Senar, Maria (BioMed Central, 2014)
    Background: RNA sequencing methods have already altered our view of the extent and complexity of bacterial and eukaryotic transcriptomes, revealing rare transcript isoforms (circular RNAs, RNA chimeras) that could play an ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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, Anna; 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 Ràfols, Francesc Xavier; 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 López, Francisco José, 1964-; 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. ...
  • Garcia Etxebarria, Koldo; Bracho, María Alma; Galán, Juan Carlos; Pumarola, Tomás; Castilla, Jesús; Ortiz de Lejarazu, Raúl; Rodríguez Domínguez, Mario; Quintela Garcia, Ines; Bonet, Núria; García Garcerà, Marc; Domínguez, Ángela; González Candelas, Fernando; Calafell i Majó, Francesc (Public Library of Science (PLoS), 2015)
    While most patients affected by the influenza A(H1N1) pandemic experienced mild symptoms, a small fraction required hospitalization, often without concomitant factors that could explain such a severe course. We hypothesize ...
  • Solé, Carme; Nadal Ribelles, Mariona, 1984-; Nadal Clanchet, Eulàlia de; 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 ...
  • Coelho, Miguel B.; Attig, Jan; Bellora Pereyra, Nicolás; König, Julian; Hallegger, Martina; Kayikci, Melis; Eyras Jiménez, Eduardo; Ule, Jernej; Smith, Christopher WJ (EMBO Press, 2015)
    Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA ...
  • 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. ...

Search


Advanced Search

Browse

My Account