Browsing by Author "Johnson, Rory"

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  • Plassais, Jocelyn; Lagoutte, Laetitia; Correard, Solenne; Paradis, Manon; Guaguère, Eric; Hédan, Benoit; Pommier, Alix; Botherel, Nadine; Cadiergues, Marie-Christine; Pilorge, Philippe; Silversides, David; Bizot, Maud; Amuels, Mark; Arnan Ros, Carme; Johnson, Rory; Hitte, Christophe; Salbert, Gilles; Méreau, Agnès; Quignon, Pascale; Derrien, Thomas; André, Catherine (Public Library of Science (PLoS), 2016)
    Human Hereditary Sensory Autonomic Neuropathies (HSANs) are characterized by insensitivity to pain, sometimes combined with self-mutilation. Strikingly, several sporting dog breeds are particularly affected by such ...
  • Ounzain, Samir; Micheletti, Rudi; Arnan Ros, Carme; Plaisance, Isabelle; Cecchi, Dario; Schroen, Blanche; Reverter, Ferran; Alexanian, Michael; Gonzales, Christine; Ng, Shi Yan; Bussotti, Giovanni, 1983-; Pezzuto, Iole; Notredame, Cedric; Heymans, Stephane; Guigó Serra, Roderic; Johnson, Rory; Pedrazzini, Thierry (Elsevier, 2015)
    Long noncoding RNAs (lncRNAs) are emerging as important regulators of developmental pathways. However, their roles in human cardiac precursor cell (CPC) remain unexplored. To characterize the long noncoding transcriptome ...
  • Frenkel-Morgenstern, Milana; Lacroix, Vincent; Ezkurdia, Iakes; Levin, Yishai; Gabashvili, Alexandra; Prilusky, Jaime; Pozo, Angela del; Tress, Michael; Johnson, Rory; Guigó Serra, Roderic; Valencia, Alfonso (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Chimeric RNAs comprise exons from two or more different genes and have the potential to encode novel proteins that alter cellular phenotypes. To date, numerous putative chimeric transcripts have been identified among the ...
  • Carlevaro-Fita, Joana; Rahim, Anisa; Guigó Serra, Roderic; Vardy, Leah A.; Johnson, Rory (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Recent footprinting studies have made the surprising observation that long noncoding RNAs (lncRNAs) physically interact with ribosomes. However, these findings remain controversial, and the overall proportion of cytoplasmic ...
  • Aparicio i Prat, Estel, 1986-; Arnan Ros, Carme; Sala, Ilaria; Bosch Roca, Núria; Guigó Serra, Roderic; Johnson, Rory (BioMed Central, 2015)
    Background. CRISPR genome-editing technology makes it possible to quickly and cheaply delete non-protein-coding regulatory elements. We present a vector system adapted for this purpose called DECKO (Double Excision CRISPR ...
  • Tilgner, Hagen, 1980-; Knowles, David G.; Johnson, Rory; Davis, Carrie A.; Chakrabortty, Sudipto; Djebali, Sarah; Curado, Joao; Snyder, Michael; Gingeras, Thomas R.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Splicing remains an incompletely understood process. Recent findings suggest that chromatin structure participates in its regulation. Here, we analyze the RNA from subcellular fractions obtained through RNA-seq in the cell ...
  • Lanzos Camaioni, Andrés Arturo; Carlevaro-Fita, Joana; Mularoni, Loris; Reverter Comes, Ferran; Palumbo, Emilio; Guigó Serra, Roderic; Johnson, Rory (Nature Publishing Group, 2017)
    Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold missing drivers of tumourigenesis, but few such “driver lncRNAs” are known. Until now, they have been discovered through changes in ...
  • Mariotti, Marco, 1984-; Santesmasses Ruiz, Didac, 1978-; Capella Gutiérrez, Salvador Jesús, 1985-; Mateo, Andrea; Arnan Ros, Carme; Johnson, Rory; D’Aniello, Salvatore; Yim, Sun Hee; Gladyshev, Vadim N.; Serras Rigalt, Florenci; Corominas Guiu, Montserrat; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press, 2015)
    Selenoproteins are proteins that incorporate selenocysteine (Sec), a nonstandard amino acid encoded by UGA, normally a stop codon. Sec synthesis requires the enzyme Selenophosphate synthetase (SPS or SelD), conserved in ...
  • Ounzain, Samir; Micheletti, Rudi; Beckmann, Tal; Schroen, Blanche; Alexanian, Michael; Pezzuto, Iole; Crippa, Stefania; Nemir, Mohamed; Sarre, Alexandre; Johnson, Rory; Dauvillier, Jérôme; Burdet, Frédéric; Ibberson, Mark; Guigó Serra, Roderic; Xenarios, Ioannis; Heymans, Stephane; Pedrazzini, Thierry (Oxford University Press, 2015)
    Aim: Heart disease is recognized as a consequence of dysregulation of cardiac gene regulatory networks. Previously, unappreciated components of such networks are the long non-coding RNAs (lncRNAs). Their roles in the heart ...
  • Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Carbonell, Silvia; Pérez-Lluch, Sílvia; Davis, Carrie A.; Gingeras, Thomas R.; Frankish, Adam; Harrow, Jennifer; Guigó Serra, Roderic; Johnson, Rory (Nature Research, 2017)
    Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene ...
  • Djebali, Sarah; Merkel, Angelika; Tanzer, Andrea; Lagarde, Julien; Röder, Maik; Curado, Joao; Derrien, Thomas; Ferreira, Pedro G.; González, David; Johnson, Rory; Kingswood, Colin; Ribeca, Paolo; Sammeth, Michael; Skancke, Jorgen; Tilgner, Hagen, 1980-; Guigó Serra, Roderic; Gingeras, Thomas R. (Nature Publishing Group, 2012)
    Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic ...
  • Mas Ponte, David; Carlevaro-Fita, Joana; Palumbo, Emilio; Hermoso Pulido, Antonio; Guigó Serra, Roderic; Johnson, Rory (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)
    The subcellular localization of long noncoding RNAs (lncRNAs) holds valuable clues to their molecular function. However, measuring localization of newly discovered lncRNAs involves time-consuming and costly experimental ...
  • 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 ...
  • Pulido-Quetglas, Carlos; Aparicio i Prat, Estel, 1986-; Arnan Ros, Carme; Polidori, Taisia; Hermoso Pulido, Antonio; Palumbo, Emilio; Ponomarenko, Julia; Guigó Serra, Roderic; Johnson, Rory (Public Library of Science (PLoS), 2017)
    CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, ...
  • Derrien, Thomas; Johnson, Rory; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Djebali, Sarah; Tilgner, Hagen, 1980-; Guernec, Gregory; Martin, David; Merkel, Angelika; Knowles, David G.; Lagarde, Julien; Veeravalli, Lavanya; Ruan, Xiaoan; Ruan, Yijun; Lassmann, Timo; Carninci, Piero; Brown, James B.; Lipovich, Leonard; González, José M.; Thomas, Mark; Davis, Carrie A.; Shiekhattar, Ramin; Gingeras, Thomas R.; Hubbard, Tim J.; Notredame, Cedric; Harrow, Jennifer; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to ...
  • Derrien, Thomas; Guigó Serra, Roderic; Johnson, Rory (Frontiers, 2012)
    The transcriptome of a cell is represented by a myriad of different RNA molecules with and without protein-coding capacities. In recent years, advances in sequencing technologies have allowed researchers to more fully ...
  • Ferreira, Pedro G.; González-Pérez, Abel; Knowles, David G.; Monlong, Jean; Johnson, Rory; Djebali, Sarah; Papasaikas, Panagiotis; Tamborero Noguera, David; Gouin, Anaïs; López Bigas, Núria; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)
    Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying ...