Browsing by Author "Ruiz Orera, Jorge, 1988-"

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  • Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
    Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva Cañas, José Luis, 1984-; Vlasova, Anna; Marcet Houben, Marina; Prieto Barja, Pablo, 1986-; Quilez Oliete, Javier; Frias, Leonor; Ribeca, Paolo; Capella Gutiérrez, Salvador Jesús, 1985-; Câmara Ferreira, Francisco; Lowy Gallego, Ernesto; Cozzuto, Luca; Erb, Ionas; Rodríguez Ales, José Luis; Ruiz Orera, Jorge, 1988-; Reverter, Ferran; Derdak, Sophia; Blanc, Julie; Gut, Marta; Lorente-Galdós, Belén, 1981-; Gut, Ivo Glynne; Guigó Serra, Roderic; Gabaldón Estevan, Juan Antonio, 1973-; Godoy, José A. (BioMed Central, 2016)
    Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective ...
  • Impact of uORFs in mediating regulation of translation in stress conditions
    Moro, Simone G.; Hermans, Cedric; Ruiz Orera, Jorge, 1988-; Albà Soler, Mar (BioMed Central, 2021)
    Background: A large fraction of genes contains upstream ORFs (uORFs) in the 5' untranslated region (5'UTR). The translation of uORFs can inhibit the translation of the main coding sequence, for example by causing premature ...
  • Long non-coding RNAs as a source of new peptides
    Ruiz Orera, Jorge, 1988-; Messeguer, Xavier; Subirana, Juan A.; Albà Soler, Mar (eLife, 2014)
    Deep transcriptome sequencing has revealed the existence of many transcripts that lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (lncRNAs). The vast majority of lncRNAs ...
  • New genes and functional innovation in mammals
    Villanueva Cañas, José Luis, 1984-; Ruiz Orera, Jorge, 1988-; Agea, M. Isabel; Gallo, María, 1989-; Andreu Martínez, David; Albà Soler, Mar (Oxford University Press, 2017)
    The birth of genes that encode new protein sequences is a major source of evolutionary innovation. However, we still understand relatively little about how these genes come into being and which functions they are selected ...
  • Origins of de novo genes in human and chimpanzee
    Ruiz Orera, Jorge, 1988-; Hernández Rodríguez, Jéssica, 1983-; Chiva, Cristina; Sabidó Aguadé, Eduard, 1981-; Kondova, Ivanela; Bontrop, Ronald E.; Marquès i Bonet, Tomàs, 1975-; Albà Soler, Mar (Public Library of Science, 2015)
    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these ...
  • Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome
    Reixachs i Solé, Marina; Ruiz Orera, Jorge, 1988-; Albà Soler, Mar; Eyras Jiménez, Eduardo (Nature Research, 2020)
    The differential production of transcript isoforms from gene loci is a key cellular mechanism. Yet, its impact in protein production remains an open question. Here, we describe ORQAS (ORF quantification pipeline for ...
  • TUNAR lncRNA encodes a microprotein that regulates neural differentiation and neurite formation by modulating calcium dynamics
    Senís, Elena; Esgleas, Miriam; Najas Sales, Sònia, 1985-; Jiménez-Sábado, Verónica; Bertani, Camilla; Giménez-Alejandre, Marta; Escriche, Alba; Ruiz Orera, Jorge, 1988-; Hergueta-Redondo, Marta; Jiménez, Mireia; Giralt, Albert; Nuciforo, Paolo G.; Albà Soler, Mar; Peinado, Héctor; Toro, Daniel; Hove-Madsen, Leif; Götz, Magdalena; Abad, María (Frontiers, 2021)
    Long noncoding RNAs (lncRNAs) are regulatory molecules which have been traditionally considered as "non-coding". Strikingly, recent evidence has demonstrated that many non-coding regions, including lncRNAs, do in fact ...
  • Uncovering de novo gene birth in yeast using deep transcriptomics
    Blevins, William Robert, 1987-; Ruiz Orera, Jorge, 1988-; Messeguer, Xavier; Blasco Moreno, Bernat, 1986-; Villanueva Cañas, José Luis, 1984-; Espinar, Lorena; Díez Antón, Juana, 1962-; Carey, Lucas, 1980-; Albà Soler, Mar (Nature Research, 2021)
    De novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new ...