Browsing by Author "Prieto Barja, Pablo, 1986-"

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  • A comparative encyclopedia of DNA elements in the mouse genome
    Yue, Feng; Breschi, Alessandra, 1988-; Pervouchine, Dmitri D.; Djebali, Sarah; Prieto Barja, Pablo, 1986-; Lagarde, Julien; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Notredame, Cedric; Guigó Serra, Roderic; Ren, Bing; The Mouse Encyclopedia of DNA Elements (ENCODE) Consortium (Nature Publishing Group, 2014)
    The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into ...
  • Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression
    Pervouchine, Dmitri D.; Djebali, Sarah; Breschi, Alessandra, 1988-; Prieto Barja, Pablo, 1986-; Lagarde, Julien; Bussotti, Giovanni, 1983-; Monlong, Jean; Notredame, Cedric; Guigó Serra, Roderic; Gingeras, Thomas R. (Nature Pub. Group, 2015)
    Mice have been a long-standing model for human biology and disease. Here we characterize, by RNA sequencing, the transcriptional profiles of a large and heterogeneous collection of mouse tissues, augmenting the mouse ...
  • 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 ...
  • Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
    Vlasova, Anna; Capella Gutiérrez, Salvador Jesús, 1985-; Erb, Ionas; Cámara, Francisco; Prieto Barja, Pablo, 1986-; Kedra, Darek; González Navarrete, Irene, 1983-; Cozzuto, Luca; Gómez Garrido, Jèssica; Aguilar Morón, María Asunción; Andreu Somavilla, Núria; Zehnsdorf, Maik; Alioto, Tyler; Notredame, Cedric; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic (BioMed Central, 2016)
    Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million ...
  • NGS applications in genome evolution and adaptation : A reproducible approach to NGS data analysis and integration
    Prieto Barja, Pablo, 1986- (Universitat Pompeu Fabra, 2017-01-12)
    In this PhD I have used NGS technologies in different organisms and scenarios such as in ENCODE, comparing the conservation and evolution of long non-coding RNA sequences between human and mouse, using experimental evidences ...
  • The impact of Docker containers on the performance of genomic pipelines
    Di Tommaso, Paolo; Palumbo, Emilio; Chatzou, Maria, 1985-; Prieto Barja, Pablo, 1986-; Heuer, Michael L.; Notredame, Cedric (PeerJ Inc., 2015)
    Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues. ...