Browsing by Author "Ribeca, Paolo"

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  • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
    Alioto, Tyler; Derdak, Sophia; Ribeca, Paolo; Castro Giner, Francesc; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon C.; Gut, Marta; Gut, Ivo Glynne (Nature Research, 2015)
    As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...
  • ChimPipe: Accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
    Rodríguez Martín, Bernardo; Palumbo, Emilio; Marco Sola, Santiago; Griebel, Thasso; Ribeca, Paolo; Alonso, Graciela; Rastrojo, Alberto; Aguado, Begoña; Guigó Serra, Roderic; Djebali, Sarah (BioMed Central, 2017)
    Background: Chimeric transcripts are commonly defined as transcripts linking two or more different genes in the genome, and can be explained by various biological mechanisms such as genomic rearrangement, read-through or ...
  • Evidence for transcript networks composed of chimeric RNAs in human cells
    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 ...
  • 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 ...
  • Fast computation and applications of genome mappability
    Derrien, Thomas; Estellé, Jordi; Marco Sola, Santiago; Knowles, David G.; Raineri, Emanuele; Guigó Serra, Roderic; Ribeca, Paolo (Public Library of Science (PLoS), 2012)
    We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of ...
  • Genome sequence of the olive tree, Olea europaea
    Cruz, Fernando; Julca, Irene; Gómez Garrido, Jèssica; Loska, Damian; Marcet Houben, Marina; Cano, Emilio; Galán Sicilia, Beatriz; Frias, Leonor; Ribeca, Paolo; Derdak, Sophia; Gut, Marta; Sánchez Fernández, Manuel; García, Jose Luis; Gut, Ivo Glynne; Vargas Gómez, Pablo; Alioto, Tyler; Gabaldón Estevan, Juan Antonio, 1973- (BioMed Central, 2016)
    Background: The Mediterranean olive tree (Olea europaea subsp. europaea) was one of the first trees to be domesticated and is currently of major agricultural importance in the Mediterranean region as the source of olive ...
  • High-throughput sequencing data compression
    Roguski, Łukasz (Universitat Pompeu Fabra, 2018-05-30)
    Thanks to advances in sequencing technologies, biomedical research has experienced a revolution over recent years, resulting in an explosion in the amount of genomic data being generated worldwide. The typical space ...
  • Landscape of transcription in human cells
    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 ...
  • Modelling and simulating generic RNA-Seq experiments with the flux simulator
    Griebel, Thasso; Zacher, Benedikt; Ribeca, Paolo; Raineri, Emanuele; Lacroix, Vincent; Guigó Serra, Roderic; Sammeth, Michael (Oxford University Press, 2012)
    High-throughput sequencing of cDNA libraries constructed from cellular RNA complements (RNA-Seq) naturally provides a digital quantitative measurement for every expressed RNA molecule. Nature, impact and mutual interference ...
  • Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
    Alioto, Tyler; Cruz, Fernando; Frias, Leonor; Gómez Garrido, Jèssica; Gut, Marta; Julca, Irene; Ribeca, Paolo; Vlasova, Anna; Gabaldón Estevan, Juan Antonio, 1973-; Arús, Pere (Wiley-VCH Verlag, 2020)
    We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short- and long-read sequencing. We obtained a genome assembly totaling 227.6 Mb of the estimated almond genome size of 238 Mb, ...