Browsing by Author "Guigó Serra, Roderic"

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  • 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 ...
  • Guigó Serra, Roderic; Manichanh, Chaysavanh; Chapple, Charles E.; Frangeul, Lionel; Gloux, Karine; Dore, Joel (Oxford University Press, 2008)
    The construction of metagenomic libraries has permitted the study of microorganisms resistant to isolation and the analysis of 16S rDNA sequences has been used for over two decades to examine bacterial biodiversity. Here, ...
  • Garrido Martín, Diego, 1992-; Calvo, Miquel (Calvo Llorca); Reverter, Ferran; Guigó Serra, Roderic (BioMed Central, 2023)
    The increasing availability of multidimensional phenotypic data in large cohorts of genotyped individuals requires efficient methods to identify genetic effects on multiple traits. Permutational multivariate analysis of ...
  • 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/none of the most challenging tasks in the postgenomic era. In this regard, alternative splicing (AS) ...
  • Breschi, Alessandra, 1988-; Muñoz-Aguirre, Manuel; Wucher, Valentin; Davis, Carrie A.; Garrido Martín, Diego, 1992-; Djebali, Sarah; Gillis, Jesse; Pervouchine, Dmitri D.; Vlasova, Anna; Dobin, Alexander; Zaleski, Chris; Drenkow, Jorg; Danyko, Cassidy; Scavelli, Alexandra; Reverter, Ferran; Snyder, Michael; Gingeras, Thomas R.; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    We have produced RNA sequencing data for 53 primary cells from different locations in the human body. The clustering of these primary cells reveals that most cells in the human body share a few broad transcriptional programs, ...
  • Garrido Martín, Diego (Universitat Pompeu Fabra, 2020-02-05)
    We have developed an efficient and reproducible pipeline for the identification of genetic variants affecting splicing (splicing quantitative trait loci or sQTLs), based on an approach that captures the intrinsically ...
  • Carithers, Latarsha J.; Guigó Serra, Roderic; GTEx Consortium (Mary Ann Liebert, Inc, 2015)
    The Genotype-Tissue Expression (GTEx) project, sponsored by the NIH Common Fund, was established to study the correlation between human genetic variation and tissue-specific gene expression in non-diseased individuals. A ...
  • 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 ...
  • Blanco, Enrique; Farré, Domènec; Albà Soler, Mar; Messeguer, Xavier; Guigó Serra, Roderic (Oxford University Press, 2006)
    Information about the genomic coordinates and the sequence of experimentally identified transcription factor binding sites is found scattered under a variety of diverse formats. The availability of standard collections of ...
  • Pérez-Lluch, Sílvia; Blanco, Enrique; Tilgner, Hagen, 1980-; Curado, Joao; Ruiz-Romero, Marina; Corominas Guiu, Montserrat; Guigó Serra, Roderic (Nature Research, 2015)
    The interplay of active and repressive histone modifications is assumed to have a key role in the regulation of gene expression. In contrast to this generally accepted view, we show that the transcription of genes temporally ...
  • Pérez-Lluch, Sílvia; Guigó Serra, Roderic; Corominas Guiu, Montserrat (Impact Journals, 2015)
    Gene expression is regulated by proteins such as transcription factors, as well as by chromatin modifications on DNA and histones. Some histone modifications have been associated to transcriptional activation (i.e. H3K4me1, ...
  • Ullrich, Sebastian (Universitat Pompeu Fabra, 2019-02-18)
    Gene regulation orchestrates the development of different cell types and organs from the same genetic blueprint. While the basic mode of gene regulation is driven by transcription factors, there are a variety of other ...
  • Guigó Serra, Roderic; Agarwal, Pankaj; Abril Ferrando, Josep Francesc; Burset Albareda, Moisès; Fickett, James W. (Cold Spring Harbor Laboratory Press-CSHL Press, 2000)
    One of the first useful products from the human genome will be a set of predicted genes. Besides its intrinsic scientific interest, the accuracy and completeness of this data set is of considerable importance for human ...
  • Stamatoyannopoulos, John A.; Guigó Serra, Roderic; Djebali, Sarah; Lagarde, Julien; Adams, Leslie B. (BioMed Central, 2012)
    To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE ...
  • ENCODE Project Consortium; Dunham, Ian; Guigó Serra, Roderic; Birney, Ewan (Nature Publishing Group, 2012)
    The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of ...
  • Carbonell Sala, Silvia; Uszczynska-Ratajczak, Barbara; Lagarde, Julien; Johnson, Rory; Guigó Serra, Roderic (Springer, 2021)
    Metazoan genomes produce thousands of long-noncoding RNAs (lncRNAs), of which just a small fraction have been well characterized. Understanding their biological functions requires accurate annotations, or maps of the precise ...
  • Alioto, Tyler; Picardi, Ernesto; Guigó Serra, Roderic; Pesole, Graziano (Hindawi, 2013)
    New genomes are being sequenced at an increasingly rapid rate, far outpacing the rate at which manual gene annotation can be performed. Automated genome annotation is thus necessitated by this growth in genome projects; ...
  • Guigó Serra, Roderic (Mary Ann Liebert, Inc, 1998)
    In a number of programs for gene structure prediction in higher eukaryotic genomic sequences, exon prediction is decoupled from gene assembly: a large pool of candidate exons is predicted and scored from features located ...
  • Steijger, Tamara; Guigó Serra, Roderic; RGASP Consortium (Nature Publishing Group, 2013)
    We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are ...
  • Guigó Serra, Roderic (Quark, 2000-01-11)

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