Browsing by Author "Guigó Serra, Roderic"

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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 ...
  • A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library
    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, ...
  • A fast non-parametric test of association for multiple traits
    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 ...
  • A general definition and nomenclature for alternative splicing events
    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) ...
  • A limited set of transcriptional programs define major cell types
    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, ...
  • A Multivariate approach to study the genetic determinants of phenotypic traits
    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 ...
  • A novel approach to high-quality postmortem tissue procurement: The GTEx Project
    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 ...
  • A short motif in Drosophila SECIS Binding Protein 2 provides differential binding affinity to SECIS RNA hairpins
    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 ...
  • ABS: a database of Annotated regulatory Binding Sites from orthologous promoters
    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 ...
  • Absence of canonical marks of active chromatin in developmentally regulated genes
    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 ...
  • Active transcription without histone modifications
    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, ...
  • Alternative mechanisms of gene regulation during hematopoiesis
    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 ...
  • An assessment of gene prediction accuracy in large DNA sequences
    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 ...
  • An encyclopedia of mouse DNA elements (Mouse ENCODE)
    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 ...
  • An integrated encyclopedia of DNA elements in the human genome
    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 ...
  • Annotation of full-length long noncoding RNAs with capture long-read sequencing (CLS)
    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 ...
  • ASPic-GeneID: a lightweight pipeline for gene prediction and alternative isoforms detection
    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; ...
  • Assembling genes from predicted exons in linear time with dynamic programming
    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 ...
  • Assessment of transcript reconstruction methods for RNA-seq
    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 ...
  • Bioinformática ¿una ciencia sin científicos?
    Guigó Serra, Roderic (Quark, 2000-01-11)

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