Browsing by Author "Hubbard, Tim J."

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  • Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
    Howald, Cédric; Tanzer, Andrea; Chrast, Jacqueline; Kokocinski, Felix; Derrien, Thomas; Walters, Nathalie; González, José M.; Frankish, Adam; Aken, Bronwen; Hourlier, Thibaut; Vogel, Jan-Hinnerk; White, Simon; Searle, Stephen; Harrow, Jennifer; Hubbard, Tim J.; Guigó Serra, Roderic; Reymond, Alexandre (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated ...
  • EGASP: the human ENCODE Genome Annotation Assessment Project
    Guigó Serra, Roderic; Flicek, Paul; Abril Ferrando, Josep Francesc; Reymond, Alexandre; Lagarde, Julien; Denoeud, France; Antonarakis, Stylianos E.; Ashburner, Michael; Bajic, Vladimir B.; Birney, Ewan; Castelo Valdueza, Robert; Eyras Jiménez, Eduardo; Ucla, Catherine; Gingeras, Thomas R.; Harrow, Jennifer; Hubbard, Tim J.; Lewis, Suzanna E.; Reese, Martin G. (BioMed Central, 2006)
    Background: We present the results of EGASP, a community experiment to assess the state-ofthe-/nart in genome annotation within the ENCODE regions, which span 1% of the human genome/nsequence. The experiment had two major ...
  • From identification to validation to gene count
    Amid, Clara; Frankish, Adam; HAVANA; Aken, Bronwen; Ezkurdia, Iakes; Kokocinski, Felix; Gilbert, James; White, Simon; Carninci, Piero; Gingeras, Thomas R.; Guigó Serra, Roderic; Searle, Stephen; Tress, Michael; Harrow, Jennifer; Hubbard, Tim J. (BioMed Central, 2010)
  • GENCODE: producing a reference annotation for ENCODE
    Harrow, Jennifer; Denoeud, France; Frankish, Adam; Reymond, Alexandre; Chen, Chao-Kung; Chrast, Jacqueline; Lagarde, Julien; Gilbert, James; Storey, Roy; Swarbreck, David; Rossier, Colette; Ucla, Catherine; Hubbard, Tim J.; Antonarakis, Stylianos E.; Guigó Serra, Roderic (BioMed Central, 2006)
    Background: The GENCODE consortium was formed to identify and map all protein-coding genes within the ENCODE regions. This was achieved by a combination of initial manual/nannotation by the HAVANA team, experimental ...
  • GENCODE: the reference human genome annotation for The ENCODE Project
    Harrow, Jennifer; Tanzer, Andrea; Guigó Serra, Roderic; Hubbard, Tim J. (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation ...
  • Prominent use of distal 5’ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    Denoeud, France; Kapranov, Philipp; Ucla, Catherine; Frankish, Adam; Castelo Valdueza, Robert; Drenkow, Jorg; Lagarde, Julien; Alioto, Tyler; Manzano, Caroline; Chrast, Jacqueline; Dike, Sujit; Wyss, Carine; Henrichsen, Charlotte N.; Holroyd, Nancy; Dickson, Mark C.; Taylor, Ruth; Hance, Zahra; Foissac, Sylvain; Myers, Richard M.; Rogers, Jane; Hubbard, Tim J.; Harrow, Jennifer; Guigó Serra, Roderic; Gingeras, Thomas R.; Antonarakis, Stylianos E.; Reymond, Alexandre (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    This report presents systematic empirical annotation of transcript products from 399 annotated protein-coding loci across the 1% of the human genome targeted by the Encyclopedia of DNA elements (ENCODE) pilot project using ...
  • Systematic evaluation of spliced alignment programs for RNA-seq data
    Engström, Pär G.; Steijger, Tamara; Sipos, Botond; Grant, Gregory R.; Kahles, André; RGASP Consortium; Rätsch, Gunnar; Goldman, Nick; Hubbard, Tim J.; Harrow, Jennifer; Guigó Serra, Roderic; Bertone, Paul (Nature Publishing Group, 2013)
    High-throughput RNA sequencing is an increasingly accessible method for studying gene structure and activity on a genome-wide scale. A critical step in RNA-seq data analysis is the alignment of partial transcript reads to ...
  • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
    Derrien, Thomas; Johnson, Rory; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Djebali, Sarah; Tilgner, Hagen, 1980-; Guernec, Gregory; Martin, David; Merkel, Angelika; Knowles, David G.; Lagarde, Julien; Veeravalli, Lavanya; Ruan, Xiaoan; Ruan, Yijun; Lassmann, Timo; Carninci, Piero; Brown, James B.; Lipovich, Leonard; González, José M.; Thomas, Mark; Davis, Carrie A.; Shiekhattar, Ramin; Gingeras, Thomas R.; Hubbard, Tim J.; Notredame, Cedric; Harrow, Jennifer; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to ...
  • The origins, evolution, and functional potential of alternative splicing in vertebrates
    Mudge, Jonathan M.; Frankish, Adam; Fernández Banet, Julio; Alioto, Tyler; Derrien, Thomas; Howald, Cédric; Reymond, Alexandre; Guigó Serra, Roderic; Hubbard, Tim J.; Harrow, Jennifer (Oxford University Press, 2011)
    Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the ...

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