Browsing Recerca: articles, congressos, llibres by Author "Harrow, Jennifer"

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Browsing Recerca: articles, congressos, llibres by Author "Harrow, Jennifer"

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  • 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 ...
  • Frankish, Adam; Uszczynska, Barbara; Ritchie, Graham RS; González, José M.; Pervouchine, Dmitri D.; Petryszak, Robert; Mudge, Jonathan M; Fonseca, Nuno; Brazma, Alvis; Guigó Serra, Roderic; Harrow, Jennifer (BioMed Central, 2015)
    Background: A vast amount of DNA variation is being identified by increasingly large-scale exome and genome sequencing projects. To be useful, variants require accurate functional annotation and a wide range of tools are ...
  • 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- art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major ...
  • 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)
  • 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 annotation by the HAVANA team, experimental ...
  • 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 ...
  • Harrow, Jennifer; Nagy, Alinda; Reymond, Alexandre; Alioto, Tyler; Patthy, Laszlo; Antonarakis, Stylianos E.; Guigó Serra, Roderic (BioMed Central, 2009)
    The vast majority of the biology of a newly sequenced genome is inferred from the set of encoded proteins. Predicting this set is therefore invariably the first step after the completion of the genome DNA sequence. Here ...
  • 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 ...
  • Zheng, Deyou; Frankish, Adam; Baertsch, Robert; Kapranov, Philipp; Reymond, Alexandre; Choo, Siew Woh; Lu, Yontao; Denoeud, France; Antonarakis, Stylianos E.; Snyder, Michael; Ruan, Yijun; Wei, Chia-Lin; Gingeras, Thomas R.; Guigó Serra, Roderic; Harrow, Jennifer; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press-CSHL Press, 2007)
    Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are “genomic fossils” valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an ...
  • 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 ...
  • 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 ...
  • 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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