Browsing by Author "Frankish, Adam"

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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-Ratajczak, Barbara; Ritchie, Graham R. S.; 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 ...
  • 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)
  • Frankish, Adam; Carbonell Sala, Silvia; Lagarde, Julien; Guigó Serra, Roderic (Oxford University Press, 2019)
    The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 ...
  • 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 ...
  • Lagarde, Julien; Uszczynska-Ratajczak, Barbara; Carbonell, Silvia; Pérez-Lluch, Sílvia; Davis, Carrie A.; Gingeras, Thomas R.; Frankish, Adam; Harrow, Jennifer; Guigó Serra, Roderic; Johnson, Rory (Nature Research, 2017)
    Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene ...
  • Pervouchine, Dmitri D.; Popov, Yaroslav; Berry, Andy; Borsari, Beatrice; Frankish, Adam; Guigó Serra, Roderic (Oxford University Press, 2019)
    Nonsense-mediated decay (NMD) is a eukaryotic mRNA surveillance system that selectively degrades transcripts with premature termination codons (PTC). Many RNA-binding proteins (RBP) regulate their expression levels by a ...
  • 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 ...
  • Steward, Charles A.; Uszczynska-Ratajczak, Barbara; Guigó Serra, Roderic; Frankish, Adam (Nature Research, 2019)
    The developmental and epileptic encephalopathies (DEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60-65% of patients without a molecular diagnosis. Here, ...
  • 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 ...