Adam Frankish

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. pmc The importance of identifying alternative splicing in vertebrate genome annotation
    Adam Frankish
    Human and Vertebrate Analysis and Annotation Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Database (Oxford) 2012:bas014. 2012
  2. pmc Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 10:R2. 2009
  3. pmc Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 11:R26. 2010
  4. pmc Quantifying the mechanisms of domain gain in animal proteins
    Marija Buljan
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 11:R74. 2010
  5. pmc Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
    Stefan Taudien
    Genomanalyse, Institut fur Molekulare Biotechnologie, Jena, Germany
    BMC Genomics 5:92. 2004
  6. pmc The Vertebrate Genome Annotation browser 10 years on
    Jennifer L Harrow
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1HH, UK
    Nucleic Acids Res 42:D771-9. 2014
  7. pmc Current status and new features of the Consensus Coding Sequence database
    Catherine M Farrell
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 42:D865-72. 2014
  8. pmc The origins, evolution, and functional potential of alternative splicing in vertebrates
    Jonathan M Mudge
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Biol Evol 28:2949-59. 2011
  9. pmc GENCODE: the reference human genome annotation for The ENCODE Project
    Jennifer Harrow
    Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 22:1760-74. 2012
  10. pmc Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
    Markus Brosch
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 21:756-67. 2011

Collaborators

Detail Information

Publications11

  1. pmc The importance of identifying alternative splicing in vertebrate genome annotation
    Adam Frankish
    Human and Vertebrate Analysis and Annotation Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Database (Oxford) 2012:bas014. 2012
    ..DATABASE URL: http://www.ensembl.org/index.html, http://vega.sanger.ac.uk/index.html...
  2. pmc Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes
    Suganthi Balasubramanian
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 10:R2. 2009
    ..The availability of genome sequences of numerous organisms allows comparative study of pseudogenes in syntenic regions. Conservation of pseudogenes suggests that they might have a functional role in some instances...
  3. pmc Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates
    Zhengdong D Zhang
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Genome Biol 11:R26. 2010
    ..They constitute only a small fraction of annotated pseudogenes in the human genome. However, as they represent distinct functional losses over time, they shed light on the unique features of humans in primate evolution...
  4. pmc Quantifying the mechanisms of domain gain in animal proteins
    Marija Buljan
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Genome Biol 11:R74. 2010
    ..By using animal gene phylogenies we were able to identify a set of high confidence domain gain events and by looking at their coding DNA investigate the causative mechanisms...
  5. pmc Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence
    Stefan Taudien
    Genomanalyse, Institut fur Molekulare Biotechnologie, Jena, Germany
    BMC Genomics 5:92. 2004
    ..1. This DEF locus, however, represents one of the regions in the euchromatic part of the final human genome sequence which contains segmental duplications, and recalcitrant gaps indicating high structural dynamics...
  6. pmc The Vertebrate Genome Annotation browser 10 years on
    Jennifer L Harrow
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1HH, UK
    Nucleic Acids Res 42:D771-9. 2014
    ..We also highlight how the user can browse manually annotated updated patches from the Genome Reference Consortium (GRC). ..
  7. pmc Current status and new features of the Consensus Coding Sequence database
    Catherine M Farrell
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 42:D865-72. 2014
    ..We also present a summary of recent and future curation targets. ..
  8. pmc The origins, evolution, and functional potential of alternative splicing in vertebrates
    Jonathan M Mudge
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    Mol Biol Evol 28:2949-59. 2011
    ..Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution...
  9. pmc GENCODE: the reference human genome annotation for The ENCODE Project
    Jennifer Harrow
    Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 22:1760-74. 2012
    ..GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers...
  10. pmc Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome
    Markus Brosch
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 21:756-67. 2011
    ..All these data have been subsequently used to improve the publicly available mouse annotation available in both the Vega and Ensembl genome browsers (http://vega.sanger.ac.uk)...
  11. ncbi request reprint GENCODE pseudogenes
    Adam Frankish
    Human and Vertebrate Analysis and Annotation Group, Wellcome Trust Sanger Institute, Morgan Building, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1HH, UK
    Methods Mol Biol 1167:129-55. 2014
    ..The activity data associated with every pseudogene is stored in the psiDR resource. ..