Adam Frankish

Summary

Affiliation: Wellcome Trust Genome Campus
Country: UK

Publications

  1. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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
  7. ncbi 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
  8. ncbi 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

Collaborators

  • Thomas Derrien
  • Jonathan M Mudge
  • David J Adams
  • Suganthi Balasubramanian
  • Michael Brent
  • Amonida Zadissa
  • Michael Tress
  • Manolis Kellis
  • Jennifer Harrow
  • Mark Gerstein
  • Toby Hunt
  • Markus Brosch
  • Zhengdong D Zhang
  • Marija Buljan
  • Stefan Taudien
  • Cédric Howald
  • Mike Kay
  • Iakes Ezkurdia
  • Alexandre Reymond
  • Daniel Barrell
  • Bronwen L Aken
  • David Haussler
  • Nathalie Walters
  • Alexandra Bignell
  • Gaurab Mukherjee
  • If Barnes
  • Gary Saunders
  • Gloria Despacio-Reyes
  • Electra Tapanari
  • Alfonso Valencia
  • Jose M Gonzalez
  • Mark Diekhans
  • Felix Kokocinski
  • Stephen Searle
  • Roderic Guigo
  • Charles Steward
  • Rachel Harte
  • Jeltje van Baren
  • Baikang Pei
  • Andrea Tanzer
  • Veronika Boychenko
  • Jose Manuel Rodriguez
  • Jacqueline Chrast
  • Tim J Hubbard
  • Michael Lin
  • Jeena Rajan
  • Tim Hubbard
  • Jyoti S Choudhary
  • Gary I Saunders
  • Mark O Collins
  • James Wright
  • Ruth Verstraten
  • Lu Yu
  • Alex Bateman
  • Roman Siddiqui
  • Kathrin Reichwald
  • Nobuyoshi Shimizu
  • Matthias Platzer
  • Klaus Huse
  • Karol Szafranski
  • Atsushi Shimizu
  • Markus Schilhabel
  • Ivan F Loncarevic
  • Petra Galgoczy
  • Shuichi Asakawa

Detail Information

Publications8

  1. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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. ncbi 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...
  7. ncbi 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)...
  8. ncbi 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...