Dr Adam Frankish | Principal Computer Biologist

This person is a member of Sanger Institute Alumni.

Frankish, Adam

As a team leader in the HAVANA group my primary responsibility is managing the production of reference gene annotation for human and mouse within the GENCODE project. My focus is driving improvement in gene annotation to support more accurate interpretation of variation in both the research and clinical environments.

Publications

  • Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

    Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D et al.

    BMC genomics 2015;16 Suppl 8;S2

  • Comparative analysis of pseudogenes across three phyla.

    Sisu C, Pei B, Leng J, Frankish A, Zhang Y et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;37;13361-6

  • Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

    Gonzàlez-Porta M, Frankish A, Rung J, Harrow J and Brazma A

    Genome biology 2013;14;7;R70

  • An integrated encyclopedia of DNA elements in the human genome.

    ENCODE Project Consortium

    Nature 2012;489;7414;57-74

  • GENCODE: the reference human genome annotation for The ENCODE Project.

    Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M et al.

    Genome research 2012;22;9;1760-74

  • The GENCODE pseudogene resource.

    Pei B, Sisu C, Frankish A, Howald C, Habegger L et al.

    Genome biology 2012;13;9;R51

  • A systematic survey of loss-of-function variants in human protein-coding genes.

    MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J et al.

    Science (New York, N.Y.) 2012;335;6070;823-8

  • Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.

    Zhang ZD, Frankish A, Hunt T, Harrow J and Gerstein M

    Genome biology 2010;11;3;R26

  • GENCODE: producing a reference annotation for ENCODE.

    Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK et al.

    Genome biology 2006;7 Suppl 1;S4.1-9

  • The DNA sequence of the human X chromosome.

    Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K et al.

    Nature 2005;434;7031;325-37

  • Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

    Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D et al.

    BMC genomics 2015;16 Suppl 8;S2

  • Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

    Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M et al.

    Human molecular genetics 2014;23;22;5866-78

  • Comparative analysis of pseudogenes across three phyla.

    Sisu C, Pei B, Leng J, Frankish A, Zhang Y et al.

    Proceedings of the National Academy of Sciences of the United States of America 2014;111;37;13361-6

  • Comparative analysis of the transcriptome across distant species.

    Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C et al.

    Nature 2014;512;7515;445-8

  • Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

    Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P et al.

    Genome biology 2014;15;6;R88

  • The Vertebrate Genome Annotation browser 10 years on.

    Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM et al.

    Nucleic acids research 2014;42;Database issue;D771-9

  • Current status and new features of the Consensus Coding Sequence database.

    Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG et al.

    Nucleic acids research 2014;42;Database issue;D865-72

  • GENCODE pseudogenes.

    Frankish A and Harrow J

    Methods in molecular biology (Clifton, N.J.) 2014;1167;129-55

  • Functional transcriptomics in the post-ENCODE era.

    Mudge JM, Frankish A and Harrow J

    Genome research 2013;23;12;1961-73

  • Integrative annotation of variants from 1092 humans: application to cancer genomics.

    Khurana E, Fu Y, Colonna V, Mu XJ, Kang HM et al.

    Science (New York, N.Y.) 2013;342;6154;1235587

  • Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

    Gonzàlez-Porta M, Frankish A, Rung J, Harrow J and Brazma A

    Genome biology 2013;14;7;R70

  • An integrated map of genetic variation from 1,092 human genomes.

    1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA et al.

    Nature 2012;491;7422;56-65

  • The GENCODE pseudogene resource.

    Pei B, Sisu C, Frankish A, Howald C, Habegger L et al.

    Genome biology 2012;13;9;R51

  • An integrated encyclopedia of DNA elements in the human genome.

    ENCODE Project Consortium

    Nature 2012;489;7414;57-74

  • Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

    Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J et al.

    Molecular biology and evolution 2012;29;9;2265-83

  • GENCODE: the reference human genome annotation for The ENCODE Project.

    Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M et al.

    Genome research 2012;22;9;1760-74

  • Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

    Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T et al.

    Genome research 2012;22;9;1698-710

  • A systematic survey of loss-of-function variants in human protein-coding genes.

    MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J et al.

    Science (New York, N.Y.) 2012;335;6070;823-8

  • The importance of identifying alternative splicing in vertebrate genome annotation.

    Frankish A, Mudge JM, Thomas M and Harrow J

    Database : the journal of biological databases and curation 2012;2012;bas014

  • The origins, evolution, and functional potential of alternative splicing in vertebrates.

    Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T et al.

    Molecular biology and evolution 2011;28;10;2949-59

  • Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

    Brosch M, Saunders GI, Frankish A, Collins MO, Yu L et al.

    Genome research 2011;21;5;756-67

  • A user's guide to the encyclopedia of DNA elements (ENCODE).

    ENCODE Project Consortium

    PLoS biology 2011;9;4;e1001046

  • Gene inactivation and its implications for annotation in the era of personal genomics.

    Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R et al.

    Genes & development 2011;25;1;1-10

  • Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.

    Zhang ZD, Frankish A, Hunt T, Harrow J and Gerstein M

    Genome biology 2010;11;3;R26

  • The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

    Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M et al.

    Genome research 2009;19;7;1316-23

  • Efficient targeted transcript discovery via array-based normalization of RACE libraries.

    Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A et al.

    Nature methods 2008;5;7;629-35

  • Determination and validation of principal gene products.

    Tress ML, Wesselink JJ, Frankish A, López G, Goldman N et al.

    Bioinformatics (Oxford, England) 2008;24;1;11-7

  • Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

    ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R et al.

    Nature 2007;447;7146;799-816

  • Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

    Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R et al.

    Genome research 2007;17;6;746-59

  • Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.

    Zheng D, Frankish A, Baertsch R, Kapranov P, Reymond A et al.

    Genome research 2007;17;6;839-51

  • The implications of alternative splicing in the ENCODE protein complement.

    Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ et al.

    Proceedings of the National Academy of Sciences of the United States of America 2007;104;13;5495-500

  • The DNA sequence and biological annotation of human chromosome 1.

    Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D et al.

    Nature 2006;441;7091;315-21

  • GENCODE: producing a reference annotation for ENCODE.

    Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK et al.

    Genome biology 2006;7 Suppl 1;S4.1-9

  • Validation of mRNA/EST-based gene predictions in human Xp11.4 revealed differences to the organization of the orthologous mouse locus.

    Wen G, Ramser J, Taudien S, Gausmann U, Blechschmidt K et al.

    Mammalian genome : official journal of the International Mammalian Genome Society 2005;16;12;934-41

  • The DNA sequence of the human X chromosome.

    Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K et al.

    Nature 2005;434;7031;325-37

  • The DNA sequence and comparative analysis of human chromosome 10.

    Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L et al.

    Nature 2004;429;6990;375-81

  • DNA sequence and analysis of human chromosome 9.

    Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE et al.

    Nature 2004;429;6990;369-74

  • The DNA sequence and analysis of human chromosome 13.

    Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL et al.

    Nature 2004;428;6982;522-8

  • The DNA sequence and analysis of human chromosome 6.

    Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL et al.

    Nature 2003;425;6960;805-11

Frankish, Adam