Dr Mark Thomas | Senior Computer Biologist

Thomas, Mark

Involved in the annotation of the human and mouse genomes, I have a particular interest in noncoding transcription.   With expertise in genome interpretation, I currently support gene targeting activities at the Wellcome Trust Sanger Institute.

I joined the Wellcome Trust Sanger Institute in 2006, as a member of the Human and Vertebrate Analysis and Annotation (HAVANA) group. Undertaking gene annotation of the human and mouse genomes, I have gained considerable expertise in genome analysis, contributing towards the GENCODE gene set. I am particularly interested in the transcription of long noncoding RNAs, which despite their functional potential, remain poorly defined within the genome.

Participating in the EUCOMM and KOMP high-throughput gene knockout programmes from an early stage, I have led the conditional design process, targeting the majority of mouse protein coding genes. I continue to be associated with the Stem Cell Engineering group at the Wellcome Trust Sanger Institute, involved in both high-throughput targeting of human ES cells and the generation of bespoke mouse models using a range of CRISPR-Cas9 strategies.

Publications

  • Health and population effects of rare gene knockouts in adult humans with related parents.

    Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ et al.

    Science (New York, N.Y.) 2016;352;6284;474-7

  • 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

  • Structural and functional annotation of the porcine immunome.

    Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H et al.

    BMC genomics 2013;14;332

  • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

    Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S et al.

    Genome research 2012;22;9;1775-89

  • 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

  • A conditional knockout resource for the genome-wide study of mouse gene function.

    Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W et al.

    Nature 2011;474;7351;337-42

  • Health and population effects of rare gene knockouts in adult humans with related parents.

    Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ et al.

    Science (New York, N.Y.) 2016;352;6284;474-7

  • 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

  • Structural and functional annotation of the porcine immunome.

    Dawson HD, Loveland JE, Pascal G, Gilbert JG, Uenishi H et al.

    BMC genomics 2013;14;332

  • The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

    Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S et al.

    Genome research 2012;22;9;1775-89

  • 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

  • A conditional knockout resource for the genome-wide study of mouse gene function.

    Skarnes WC, Rosen B, West AP, Koutsourakis M, Bushell W et al.

    Nature 2011;474;7351;337-42

Thomas, Mark