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 editing activities at the Wellcome 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. In 2017, the HAVANA group moved to the European Bioinformatics Institute (EMBL-EBI) and I continue to be associated with gene annotation as a visiting scientist.

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 involved in gene editing at the Wellcome Sanger Institute, including high-throughput targeting of human ES cells and the generation of bespoke mouse models using a range of CRISPR-Cas9 strategies.

Publications

  • Best practice for CRISPR design using current tools and resources.

    Thomas M, Parry-Smith D and Iyer V

    Methods (San Diego, Calif.) 2019;164-165;3-17

  • Collateral damage and CRISPR genome editing.

    Thomas M, Burgio G, Adams DJ and Iyer V

    PLoS genetics 2019;15;3;e1007994

  • Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

    Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J et al.

    Nature genetics 2018;50;11;1574-1583

  • No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice.

    Iyer V, Boroviak K, Thomas M, Doe B, Riva L et al.

    PLoS genetics 2018;14;7;e1007503

  • 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

  • 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

  • Best practice for CRISPR design using current tools and resources.

    Thomas M, Parry-Smith D and Iyer V

    Methods (San Diego, Calif.) 2019;164-165;3-17

  • An Orphan CpG Island Drives Expression of a let-7 miRNA Precursor with an Important Role in Mouse Development.

    Koerner MV, Chhatbar K, Webb S, Cholewa-Waclaw J, Selfridge J et al.

    Epigenomes 2019;3;1;7

  • Collateral damage and CRISPR genome editing.

    Thomas M, Burgio G, Adams DJ and Iyer V

    PLoS genetics 2019;15;3;e1007994

  • Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

    Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J et al.

    Nature genetics 2018;50;11;1574-1583

  • No unexpected CRISPR-Cas9 off-target activity revealed by trio sequencing of gene-edited mice.

    Iyer V, Boroviak K, Thomas M, Doe B, Riva L et al.

    PLoS genetics 2018;14;7;e1007503

  • 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