Dr Greg Deakin

Bioinformatician
Department:Crop Science and Production Systems
Tel:+44 (0)1732 843833
DD:+44 (0)1732 523757
Fax:+44 (0)1732 849067

Research Interests

I am currently a post-doctoral Bioinformation in the PPE program. My main research interest is using bioinformatics to understand disease interactions. The focus of this work is in the complex diseases of Apple Replant and Mushroom Virus X. I have developed several reusable bioinformatics pipelines at NIAB-EMR, including a Metabarcoding pipeline to identify and quantify bacteria, fungi, oomycetes and nematodes from Illumina Miseq data, and RNA and allele-seq pipelines. I have recently completed my PhD under the supervision of Dr Kerry Burton of EMR and Helen Grogan and Ian M Jones of University of Reading with a project entitled ‘Understanding the biology of Mushroom Virus X by molecular characterisation, location and translocation of RNA and their role in disease epidemiology’.

Selected Publications

  • Morin E, Kohler A, Baker AR, Foulongne-Oriol M, Lombard V, Nagy LG, Ohm RA, Patyshakuliyeva A, Brun A, Aerts AL, Bailey AM, Billette C, Coutinho PM, Deakin G, Doddapaneni H, Floudas D, Grimwood J, Hildén K, Kües U, Labutti KM, Lapidus A, Lindquist EA, Lucas SM, Murat C, Riley RW, Salamov AA, Schmutz J, Subramanian V, Wösten HA, Xu J, Eastwood DC, Foster GD, Sonnenberg AS, Cullen D, de Vries RP, Lundell T, Hibbett DS, Henrissat B, Burton KS, Kerrigan RW, Challen MP, Grigoriev IV, Martin F. (2012). Genome sequence of the button mushroom Agaricus bisporus reveals mechanisms governing adaptation to a humic-rich ecological niche. Proc Natl Acad Sci U S A. 2012 Oct 23;109(43). 17501-6. doi: 10.1073/pnas.1206847109. Epub 2012 Oct 8.

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