Biography
I am a bioinformatics specialist with a focus on second and third generation sequence analysis. My post was created at the start of the next generation sequencing era and I am one of the early pioneers of applying these technologies to crop plants. I was part of the consortia for the barley genome projects in 2012 and 2017 and a co-author on several high-impact publications revolving around the analysis of genetic variation in barley. I was also the lead bioinformatician for the last two barley genotyping platforms, the Illumina iSelect 9k and 50k genotyping chips. I have been involved in two barley reference transcriptome projects, leading to high-quality barley reference transcript datasets (BART1 and BART2). Other projects I have been involved in include the identification of Rhynchosporium resistance genes, candidate genes for diastatic power and diagnostic markers for epiheterodendrin (EPH). More recently, I have been involved in the barley pan-genome, pan-transcriptome and pan-Hordeum projects, as well as the creation of the EORNA database (https://ics.hutton.ac.uk/eorna/index.html). I also have an active interest in RenSeq (https://doi.org/10.1111/tpj.12307) and related technologies, in both potato and barley.
Research
- BBSRC European Partnership Award “The exploitation and sharing of barley resources” 2021-2025 (Co-I)
- BBSRC Responsive mode “The Generation Gap – Mechanisms of maternal control on grain” 2021-2024 (Co-PI)
- BBSRC Responsive mode “R-EVOLVE” 2021-2025 (subcontract)
- BBSRC Responsive mode “Developing nutrient-enriched cereal grains with large embryos” 2019-2022 (named researcher)
- BBSRC BBR “A Reference Transcript Dataset for improved analysis of RNA-seq data from barley” 2018-2020 (subcontract)
- ERA-CAPS network “BARley yield associated Network (BARN)” 2018-2021 (subcontract)
- BBSRC Responsive mode “Mechanisms underlying variation in barley hull adhesion” 2018-2021 (subcontract)
- Innovate UK “EPH Elimination from Malting Barley for Scotch Whisky Production” 2017-2018 (Co-I)
- TSB/BBSRC AgriTech Catalyst “Breeding Targets for Durable Resistance to Rhynchosporium (DRRUM)” 2016-2019 (Co-I)
- HGCA/AHDB “A genome wide analysis of key genes controlling diastatic power activity in UK barley” 2015-2017 (Co-I)
- BBSRC Crop Improvement Research Club (CIRC) “Fungal effectors as activators of novel resistances in cereals.” 2012-2016 (Researcher Co-I)
- BBSRC Responsive mode “The diversity and evolution of the gene component of barley peri-centromeric heterochromatin” 2011-2014 (named researcher)
Past research
- May2008 – present: Bioinformatics Specialist, The James Hutton Institute (prev. SCRI)
- March 2006 – May2008: Software Developer, Scottish Bioinformatics Research Network (SBRN), SCRI
- September 2003 – February 2006: Grid Developer, National e-Science Centre (Glasgow Hub), University of Glasgow
- September 2002 – September 2003: MSc Information Technology, Glasgow University
- July 1998 – August 2002: Postdoctoral Researcher, Royal Botanic Garden Edinburgh
- February 1998 – June 1998: Postdoctoral Research Fellow, Gatty Marine Laboratory, St Andrews University
- June 1994 – January 1998: PhD Marine Biology, St Andrews University
Publications
The following Publications have not yet been migrated to the James Hutton Institute's Pure service and relate to the research outputs from the two legacy organisations: The Macaulay Land Use Research Institute and The Scottish Crop Research Institute.
Journals
- Russell, J.R.; Bayer, M.M.; Booth, C.; Cardle, L.; Hackett, C.A.; Hedley, P.E.; Jorgensen, L.; Morris, J.A.; Brennan, R.M. (2011) Identification, utilisation and mapping of novel transcriptome-based markers from blackcurrant (Ribes nigrum)., BMC Plant Biology, 11, 147.
- Graham, J.; Hackett, C.A.; Smith, K.; Woodhead, M.; MacKenzie, K.; Tierney, I.; Cooke, D.E.L.; Bayer, M.M.; Jennings, N. (2011) Towards an understanding of the nature of resistance to Phytophthora root rot in red raspberry., Theoretical and Applied Genetics, 123, 585-601.
- Bayer, M.M.; Milne, I.; Stephen, G.; Shaw, P.; Cardle, L.; Wright, F.; Marshall, D.F. (2011) Comparative visualization of genetic and physical maps with Strudel., Bioinformatics, 27, 1307-1308.
- Liu, H.; McNicol, J.W.; Bayer, M.M.; Morris, J.A.; Cardle, L.; Marshall, D.F.; Schulte, D.; Stein, N.; Shi, B.; Tandien, S.; Waugh, R.; Hedley, P.E. (2011) Highly parallel gene-to-BAC addressing using microarrays., Biotechniques, 50, 165-174.
- Milne, I.; Shaw, P.J.; Stephen, G.; Bayer, M.M.; Cardle, L.; Thomas, W.T.B.; Flavell, A.J.; Marshall, D.F. (2010) Flapjack – graphical genotype visualization., Bioinformatics, 26, 3133-3134.
- Chen, X.W.; Hackett, C.A.; Niks, R.E.; Hedley, P.E.; Booth, C.; Druka, A.; Marcel, T.C.; Vels, A.; Bayer, M.M.; Milne, I.; Morris, J.; Ramsay, L.; Marshall, D.F.; Cardle, L.; Waugh, R. (2010) An eQTL analysis of partial resistance to Puccinia hordei in barley., PLoS ONE, 5, 1-15.
- Milne, I.; Bayer, M.M.; Cardle, L.; Shaw, P.; Stephen, G.; Wright, F.; Marshall, D.F. (2010) Tablet – next generation sequence assembly visualization., Bioinformatics, 26, 401-402.
- Milne, I.; Lindner, D.; Bayer, M.M.; Husmeier, D.; McGuire, G.; Marshall, D.F.; Wright, F. (2009) TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops., Bioinformatics, 25, 126-127.
- Mann, D.G.; Bayer, M.M.; Droop, S.J.M.; Hicks, Y.A.; Marshall, A.D.; Martin, R.R.; Rosin, P.L. (2007) New methods for preparing, imaging and typifying desmids (Chlorophyta, Zygnematophyceae), including extended depth of focus and 3-D reconstruction., Phycologia, 46, 29-45.
Technical / contract reports
- Milne, I.; Shaw, P.; Milne, L.; Bayer, M.; Stephen, G.; Marshall, D.F. (2010) Visualising genetic diversity., Annual Report of the Scottish Crop Research Institute for 2009, pp21-22.
Conference papers
- Bayer, M.M.; Russell, J.R.; Milne, L.; Hedley, P.E.; Marshall, D.F. (2010) SNP discovery in barley Illumina data using Mosaik, GigaBayes and Tablet., 2nd Workshop of COST StatSeq Action (TD0801), Ghent, Belgium, 20-21 May 2010.
- Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.; Thomas, W.T.B.; Grzebyta, J.; Bayer, M.; Marshall, D.F. (2009) Germinate 2: A platform for Illumina SNP genotyping experiments and high volume phenotypic data., Plant & Animal Genome XVII, San Diego, California, 10-14 January 2009.
Conference posters / abstracts
- Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Flavell, A.J.; Stephen, G.; Bayer, M.; Graham, M.; Kennedy, J.; Marshall, D.F. (2011) Germinate 2 – Storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
- Flavell, A.J.; Syed, N.H.; Ho, T.; Cardle, L.; Xu, X.; Bayer, M.M.; Marshall, D.F. (2011) Genome-Tagged Amplification (GTA) – A PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing., Plant and Animal Genome XIX, San Diego, California, USA, 15-19 January 2011. (Poster)
- Woodhead, M.; Williamson, S.; Weir, A.; Smith, K.; Jennings, N.; McCallum, S.; Hackett, C.A.; Hedley, P.E.; Bayer, M.M.; Graham, J. (2011) Identification of cane splitting QTLs in raspberry., Scottish Society for Crop Research, The James Hutton Institute, Dundee, 9 March 2011. (Poster)
- Marshall, D.F.; Milne, I.; Bayer, M.; Shaw, P.; Cardle, L.; Stephen, G.; Ramsay, L.; Comadran, J.; Thomas, W.T.B.; Russell, J.R.; Flavell, A.J.; Waugh, R. (2010) What you see is what you get: SCRI visualization tools for SNP discovery, genotype analysis and comparative mapping., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Abstract).
- Marshall, D.F.; Milne, I.; Bayer, M.; Shaw, P.; Cardle, L.; Stephen, G.; Ramsay, L.; Comadran, J.; Thomas, W.T.B.; Russell, J.R.; Flavell, A.J.; Waugh, R. (2010) Tablet, flapjack and strudel; SCRI visualization tools to support SNP discovery, genotype analysis and comparative mapping., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Poster).
- Shaw, P.; Cardle, L.; Milne, I.; Waugh, R.; Flavell, A.J.; Stephen, G.; Bayer, M.M.; Graham, M.; Kennedy, J.; Marshall, D.F. (2010) Germinate 2 – storage, visualization and analysis of high volume genotypic, phenotypic and pedigree data., Plant & Animal Genome XVIII, San Diego, California, USA, 9-13 January 2010 (Abstract).
