Micha Bayer
I am a bioinformatics specialist with a focus on second and third generation sequence analysis and 14 years of experience in barley genomics, variomics and transcriptomics. 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 barley. 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 the 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).
- Bioinformatics Specialist, Information and Computational Sciences group
- Specialises in analysis of Next Generation Sequencing data from crop plants
- Main focus: genomics and variomics (in particular in barley)
Current research interests
Over the years I have been involved in a large variety of projects across most of our crop plant species, but most of my research currently relates to barley. My particular interest is in barley variomics and genomics. I have been actively involved in the last two barley genome projects, and also in the development of the last two barley high throughout genotyping platforms. I have an active interest in the quality issues Next Generation Sequencing data and its analysis suffer from, and as part of this I recently supervised a PhD project looking at the generation of false positive SNPs during variant calling. Due to the high demand for bioinformatics analysis skills, I now also spend a substantial amount of my time teaching, supervising and mentoring both staff and students. I have been involved in delivering bioinformatics training courses both internationally and locally, at the James Hutton Institute and University of Dundee.
- 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 (species identification of algae by computer vision)
- February 1998 – June 1998: Postdoctoral Research Fellow, Gatty Marine Laboratory, St Andrews University (development of microsatellites for population genetics in marine invertebrates)
- June 1994 – January 1998: PhD Marine Biology, St Andrews University (phenotypic plasticity in marine bryozoans)
Bibliography
- Adams, T.M.; Smith, M.; Wang, Y.; Brown, L.H.; Bayer, M.M.; Hein, I. (2023) HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes, BMC Bioinformatics, 24(1), Art. 204
- Coulter, M.; Entizne, J.C.; Guo, W.; Bayer, M.; Wonneberger, R.; Milne, L.; Schreiber, M.; Haaning, A.; Muehlbauer, G.J.; McCallum, N.; Fuller, J.; Simpson, C.; Stein, N.; Brown, J.W.S.; Waugh, R.; Zhang, R. (2022) BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification, The Plant Journal,111(4),1183-1202
- Liu, L.; B. Jose, S.; Campoli, C.; Bayer, M.; A. Sánchez-Diaz, M.; Mcallister, T.; Zhou, Y.; Eskan, M.; Milne, L.; Schreiber, M.; Batstone, T.; D. Bull, I.; Ramsay, L.; von Wettstein-Knowles, P.; Waugh, R.; M. Hetherington, A.; McKim, S. (2022) Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley, Nature Communications, 13, Art. 6050
- Chen, Y.; Schreiber, M.; Bayer, M.; Dawson, I.; Hedley, P.; Lei, L.; Akhunova, A.; Liu, C.; Smith, K.; Fay, J.; Muehlbauer, G.; Steffenson, B.; Morrell, P.; Waugh, R.; Russell, J. (2022) The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication, The Plant Journal, 111(6), 1580-1594
- Thauvin, J.; Russell, J.; Vequaud, D.; Looseley, M.; Bayer, M.; Le Roux, P.; Pin, P.; Waugh, R.; Avrova, A. (2022) Genome-Wide Association Study for Resistance to Rhynchosporium in a Diverse Collection of Spring Barley Germplasm, Agronomy, 12(4), Art. 782
- Milne, L.; Bayer, M.; Rapazote-Flores, P.; Mayer, C-D.; Waugh, R.; Simpson, C.G. (2021) EORNA, a barley gene and transcript abundance database., Scientific Data, 8(1), Article No. 90
- Houston, K.; Qiu, J.; Wege, S.; Hrmova, M.; Oakey, H.; Qu, Y.; Smith, P.; Situmorang, A.; Macaulay, M.; Flis, P.; Bayer, M.; Roy, S.; Halpin, C.; Russell, J.; Schreiber, M.; Byrt, C.; Gilliham, M.; Salt, D.E.; Waugh, R. (2020) Barley sodium content is regulated by natural variants of the Na+ transporter HvHKT1;5., Communications Biology, 3, Article No. 258.
- Looseley, M.E.; Griffe, L.L.; Büttner, B.; Wright, K.M.; Bayer, M.M.; Coulter, M.; Thauvin, J-N.; Middlefell-Williams, J.; Maluk, M.; Okpo, A.; Kettles, N.; Werner, P.; Byrne, E.; Avrova, A. (2020) Characterisation of barley landraces from Syria and Jordan for resistance to rhynchosporium and identification of diagnostic markers for Rrs1Rh4., Theoretical and Applied Genetics, 133, 1243-1264.
- Coulter, M.; Büttner, B.; Hofmann, K.; Bayer, M.; Ramsay, L.; Schweizer, G.; Waugh, R.; Looseley, M.E.; Avrova, A. (2019) Characterisation of barley resistance to rhynchosporium on chromosome 6HS., Theoretical and Applied Genetics, 132, 1089-1107.
- Rapazote-Flores, P.; Bayer, M.; Milne, L.; Mayer, C-D.; Fuller, J.; Guo, W.; Hedley, P.E.; Morris, J.; Halpin, C.; Kam, J.; McKim, S.M.; Zwirek, M.; Casao, C.; Barakate, A.; Schreiber, M.; Stephen, G.; Zhang, R.; Brown, J.W.S.; Waugh, R.; Simpson, C.G. (2019) BaRTv1.0: a barley reference transcript dataset for quantitative measurement barley transcriptomes using RNA-seq., BMC Genomics, 20, Article No. 968.
- Bayer, M.; Morris, J.; Booth, C.; Booth, A.; Uzrek, N.; Russell, J.R.; Waugh, R.; Hedley, P.E. (2019) Exome capture for variant discovery and analysis in barley, In: Harwood, W.A. (ed.) Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, 283-310
- Okagaki, R.J.; Haaning, A.; Bilgic, H.; Heinen, S.; Druka, A.; Bayer, M.; Waugh, R.; Muehlbauer, G.J. (2018) ELIGULUM-A regulates lateral branch and leaf development in barley., Plant Physiology, 176, 2750-2760.
- Chen, X.; Lewandowska, D.; Armstrong, M.R.; Baker, K.; Lim, T.Y.; Bayer, M.; Harrower, B.; McLean, K.; Jupe, F.; Witek, K.; Lees, A.K.; Jones, J.D.; Bryan, G.J.; Hein, I. (2018) Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies, Theoretical and Applied Genetics, 131(6), 1287-1297
- Simpson, C.G.; Barrero, R.A.; Bayer, M.; Flavell, A.; Rapazote-Flores, P.; Bellgard, M.I.; Hedley, P.E.; Zhang, R.; Waugh, R. (2018) The expressed portion of the barley genome, In: Stein, N. & Muehlbauer, G. (eds.) The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, 789-107
- Twardziok, S.; Gundlach, H.; Hedley, P.E.; Bayer, M.; Platzer, M.; Groth, M.; Waugh, R.; Spannagl, M. (2018) Gene prediction in the barley genome, In: Stein, N. & Muehlbauer, G. (eds.) The Barley Genome, Compendium of Plant Genomes. Switzerland: Springer, Cham, 73-88
- Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S.O.; Wicker, T.; Radchuk, V.; Dockter, C.; Hedley, P.E.; Russell, J.; Bayer, M.; Ramsay, L.; Liu, H.; Haberer, G.; Zhang, X.; Zhang, Q.; Barrero, R.A.; Li, L.; Taudien, S.; Groth, M.; Felder, M.; Hastie, A.; Simkova, H.; Stankova, H.; Vrana, J.; Chan, S.; Munoz-Amatriain, M.; Ounit, R.; Wanamaker, S.; Bolser, D.; Colmsee, C.; Schmutzer, T.; Aliyeva-Schnorr, L.; Grasso, S.; Tanskanen, J.; Chailyan, A.; Sampath, D.; Heavens, D.; Clissold, L.; Cao, S.; Chapman, B.; Dai, F.; Han, Y.; Li, H.; Li, X.; Lin, C.; McCooke, J.K.; Tan, C.; Wang, P.; Wang, S.; Yin, S.; Zhou, G.; Poland, J.A.; Bellgard, M.I.; Borisjuk, L.; Houben, A.; Dolezel, J.; Ayling, S.; Lonardi, S.; Kersey, P.; Langridge, P.; Muehlbauer, G.J.; Clark, M.D.; Caccamo, M.; Schulman, U.; Mayer, K.F.X.; Platzer, M.; Close, T.J.; Scholz, U.; Hansson, M.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh. R.; Stein, N. (2017) A chromosome conformation capture ordered sequence of the barley genome , Nature, 544, 427-433.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- Looseley, M.E.; Bayer, M.; Bull, H.; Ramsay, L.; Thomas, W.; Booth, A.; De La Fuente Canto, C.; Morris, J.; Hedley, P.E.; Russell, J. (2017) Association mapping of diastatic power in UK winter and spring barley by exome sequencing of phenotypically contrasting variety sets., Frontiers in Plant Science, 8, Article No. 1566.
- Beier, S.; Himmelbach, A.; Colmsee, C.; Zhang, X.Q.; Barrero, R.A.; Zhang, Q.S.; Li, L.; Bayer, M.; Bolser, D.; Taudien, S.; Groth, M.; Felder, M.; Hastie, A.; Simkova, H.; Stankova, H.; Vrana, J.; Chan, S.K.; Munoz-Amatriain, M.; Ounit, R.; Wanamaker, S.; Schmutzer, T.; Aliyeva-Schnorr, L.; Grasso, S.; Tanskanen, J.; Sampath, D.; Heavens, D.; Cao, SJ; Chapman, B; Dai, F; Han, Y; Li, H; Li, X; Lin, CY; McCooke, JK; Tan, C; Wang, SB; Yin, SY; Zhou, GF; Poland, JA; Bellgard, MI; Houben, A; Dolezel, J; Ayling, S; Lonardi, S.; Langridge, P.; Muehlbauer, G.J.; Kersey, P.; Clark, M.D.; Caccamo, M.; Schulman, A.H.; Platzer, M.; Close, T.J.; Hansson, M.; Zhang, G.P.; Braumann, I.; Li, C.D.; Waugh, R.; Scholz, U.; Stein, N.; Mascher, M. (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L., Scientific Data, 4, Article No. 170044.
- Russell, J.; Mascher, M.; Dawson, I.K.; Kyriakidis, S.; Calixto, C.; Freund, F.; Bayer, M.; Milne, I.; Marshall-Griffiths, T.; Heinen, S.; Hofstad, A.; Sharma, R.; Himmelbach, A.; Knauft, M.; van Zonneveld, M.; Brown, J.W.S.; Schmid, K.; Kilian, B.; Muehlbauer, G.J.; Stein, N.; Waugh R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation., Nature Genetics, 48, 1024-1030.
- Milne, I.; Bayer, M.; Stephen, G.; Cardle, L.; Marshall, D. (2016) Tablet: visualizing next-generation sequence assemblies and mappings., In: Edwards, D. (ed.). Plant Bioinformatics: Methods and Protocols, Methods in Molecular Biology. Springer Science+Business Media, New York, 14, pp253-268.
- Baker, K.; Dhillon, T.; Colas, I.; Cook, N.; Milne, I.; Milne, L.; Bayer, M.; Flavell, A.J. (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance., Plant Journal, 84, 111-124.
- Ribeiro, A.; Golicz, A.; Hackett, C.A.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J.; Bayer, M. (2015) An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryotic genome., BMC Bioinformatics, 16, Article No.382.
- Comadira, G.; Rasool, B.; Kaprinska, B.; Garcia, B.M.; Morris, J.; Verrall, S.R.; Bayer, M.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2015) WHIRLY1 functions in the control of responses to nitrogen deficiency but not aphid infestation in barley., Plant Physiology, 168, 1140-1151.
- Baker, K.; Bayer, M.; Cook, N.; Dreizig, S.; Dhillon, T.; Russell, J.; Hedley, P.E.; Morris, J.; Ramsay, L.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression., The Plant Journal, 79, 981-992.
- Liu, H.; Bayer, M.; Druka, A.; Russell, J.; Hackett, C.; Poland, J.; Ramsay, L.; Hedley, P.; Waugh, R. (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley., BMC Genomics, 15, Article No.104.
- Russell, J.; Hackett, C.; Hedley, P.; Lui, H.; Milne, L.; Bayer, M.; Marshall, D.; Jorgensen, L.; Gordon, S.; Brennan, R. (2014) The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences., Molecular Breeding, 33, 835-849.
- Wu, X.; Hornyik, C.; Bayer, M.; Marshall, D.; Waugh, R.; Zhang, R.X. (2014) In silico identification and characterization of conserved plant microRNAs in barley., Central European Journal of Biology, 9, 841-852.
- Ho, T.; Cardle, L.; Xu, X.; Bayer, M.; Prince, S.J.; Mutava, R.N.; Marshall, D.F.; Syed, N.H. (2014) Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing., Molecular Breeding, 34, 977-988.
- Gamble, L.; Munsterkotter, M.; Bayer, M.; Knogge, W.; Newton, A.C.; Birch, P.R.J.; Avrova, A. (2014) On the path of discovery: Rhynchosporium commune effectors activating scald resistance in barley., Crop Protection in Northern Britain, Environmental Management and Crop Protection, West Park Conference Centre, Dundee, 25-26 February 2014.
- Adams, T.M.; Smith, M.; Wang, Y.; Brown, L.H.; Bayer, M.M.; Hein, I. (2023) HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes, BMC Bioinformatics, 24(1), Art. 204
- Coulter, M.; Entizne, J.C.; Guo, W.; Bayer, M.; Wonneberger, R.; Milne, L.; Schreiber, M.; Haaning, A.; Muehlbauer, G.J.; McCallum, N.; Fuller, J.; Simpson, C.; Stein, N.; Brown, J.W.S.; Waugh, R.; Zhang, R. (2022) BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification, The Plant Journal,111(4),1183-1202
- Liu, L.; B. Jose, S.; Campoli, C.; Bayer, M.; A. Sánchez-Diaz, M.; Mcallister, T.; Zhou, Y.; Eskan, M.; Milne, L.; Schreiber, M.; Batstone, T.; D. Bull, I.; Ramsay, L.; von Wettstein-Knowles, P.; Waugh, R.; M. Hetherington, A.; McKim, S. (2022) Conserved signalling components coordinate epidermal patterning and cuticle deposition in barley, Nature Communications, 13, Art. 6050
- Chen, Y.; Schreiber, M.; Bayer, M.; Dawson, I.; Hedley, P.; Lei, L.; Akhunova, A.; Liu, C.; Smith, K.; Fay, J.; Muehlbauer, G.; Steffenson, B.; Morrell, P.; Waugh, R.; Russell, J. (2022) The evolutionary patterns of barley pericentromeric chromosome regions, as shaped by linkage disequilibrium and domestication, The Plant Journal, 111(6), 1580-1594
- Thauvin, J.; Russell, J.; Vequaud, D.; Looseley, M.; Bayer, M.; Le Roux, P.; Pin, P.; Waugh, R.; Avrova, A. (2022) Genome-Wide Association Study for Resistance to Rhynchosporium in a Diverse Collection of Spring Barley Germplasm, Agronomy, 12(4), Art. 782
- Milne, L.; Bayer, M.; Rapazote-Flores, P.; Mayer, C-D.; Waugh, R.; Simpson, C.G. (2021) EORNA, a barley gene and transcript abundance database., Scientific Data, 8(1), Article No. 90
- Houston, K.; Qiu, J.; Wege, S.; Hrmova, M.; Oakey, H.; Qu, Y.; Smith, P.; Situmorang, A.; Macaulay, M.; Flis, P.; Bayer, M.; Roy, S.; Halpin, C.; Russell, J.; Schreiber, M.; Byrt, C.; Gilliham, M.; Salt, D.E.; Waugh, R. (2020) Barley sodium content is regulated by natural variants of the Na+ transporter HvHKT1;5., Communications Biology, 3, Article No. 258.
- Looseley, M.E.; Griffe, L.L.; Büttner, B.; Wright, K.M.; Bayer, M.M.; Coulter, M.; Thauvin, J-N.; Middlefell-Williams, J.; Maluk, M.; Okpo, A.; Kettles, N.; Werner, P.; Byrne, E.; Avrova, A. (2020) Characterisation of barley landraces from Syria and Jordan for resistance to rhynchosporium and identification of diagnostic markers for Rrs1Rh4., Theoretical and Applied Genetics, 133, 1243-1264.
- Coulter, M.; Büttner, B.; Hofmann, K.; Bayer, M.; Ramsay, L.; Schweizer, G.; Waugh, R.; Looseley, M.E.; Avrova, A. (2019) Characterisation of barley resistance to rhynchosporium on chromosome 6HS., Theoretical and Applied Genetics, 132, 1089-1107.
- Rapazote-Flores, P.; Bayer, M.; Milne, L.; Mayer, C-D.; Fuller, J.; Guo, W.; Hedley, P.E.; Morris, J.; Halpin, C.; Kam, J.; McKim, S.M.; Zwirek, M.; Casao, C.; Barakate, A.; Schreiber, M.; Stephen, G.; Zhang, R.; Brown, J.W.S.; Waugh, R.; Simpson, C.G. (2019) BaRTv1.0: a barley reference transcript dataset for quantitative measurement barley transcriptomes using RNA-seq., BMC Genomics, 20, Article No. 968.
- Okagaki, R.J.; Haaning, A.; Bilgic, H.; Heinen, S.; Druka, A.; Bayer, M.; Waugh, R.; Muehlbauer, G.J. (2018) ELIGULUM-A regulates lateral branch and leaf development in barley., Plant Physiology, 176, 2750-2760.
- Chen, X.; Lewandowska, D.; Armstrong, M.R.; Baker, K.; Lim, T.Y.; Bayer, M.; Harrower, B.; McLean, K.; Jupe, F.; Witek, K.; Lees, A.K.; Jones, J.D.; Bryan, G.J.; Hein, I. (2018) Identification and rapid mapping of a gene conferring broad-spectrum late blight resistance in the diploid potato species Solanum verrucosum through DNA capture technologies, Theoretical and Applied Genetics, 131(6), 1287-1297
- Mascher, M.; Gundlach, H.; Himmelbach, A.; Beier, S.; Twardziok, S.O.; Wicker, T.; Radchuk, V.; Dockter, C.; Hedley, P.E.; Russell, J.; Bayer, M.; Ramsay, L.; Liu, H.; Haberer, G.; Zhang, X.; Zhang, Q.; Barrero, R.A.; Li, L.; Taudien, S.; Groth, M.; Felder, M.; Hastie, A.; Simkova, H.; Stankova, H.; Vrana, J.; Chan, S.; Munoz-Amatriain, M.; Ounit, R.; Wanamaker, S.; Bolser, D.; Colmsee, C.; Schmutzer, T.; Aliyeva-Schnorr, L.; Grasso, S.; Tanskanen, J.; Chailyan, A.; Sampath, D.; Heavens, D.; Clissold, L.; Cao, S.; Chapman, B.; Dai, F.; Han, Y.; Li, H.; Li, X.; Lin, C.; McCooke, J.K.; Tan, C.; Wang, P.; Wang, S.; Yin, S.; Zhou, G.; Poland, J.A.; Bellgard, M.I.; Borisjuk, L.; Houben, A.; Dolezel, J.; Ayling, S.; Lonardi, S.; Kersey, P.; Langridge, P.; Muehlbauer, G.J.; Clark, M.D.; Caccamo, M.; Schulman, U.; Mayer, K.F.X.; Platzer, M.; Close, T.J.; Scholz, U.; Hansson, M.; Zhang, G.; Braumann, I.; Spannagl, M.; Li, C.; Waugh. R.; Stein, N. (2017) A chromosome conformation capture ordered sequence of the barley genome , Nature, 544, 427-433.
- Bayer, M.; Ganal, M.; Hedley, P.E.; Macaulay, M.; Plieske, J.; Ramsay, L.; Rapazote-Flores, P.; Russell, J.; Shaw, P.; Thomas, W.; Waugh, R. (2017) Development and evaluation of a barley 50k iSelect SNP array., Frontiers in Plant Science, 8, Article No. 1792.
- Looseley, M.E.; Bayer, M.; Bull, H.; Ramsay, L.; Thomas, W.; Booth, A.; De La Fuente Canto, C.; Morris, J.; Hedley, P.E.; Russell, J. (2017) Association mapping of diastatic power in UK winter and spring barley by exome sequencing of phenotypically contrasting variety sets., Frontiers in Plant Science, 8, Article No. 1566.
- Beier, S.; Himmelbach, A.; Colmsee, C.; Zhang, X.Q.; Barrero, R.A.; Zhang, Q.S.; Li, L.; Bayer, M.; Bolser, D.; Taudien, S.; Groth, M.; Felder, M.; Hastie, A.; Simkova, H.; Stankova, H.; Vrana, J.; Chan, S.K.; Munoz-Amatriain, M.; Ounit, R.; Wanamaker, S.; Schmutzer, T.; Aliyeva-Schnorr, L.; Grasso, S.; Tanskanen, J.; Sampath, D.; Heavens, D.; Cao, SJ; Chapman, B; Dai, F; Han, Y; Li, H; Li, X; Lin, CY; McCooke, JK; Tan, C; Wang, SB; Yin, SY; Zhou, GF; Poland, JA; Bellgard, MI; Houben, A; Dolezel, J; Ayling, S; Lonardi, S.; Langridge, P.; Muehlbauer, G.J.; Kersey, P.; Clark, M.D.; Caccamo, M.; Schulman, A.H.; Platzer, M.; Close, T.J.; Hansson, M.; Zhang, G.P.; Braumann, I.; Li, C.D.; Waugh, R.; Scholz, U.; Stein, N.; Mascher, M. (2017) Construction of a map-based reference genome sequence for barley, Hordeum vulgare L., Scientific Data, 4, Article No. 170044.
- Russell, J.; Mascher, M.; Dawson, I.K.; Kyriakidis, S.; Calixto, C.; Freund, F.; Bayer, M.; Milne, I.; Marshall-Griffiths, T.; Heinen, S.; Hofstad, A.; Sharma, R.; Himmelbach, A.; Knauft, M.; van Zonneveld, M.; Brown, J.W.S.; Schmid, K.; Kilian, B.; Muehlbauer, G.J.; Stein, N.; Waugh R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation., Nature Genetics, 48, 1024-1030.
- Baker, K.; Dhillon, T.; Colas, I.; Cook, N.; Milne, I.; Milne, L.; Bayer, M.; Flavell, A.J. (2015) Chromatin state analysis of the barley epigenome reveals a higher-order structure defined by H3K27me1 and H3K27me3 abundance., Plant Journal, 84, 111-124.
- Ribeiro, A.; Golicz, A.; Hackett, C.A.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J.; Bayer, M. (2015) An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryotic genome., BMC Bioinformatics, 16, Article No.382.
- Comadira, G.; Rasool, B.; Kaprinska, B.; Garcia, B.M.; Morris, J.; Verrall, S.R.; Bayer, M.; Hedley, P.E.; Hancock, R.D.; Foyer, C.H. (2015) WHIRLY1 functions in the control of responses to nitrogen deficiency but not aphid infestation in barley., Plant Physiology, 168, 1140-1151.
- Baker, K.; Bayer, M.; Cook, N.; Dreizig, S.; Dhillon, T.; Russell, J.; Hedley, P.E.; Morris, J.; Ramsay, L.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The low recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression., The Plant Journal, 79, 981-992.
- Liu, H.; Bayer, M.; Druka, A.; Russell, J.; Hackett, C.; Poland, J.; Ramsay, L.; Hedley, P.; Waugh, R. (2014) An evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley., BMC Genomics, 15, Article No.104.
- Russell, J.; Hackett, C.; Hedley, P.; Lui, H.; Milne, L.; Bayer, M.; Marshall, D.; Jorgensen, L.; Gordon, S.; Brennan, R. (2014) The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences., Molecular Breeding, 33, 835-849.
- Wu, X.; Hornyik, C.; Bayer, M.; Marshall, D.; Waugh, R.; Zhang, R.X. (2014) In silico identification and characterization of conserved plant microRNAs in barley., Central European Journal of Biology, 9, 841-852.
- Ho, T.; Cardle, L.; Xu, X.; Bayer, M.; Prince, S.J.; Mutava, R.N.; Marshall, D.F.; Syed, N.H. (2014) Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing., Molecular Breeding, 34, 977-988.
- Milne, I.; Stephen, G.; Bayer, M.M.; Cock, P.J.A.; Pritchard, L.; Cardle, L.; Shaw, P.; Marshall, D.F. (2013) Using Tablet for visual exploration of second generation sequencing data., Briefings in Bioinformatics, 14, 193-202.
- The International Barley Genome Sequencing Consortium (IBSC). (including: Waugh, R.; Hedley, P.; Liu, H.; Morris, J.; Brown, J.W.S.; Russell, J.; Druka, A.; Marshall, D.; Bayer, M.). (2012) A physical, genetic and functional sequence assembly of the barley genome., Nature, 491, 711-716.
- Comadran, J.; Kilian, B.; Russell, J.R.; Ramsay, L.; Stein, N.; Ganal, M.; Shaw, P.; Bayer, M.; Thomas, W.T.B.; Marshall, D.F.; Hedley, P.E.; Tondelli, A.; Pecchioni, N.; Francia, E.; Korzun, V.; Walther, A.; Waugh, R. (2012) Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley., Nature Genetics, 44, 1388-1392.
- 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.
- 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.
- Bayer, M.; Morris, J.; Booth, C.; Booth, A.; Uzrek, N.; Russell, J.R.; Waugh, R.; Hedley, P.E. (2019) Exome capture for variant discovery and analysis in barley, In: Harwood, W.A. (ed.) Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, 283-310
- Simpson, C.G.; Barrero, R.A.; Bayer, M.; Flavell, A.; Rapazote-Flores, P.; Bellgard, M.I.; Hedley, P.E.; Zhang, R.; Waugh, R. (2018) The expressed portion of the barley genome, In: Stein, N. & Muehlbauer, G. (eds.) The Barley Genome, Compendium of Plant Genomes. Springer, Cham, Switzerland, 789-107
- Twardziok, S.; Gundlach, H.; Hedley, P.E.; Bayer, M.; Platzer, M.; Groth, M.; Waugh, R.; Spannagl, M. (2018) Gene prediction in the barley genome, In: Stein, N. & Muehlbauer, G. (eds.) The Barley Genome, Compendium of Plant Genomes. Switzerland: Springer, Cham, 73-88
- Milne, I.; Bayer, M.; Stephen, G.; Cardle, L.; Marshall, D. (2016) Tablet: visualizing next-generation sequence assemblies and mappings., In: Edwards, D. (ed.). Plant Bioinformatics: Methods and Protocols, Methods in Molecular Biology. Springer Science+Business Media, New York, 14, pp253-268.
- 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.
- Chen, X.; Bayer, M.; Harrower, B.; Stevens, L.; Chapman, S.; Gilroy, E.; van Weymers, P.; Jupe, F.; Witek, K.; Jones, J.; Birch, P.; Bryan, G.; Hein, I. (2014) Using the potato genome to map and clone durable resistance genes more rapidly., Crop Protection in Northern Britain, Environmental Management and Crop Protection, West Park Conference Centre, Dundee, 25-26 February 2014.
- Avrova, A.; Gamble, L.; Griffe, L.; Ruiz, O.; Munsterkotter, M.; Bayer, M.; Looseley, M.E.; Knogge, W.; Newton, A.C.; Birch, P.R.; Hammond-Kosack K.E.; Kanyuka, K. (2014) From Rhynchosporium commune genome sequence to barley resistance., Crop Protection in Northern Britain, Environmental Management and Crop Protection, West Park Conference Centre, Dundee, 25-26 February 2014.
- Gamble, L.; Munsterkotter, M.; Bayer, M.; Knogge, W.; Newton, A.C.; Birch, P.R.J.; Avrova, A. (2014) On the path of discovery: Rhynchosporium commune effectors activating scald resistance in barley., Crop Protection in Northern Britain, Environmental Management and Crop Protection, West Park Conference Centre, Dundee, 25-26 February 2014.
- Shaw, P.; Milne, I.; Cardle, L.; Waugh, R.; Thomas, W.T.B.; Ramsay, L.; Comadran, J.; Stephen G.; Bayer, M.; Graham, M.; Kennedy J.; Oakey, H.; Marshall, D.F. (2012) Visualizing genetic transmission patterns in plant pedigrees., Plant and Animal Genome XX, San Diego, California, 14-18 January 2012.
- Bayer, M.; Liu, H.; Marshall, D.F.; Russell, J.; Hedley, P.E.; Milne, I.; Stephen G.; Waugh, R.; (2011) A GBS data processing pipeline for barley., StatSeq Meeting on Genotyping by Sequencing. Wageningen, Netherlands, 3-4 November 2011 (Talk).
- 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.
- Shaw, P.; Raubach, S.; Macaulay, M.; Schreiber, M.; Milne, I.; Bayer, M.; Kilian, B. (2023) Going for BOLD Supporting the Biodiversity for Opportunities, Livelihoods and Development Project with Germinate and GridScore, Plant and Animal Genome 30, 13-18 January 2023. San Diego, USA & Online.
- Sharma, S.K.; Bayer, M.; MacKenzie, K.; McLean, K.; Dale, F.; Taylor, M.; Bryan, G.J. (2018) Sequence-based genotyping and trait analysis in potato., 15th Solanaceae Conference (SOL2018), Chiang Mai, Thailand, 30 September - 4 October 2018. Abstract
- Rapazote-Flores, P.; Mayer, C-D.; Hedley, P.E.; Morris, J.; Fuller, J.; Milne, L.; Stephen, G.; Raeside, A.; Bayer, M.; Brown, J.W.S.; Calixto, C.P.G.; de la Vega, J.; Ayling, S.; Sampath, D.; Caccamo, M.; Waugh, R. (2016) Organ specific expression and alternative splicing in Barley (Hordeum vulgare)., Poster, September 2016.
- Looseley, M.E.; Bayer, M.; Hedley, P.E.; Bull, H.; Booth, A.; Thomas, W.T.B.; Ramsay, L.; Morris, J.; Waugh, R.; Russell, J.R. (2016) A genome wide analysis of key genes controlling diastatic power activity in winter and spring barley., International Barley Genetics Symposium, 12th, Minneapolis, USA, 26-30 June 2016. Poster
- Sharma, S.K.; Bayer, M.; McLean, K.; MacKenzie, K.; Daniels, S.; Dale, F.; Bryan, G. (2015) Application of genotyping-by-sequencing and genome-wide association analysis in tetraploid potato, 3rd Plant Genomics Congress, 11-12 May 2015, London, UK.
- Sharma, S.K.; Bayer, M.; McLean, K.; MacKenzie, K.; Daniels, S.; Dale, F.; Bryan, G. (2015) Genome-wide association studies using high-throughput SNP analysis in tetraploid potato, 12th Solanaceae Conference (SOL 2015), 25-29 October 2015, Bordeaux, France.
- Sharma, S.K.; Bayer, M.; McLean, K.; MacKenzie, K.; Daniels, S.; Dale, F.; Bryan, G. (2014) Application of genotyping-by-sequencing for identifying SNP variation and performing genome-wide association studies in a tetraploid potato association panel, 19th Triennial Conference of the European Association for Potato Research (EAPR), 6-11 July 2014, Brussels, Belgium.
- Sharma, S.K.; Bayer, M.; McLean, K.; MacKenzie, K.; Daniels, S.; Dale, F.; Bryan, G. (2014) Genotyping-by-sequencing and genome-wide association analysis in tetraploid potato, 11th Solanaceae Conference (SOL 2014), 2-6 November 2014, Porto Seguro-BA, Brazil.
- Baker, K.; Cook, N.; Bayer, M.; Colas, I.; Ramsay, L.; Russell, J.; Flavell, A.J. (2014) Epigenome of barley: Development and optimisation of a ChiP-Seq protocol to investigate histone modification in barley., Plant and Animal Genome XXII, San Diego, California, USA, 12-16 January 2014.
- Baker, K.; Bayer, M.; Cook, N.; Dreissig, S.; Dhillon, T.; Russell, J.; Hedley, P.; Morris, J.; Colas, I.; Waugh, R.; Steffenson, B.; Milne, I.; Stephen, G.; Marshall, D.; Flavell, A.J. (2014) The peri-centromeric heterochromatin of barley is a permissive environment for gene diversity, expression and evolution., Plant and Animal Genome XXII, San Diego, California, USA, 12-16 January 2014.
- Stephen, G.; Milne, I.; Bayer, M.; Shaw, P.D.; Raubach, S.; Hearne, S.; Singh, S.; Wenzl, P.; Marshall, D. (2014) Graphical applications for visualizing and analysing genotype data sets., VizBi 2014, 2nd EMBO Conference on Visualizing Biological Data, EML-Heidelberg, Germany, 5-7 March 2014.
- Milne, I.; Stephen, G.; Bayer, M.; Shaw, P.D.; Raubach, S.; Hearne, S.; Singh, S.; Wenzl, P.; Marshall, D. (2014) Graphical applications for visualizing and analysing genotype data sets., International Plant and Animal Genome XXII, San Diego, CA, USA, 11-15 January 2014.
- Pritchard, L.; Bayer, M.; Cock, P.; Flores, P.; Jones, S.; Milne, I.; Shaw, P.; Marshall, D. (2014) James Hutton Institute Bioinformatics Grouping., Data Science Research Day, University of Edinburgh, 12 September 2014.
- Milne, I.; Stephen, G.; Bayer, M.; Cardle, L.; Shaw, P.; Marshall, D. (2013) Optimisation of SNP and alternative splicing discovery using the Tablet NGS viewer., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013, P0971.
- Tondelli, A.; Xu, X.; Schnaithmann, F.; Sharma, R.; Ingvardsen C.; Comadran, J.; Thomas, W.T.B.; Russell, J.; Bayer, M.; Hedley, P.E.; Waugh, R.; Schulman, A.H.; Pillen K.; Kilian B.; Rasmussen, S.K.; Cattivelli, L.; Flavell, A.J. (2012) Structural and temporal variation in the genetic diversity of a European collection of barley cultivars and utility for association mapping of quantitative traits., Plant and Animal Genome XX, San Diego, USA, 11-15 January 2012 (Abstract).
- Tondelli, A.; Xu, X.; Schnaithmann, F.; Sharma, R.; Ingvardsen C.; Comadran, J.; Thomas, W.T.B.; Russell, J.; Bayer, M.; Hedley, P.E.; Waugh, R.; Schulman, A.H.; Pillen K.; Kilian B.; Rasmussen, S.K.; Cattivelli, L.; Flavell, A.J. (2012) Structural and temporal variation in the genetic diversity of a European collection of barley cultivars and utility for association mapping of quantitative traits., 11th International Barley Genetics Symposium, Hangzhou, China, 15-20 April 2012, No. 89 (Abstract).
- 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).
