Linda Milne
Current research interests
- Genome assembly, SNP discovery, marker/microarray design, genome annotation.
- Development of visualization and analysis tools for sequence and genetic data.
- Database and information management systems for Institute research projects.
- Automated data pipelines for producing good quality, contaminant-free DNA sequences, contig assemblies and sequence annotation.
Past research
As Bioinformatics Specialist at the Institute I create databases of plant genetic data and create interactive websites to deliver that data to a world-wide audience. Much of my research involves the design and implementation of new methods of visualizing data. The online databases use custom designed mySQL databases and Perl/CGI scripts for the back-end programming and generation of images, and use a combination of CSS and JavaScript for the website design. I also develop strategies for comparing large datasets of sequences (both within and between species), and write software for automating and streamlining the processing of large quantities of sequence data.
Bibliography
- 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, Article No. 90.
- Dreissig, S.; Maurer, A.; Sharma, R.; Milne, L.; Flavell, A.J.; Schmutzer, T.; Pillen, K. (2020) Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley., New Phytologist, 228, 1852-1863.
- 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.
- Simpson, C.G.; Fuller, J.; Flores, J.; Mayer, C-D.; Calixto, C.P.G.; Milne, L.; Hedley, P.E.; Booth, C.; Waugh, R.; Brown, J.W.S. (2019) High resolution RT-PCR analysis of alternative barley transcripts., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 17, pp269-281.
- Jarret, D.A.; Morris, J.; Cullen, D.W.; Gordon, S.L.; Verrall, S.R.; Milne, L.; Hedley, P.E.; Allwood, J.W.; Brennan, R.M.; Hancock, R.D. (2018) A transcript and metabolite atlas of blackcurrant fruit development highlights hormonal regulation and reveals the role of key transcription factors., Frontiers in Plant Science, 9, Article No. 1235.
- Herzig, P.; Maurer, A.; Draba, V.; Sharma, R.; Draicchio, F.; Bull, H.; Milne, L.; Thomas, W.T.B.; Flavell, A.J.; Pillen, K. (2018) Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping., Journal of Experimental Botany, 69, 1517-1531.
- Hackett, C.; Milne, L.; Smith, K.; Hedley, P.; Morris, J.; Simpson, C.; Preedy, K.; Graham, J. (2018) Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening., BMC Genetics, 19, Article No. 59.
- Ferdous, J.; Sanchez-Ferrero, J.C.; Langridge, P.; Milne, L.; Chowdhury, J.; Brien, C.; Tricker, P.J. (2017) Differential expression of microRNAs and potential targets under drought stress in barley., Plant Cell and Environment, 40, 11-24.
- Zhang, R.X.; Tucker, M.R.; Burton, R.A.; Shirley, N.J.; Little, A.; Morris, J.; Milne, L.; Houston, K.; Hedley, P.E.; Waugh, R.; Fincher, G.B. (2016) The dynamics of transcript abundance during cellularization of developing barley endosperm., Plant Physiology, 170, 1549-1565.
- Velmurugan, J.; Mollison, E.; Barth, S.; Marshall, D.; Milne, L.; Creevey, C.J.; Lynch, B.; Meally, H.; McCabe, M.; Milbourne, D. (2016) An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly., Annals of Botany, 118, 71-87.
- 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.
- Chowdappa, P.; Kumar, N.B.J.; Madhura, S.; Kumar, M.S.P.; Myers, K.L.; Fry, W.E.; Cooke, D.E.L. (2015) Severe outbreaks of late blight on potato and tomato in South India caused by recent changes in the Phytophthora infestans population., Plant Pathology, 64, 191-199.
- Wiesel, L.; Davis, J.L.; Milne, L.; Fernandez, V.R.; Herold, M.B.; Williams, J.M.; Morris, J.; Hedley, P.E.; Harrower, B.; Newton, A.C.; Birch, P.R.J.; Gilroy, E.M.; Hein, I. (2015) A transcriptional reference map of defence hormone responses in potato., Scientific Reports, 5, Article No. 15229.
- Graham, J.; Smith, K.; McCallum, S.; Hedley, P.E.; Cullen, D.W.; Dolan, A.; Milne, L.; McNicol, J.W.; Hackett, C.A. (2015) Towards an understanding of the control of 'crumbly' fruit in red raspberry., SpringerPlus, 4, Article No. 223.
- Russell, J.R.; Hedley, P.E.; Cardle, L.; Dancey, S.; Morris, J.; Booth, A.; Odee, D.; Mwaura, L.; Omondi, W.; Angaine, P.; Machua, J.; Muchugi, A.; Milne, I.; Kindt, R.; Jamnadass, R.; Dawson, I.K. (2014) tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species., PLoS ONE, 9, Article No. e102502.
- 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.
- 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.
- Mollison, E.M.B.; Barth, S.; Milbourne, D.; Milne, L.; Halpin, C.; McCabe, M.; Creevey, C.; Marshall, D.F. (2014) Genome assembly of perennial ryegrass, Lolium perenne., Agricultural Research Forum 2014, Tullamore Court Hotel, Ireland, 10-11 March 2014.
- McCallum, S.; Cullen, D.W.; Hedley, P.; Simpson, C.; Hancock, R.D.; Milne, L.; Hackett, C.A.; Graham J. (2013) Control of fruit quality traits in red raspberry, a review from the James Hutton Institute., Aspects of Applied Biology, 119, 1-16.
- Jupe, F.; Witek, K.; Verweij, W.; Sliwka, J.; Pritchard, L.; Etherington, G.J.; Maclean, D.; Cock, P.J.; Leggett, R.M.; Bryan, G.J.; Cardle, L.; Hein, I.; Jones, J.D.G. (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations., Plant Journal, 76, 530-544.
- 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.
- Sharma, S.K.; Bolser, D.; de Boer, J.; Sonderkaer, M.; Amoros, W.; Carboni, M.F.; D'Ambrosio, J.M.; de la Cruz, G.; Di Genova, A.; Douches, D.S.; Eguiluz, M.; Guo, X.; Guzman, F.; Hackett, C.A.; Hamilton, J.P.; Li, G.C.; Li, Y.; Lozano, R.; Maass, A.; Marshall, D.; Martinez, D.; McLean, K.; Mejia, N.; Milne, L.; Munive, S.; Nagy, I.; Ponce, O.; Ramirez, M.; Simon, R.; Thomson, S.J.; Torres, Y.; Waugh, R.; Zhang, Z.H.; Huang, S.W.; Visser, R.G.F.; Bachem, C.W.B.; Sagredo, B.; Feingold, S.E.; Orjeda, G.; Veilleux, R.E.; Bonierbale, M.; Jacobs, J.M.E.; Milbourne, D.; Martin, D.M.A.; Bryan, G.J. (2013) Construction of reference chromosome-scale Pseudomolecules for potato: integrating the potato genome with genetic and physical maps., G3-Genomes Genomes Genetics, 3, 2031-2047.
- Cullen, D.W.; McCallum, S.; Paterson, A.; Hedley, P.E.; Simpson, C.G.; Milne L.; Graham, J. (2013) Fruit quality in red raspberry., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013.
- McCallum, S.; Cullen, D.W.; Hedley, P.; Simpson, C.; Hancock, R.D.; Milne, L.; Hackett, C.A.; Graham J. (2013) Control of fruit quality traits in red raspberry, a review from James Hutton Institute., Fruits and Roots: A Celebration and Forward look, East Malling Research, Kent, 6-7 November 2013.
- Kalyna, M.; Simpson, C.G.; Syed, N.H.; Lewandowska, D.; Marquez, Y.; Kusenda, B.; Marshall, J.; Fuller, J.; Cardle, L.; McNicol, J.W.; Dihn, H.; Barta, A.; Brown, J.W.S. (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis., Nucleic Acids Research, 40, 2454-2469.
- 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.
- Cook, N.; Aziz, N.; Hedley, P.E.; Morris, J.; Milne, L.; Karley, A.J.; Hubbard, S.F.; Russell, J.R. (2011) Transcriptome sequencing of an ecologically important graminivorous sawfly: a resource for marker development., Conservation Genetics Resources, 3, 789-795.
- 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.
- Yong, SY.C.; Choong, C.Y.; Cheong, P.L.; Pang, S.L.; Amalina, R.N.; Harikrishna, J.A.; Mat-Isa, M.N.; Hedley, P.E.; Milne, L.; Vaillancourt, R.E.; Wickneswari, R. (2011) Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid., Tree Genetics and Genomes, 7, 143-152.
- 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.
- Hedley, P.E.; Russell, J.R.; Jorgensen, L.; Gordon, S.; Morris, J.A.; Hackett, C.A.; Cardle, L.; Brennan, R.M. (2010) Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.)., BMC Plant Biology, 10, 1-13.
- Druka, A.; Franckowiak, J.D.; Lundqvist, U.; Bonar, N.; Alexander, J.; Guzy-Wrobelska, J.; Ramsay, L.; Druka, I.; Grant, I.; Macaulay, M.; Vendramin, V.; Shahinnia, F.; Radovic, S.; Houston, K.; Harrap, D.; Cardle, L.; Marshall, D.F.; Morgante, M.; Stein, N.; Waugh, R. (2010) Exploiting induced variation to dissect quantitative traits in barley., Biochemical Society Transactions, 38, 683-688.
- 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.
- 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.
- 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.
- 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.
- Schena, L.; Cardle, L.; Cooke, D.E.L. (2008) Use of genome sequence data in the design and testing of SSR markers for Phytophthora species., BMC Genomics, 9, 620-643.
- 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, Article No. 90.
- Dreissig, S.; Maurer, A.; Sharma, R.; Milne, L.; Flavell, A.J.; Schmutzer, T.; Pillen, K. (2020) Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley., New Phytologist, 228, 1852-1863.
- 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.
- Jarret, D.A.; Morris, J.; Cullen, D.W.; Gordon, S.L.; Verrall, S.R.; Milne, L.; Hedley, P.E.; Allwood, J.W.; Brennan, R.M.; Hancock, R.D. (2018) A transcript and metabolite atlas of blackcurrant fruit development highlights hormonal regulation and reveals the role of key transcription factors., Frontiers in Plant Science, 9, Article No. 1235.
- Herzig, P.; Maurer, A.; Draba, V.; Sharma, R.; Draicchio, F.; Bull, H.; Milne, L.; Thomas, W.T.B.; Flavell, A.J.; Pillen, K. (2018) Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping., Journal of Experimental Botany, 69, 1517-1531.
- Hackett, C.; Milne, L.; Smith, K.; Hedley, P.; Morris, J.; Simpson, C.; Preedy, K.; Graham, J. (2018) Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening., BMC Genetics, 19, Article No. 59.
- Ferdous, J.; Sanchez-Ferrero, J.C.; Langridge, P.; Milne, L.; Chowdhury, J.; Brien, C.; Tricker, P.J. (2017) Differential expression of microRNAs and potential targets under drought stress in barley., Plant Cell and Environment, 40, 11-24.
- Zhang, R.X.; Tucker, M.R.; Burton, R.A.; Shirley, N.J.; Little, A.; Morris, J.; Milne, L.; Houston, K.; Hedley, P.E.; Waugh, R.; Fincher, G.B. (2016) The dynamics of transcript abundance during cellularization of developing barley endosperm., Plant Physiology, 170, 1549-1565.
- Velmurugan, J.; Mollison, E.; Barth, S.; Marshall, D.; Milne, L.; Creevey, C.J.; Lynch, B.; Meally, H.; McCabe, M.; Milbourne, D. (2016) An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly., Annals of Botany, 118, 71-87.
- 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.
- Chowdappa, P.; Kumar, N.B.J.; Madhura, S.; Kumar, M.S.P.; Myers, K.L.; Fry, W.E.; Cooke, D.E.L. (2015) Severe outbreaks of late blight on potato and tomato in South India caused by recent changes in the Phytophthora infestans population., Plant Pathology, 64, 191-199.
- Wiesel, L.; Davis, J.L.; Milne, L.; Fernandez, V.R.; Herold, M.B.; Williams, J.M.; Morris, J.; Hedley, P.E.; Harrower, B.; Newton, A.C.; Birch, P.R.J.; Gilroy, E.M.; Hein, I. (2015) A transcriptional reference map of defence hormone responses in potato., Scientific Reports, 5, Article No. 15229.
- Graham, J.; Smith, K.; McCallum, S.; Hedley, P.E.; Cullen, D.W.; Dolan, A.; Milne, L.; McNicol, J.W.; Hackett, C.A. (2015) Towards an understanding of the control of 'crumbly' fruit in red raspberry., SpringerPlus, 4, Article No. 223.
- Russell, J.R.; Hedley, P.E.; Cardle, L.; Dancey, S.; Morris, J.; Booth, A.; Odee, D.; Mwaura, L.; Omondi, W.; Angaine, P.; Machua, J.; Muchugi, A.; Milne, I.; Kindt, R.; Jamnadass, R.; Dawson, I.K. (2014) tropiTree: an NGS-based EST-SSR resource for 24 tropical tree species., PLoS ONE, 9, Article No. e102502.
- 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.
- 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.
- McCallum, S.; Cullen, D.W.; Hedley, P.; Simpson, C.; Hancock, R.D.; Milne, L.; Hackett, C.A.; Graham J. (2013) Control of fruit quality traits in red raspberry, a review from the James Hutton Institute., Aspects of Applied Biology, 119, 1-16.
- Jupe, F.; Witek, K.; Verweij, W.; Sliwka, J.; Pritchard, L.; Etherington, G.J.; Maclean, D.; Cock, P.J.; Leggett, R.M.; Bryan, G.J.; Cardle, L.; Hein, I.; Jones, J.D.G. (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations., Plant Journal, 76, 530-544.
- 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.
- Sharma, S.K.; Bolser, D.; de Boer, J.; Sonderkaer, M.; Amoros, W.; Carboni, M.F.; D'Ambrosio, J.M.; de la Cruz, G.; Di Genova, A.; Douches, D.S.; Eguiluz, M.; Guo, X.; Guzman, F.; Hackett, C.A.; Hamilton, J.P.; Li, G.C.; Li, Y.; Lozano, R.; Maass, A.; Marshall, D.; Martinez, D.; McLean, K.; Mejia, N.; Milne, L.; Munive, S.; Nagy, I.; Ponce, O.; Ramirez, M.; Simon, R.; Thomson, S.J.; Torres, Y.; Waugh, R.; Zhang, Z.H.; Huang, S.W.; Visser, R.G.F.; Bachem, C.W.B.; Sagredo, B.; Feingold, S.E.; Orjeda, G.; Veilleux, R.E.; Bonierbale, M.; Jacobs, J.M.E.; Milbourne, D.; Martin, D.M.A.; Bryan, G.J. (2013) Construction of reference chromosome-scale Pseudomolecules for potato: integrating the potato genome with genetic and physical maps., G3-Genomes Genomes Genetics, 3, 2031-2047.
- Kalyna, M.; Simpson, C.G.; Syed, N.H.; Lewandowska, D.; Marquez, Y.; Kusenda, B.; Marshall, J.; Fuller, J.; Cardle, L.; McNicol, J.W.; Dihn, H.; Barta, A.; Brown, J.W.S. (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis., Nucleic Acids Research, 40, 2454-2469.
- 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.
- Cook, N.; Aziz, N.; Hedley, P.E.; Morris, J.; Milne, L.; Karley, A.J.; Hubbard, S.F.; Russell, J.R. (2011) Transcriptome sequencing of an ecologically important graminivorous sawfly: a resource for marker development., Conservation Genetics Resources, 3, 789-795.
- 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.
- Yong, SY.C.; Choong, C.Y.; Cheong, P.L.; Pang, S.L.; Amalina, R.N.; Harikrishna, J.A.; Mat-Isa, M.N.; Hedley, P.E.; Milne, L.; Vaillancourt, R.E.; Wickneswari, R. (2011) Analysis of ESTs generated from inner bark tissue of an Acacia auriculiformis x Acacia mangium hybrid., Tree Genetics and Genomes, 7, 143-152.
- 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.
- Hedley, P.E.; Russell, J.R.; Jorgensen, L.; Gordon, S.; Morris, J.A.; Hackett, C.A.; Cardle, L.; Brennan, R.M. (2010) Candidate genes associated with bud dormancy release in blackcurrant (Ribes nigrum L.)., BMC Plant Biology, 10, 1-13.
- Druka, A.; Franckowiak, J.D.; Lundqvist, U.; Bonar, N.; Alexander, J.; Guzy-Wrobelska, J.; Ramsay, L.; Druka, I.; Grant, I.; Macaulay, M.; Vendramin, V.; Shahinnia, F.; Radovic, S.; Houston, K.; Harrap, D.; Cardle, L.; Marshall, D.F.; Morgante, M.; Stein, N.; Waugh, R. (2010) Exploiting induced variation to dissect quantitative traits in barley., Biochemical Society Transactions, 38, 683-688.
- 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.
- Schena, L.; Cardle, L.; Cooke, D.E.L. (2008) Use of genome sequence data in the design and testing of SSR markers for Phytophthora species., BMC Genomics, 9, 620-643.
- Lyons, M.; Cardle, L.; Rostoks, N.; Waugh, R.; Flavell, A.J. (2008) Isolation, analysis and marker utility of novel miniature inverted repeat transposable elements from the barley genome., Molecular Genetics and Genomics, 280, 275-285.
- Woodhead, M.; McCallum, S.; Smith, K.; Cardle, L.; Mazzitelli, L.; Graham, J. (2008) Identification, characterisation and mapping of simple sequence repeat (SSR) markers from raspberry root and bud ESTs., Molecular Breeding, 22, 555-563.
- Woodhead, M.; Russell, J.R.; Squirrell, J.; Hollingsworth, P.M.; Cardle, L.; Gibby, M.; Powell, W. (2007) Development of EST-derived microsatellite markers for Arabidopsis lyrata subspecies petraea (L.)., Molecular Ecology Notes, 7, 631-634.
- Rostoks, N.; Ramsay, L.; MacKenzie, K.; Cardle, L.; Bhat, P.R.; Roose, M.L.; Svensson, J.T.; Stein, N.; Varshney, R.K.; Marshall, D.F.; Graner, A.; Close, T.J.; Waugh, R. (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties., Proceedings of the National Academy of Sciences of the United States of America (PNAS), 103, 18656-18661.
- Rostoks, N.; Mudie, S.; Cardle, L.; Russell, J.R.; Ramsay, L.; Booth, A.; Svensson, J.T.; Wanamaker, S.I.; Walia, H.; Rodriguez, E.M.; Hedley, P.E.; Liu, H.; Morris, J.; Close, T.J.; Marshall, D.F.; Waugh, R. (2005) Genome wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress., Molecular Genetics and Genomics, 274, 515-527.
- Rostoks, N.; Borevitz, J.O.; Hedley, P.E.; Russell, J.R.; Mudie, S.; Morris, J.; Cardle, L.; Marshall, D.F.; Waugh, R. (2005) Single feature polymorphism discovery in the barley transcriptome., Genome Biology, 6, 1-10.
- Ibrahim, A.F.M.; Hedley, P.E.; Cardle, L.; Kruger, W.; Marshall, D.F.; Muehlbauer, G.; Waugh, R. (2005) A comparative analysis of transcript abundance using SAGE and Affymetrix arrays., Functional and Integrative Genomics, 5, 163-174.
- Furlanetto, C.; Cardle, L.; Brown, D.J.F.; Jones, J.T. (2005) Analysis of Expressed Sequence Tags from the ectoparasitic nematode Xiphinema index., Nematology, 7, 95-104.
- Simpson, C.G.; Fuller, J.; Flores, J.; Mayer, C-D.; Calixto, C.P.G.; Milne, L.; Hedley, P.E.; Booth, C.; Waugh, R.; Brown, J.W.S. (2019) High resolution RT-PCR analysis of alternative barley transcripts., In: Harwood, W.A. (ed.). Barley: Methods and Protocols. Methods in Molecular Biology, Humana Press, New York, Volume 1900, Chapter 17, pp269-281.
- 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.
- Ramsay, L.; Hedley, P.E.; Liu, H.; McCallum, N.; Mudie, S.; Cardle, L.; Harrower, B.E.; Machray, G.C.; Marshall, D.F.; Waugh, R. (2002) Barley transcriptome resources., Annual Report of the Scottish Crop Research Institute for 2001/2002, pp151-152.
- Cardle, L.; Macaulay, M.; Marshall, D.F.; Milbourne, D.; Ramsay, L.; Waugh, R. (2000) SSR frequency and occurrence in plant genomes., Annual Report of the Scottish Crop Research Institute for 1999/2000, pp108-110.
- Mollison, E.M.B.; Barth, S.; Milbourne, D.; Milne, L.; Halpin, C.; McCabe, M.; Creevey, C.; Marshall, D.F. (2014) Genome assembly of perennial ryegrass, Lolium perenne., Agricultural Research Forum 2014, Tullamore Court Hotel, Ireland, 10-11 March 2014.
- Cullen, D.W.; McCallum, S.; Paterson, A.; Hedley, P.E.; Simpson, C.G.; Milne L.; Graham, J. (2013) Fruit quality in red raspberry., Plant and Animal Genome XXI, San Diego, CA, USA, 12-16 January 2013.
- McCallum, S.; Cullen, D.W.; Hedley, P.; Simpson, C.; Hancock, R.D.; Milne, L.; Hackett, C.A.; Graham J. (2013) Control of fruit quality traits in red raspberry, a review from James Hutton Institute., Fruits and Roots: A Celebration and Forward look, East Malling Research, Kent, 6-7 November 2013.
- 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.
- Rostoks, N.; Mudie, S.; Bonar, N.; Cardle, L.; Marshall, D.F.; Waugh, R. (2007) SNP and haplotype diversity in coding and non-coding regions of European spring and winter barley., II International Vavilov Conference Crop Genetic Resources in the 21st Century, St Petersburg, Russia, 26-30 November 2007.
- Rostoks, N.; Mudie, S.; Bonar, N.; Cardle, L.; Marshall, D.F.; Waugh, R. (2005) Single nucleotide polymorphism discovery and mapping in barley., Plant & Animal Genome Conference (PAG) XIII, San Diego, California, 15-19 January 2005.
- Marshall, D.F.; Shaw, P.; Cardle, L. (2005) The plant genomics database infrastructure at the Scottish Crop Research Institute., Plant & Animal Genome XII, San Diego, California, 15-19 January 2005 (Abstract).
- Rostoks, N.; Cardle, L.; Mudie, S.; Svensson, J.T.; Walia, H.; Rodriguez, E.M.; Wanamaker, S.; Hedley, P.E.; Liu, H.; Ramsay, L.; Russell, J.R.; Close, T.J.; Marshall, D.F.; Waugh, R. (2004) Single nucleotide polymorphism mapping of the barley genes involved in abiotic stresses., Barley Genetics IX, Proceedings of 9th International Barley Genetics Symposium, Brno, Czech Republic, 20-26 June 2004.
- Russell, J.R.; Ramsay, L.; Booth, A.; Macaulay, M.; Cardle, L.; Marshall, D.F.; Powell, W.; Waugh, R. (2004) Development of gene based molecular markers in barley., Barley Genetics IX, Proceedings of 9th International Barley Genetics Symposium, Brno, Czech Republic, 20-26 June 2004.
- Ibrahim, A.F.M.; Hedley, P.E.; Cardle, L.; Marshall, D.F.; Waugh, R. (2004) Analysis of patterns of gene expression during barley grain development using Serial Analysis of Gene Expression (SAGE)., Barley Genetics IX, Proceedings of the 9th International Barley Genetics Symposium, Brno, Czech Republic, 20-26 June 2004.
- Ibrahim, A.F.M.; Hedley, P.E.; Cardle, L.; Kruger, W.; Marshall, D.F.; Muehlbauer, G.J.; Waugh, R. (2004) A comparative study of sage and microarray analysis in transcript profiling in barley., Plant & Animal Genome XII, San Diego, 10-14 January 2004, 120.
- McNicoll, J.; Tierney, I.; Milbourne, D.; Isidore, E.; McLean, K.; Williamson, S.; Cardle, L.; Purvis, A.; Waugh, R.; Bryan, G.J. (2003) Progress towards construction of a targeted physical map of a region of potato chromosome V., Plant and Animal Genome XI, San Diego, USA, 13-17January 2003.
- Taleb, N.; Avrova, A.O.; Stewart, H.E.; Cardle, L.; Jauffeerally-Fakim, Y.; Birch, P.R.J. (2002) Unravelling the molecular mechanisms of resistance in potato to Phytophthora infestans the causal agent of late blight., BSSP Presidential Conference: Plant Pathology and Global Food Security, Imperial College, London, 8-10 July 2002.
- Rokka, V.; Avrova, A.O.; Hein, I.; Gilroy, E.M.; Cardle, L.; Birch, P.R.J. (2002) Unravelling signalling processes in the potato R gene resistance response to Phytophthora infestans., GILB GILB'02 conference - Late Blight: Managing the Global Threat, Hamburg, Germany, 11-13 July 2002, 152.
- Woodhead, M.; Russell, J.R.; Squirrell, J.; Hollingsworth, P.M.; Cardle, L.; Ramsay, L.; Gibby, M.; Powell, W. (2002) The application of EST-derived SSRs in plant conservation genetics., Plant Conservation in Scotland Conference, September 2002.
- Woodhead, M.; Russell, J.R.; Ramsay, L.; Cardle, L.; Powell, W. (2002) The development and utility of SSRs derived from expressed sequence tags. Poster., Ecological Genetics Group Meeting.
- Marshall, D.F.; Cardle, L.; Ramsay, L.; Biscoe, P.V. (2001) Barley and potato bioinformatics at SCRI., Proceedings of Plant and Animal Genome, p673.
- Bell, K.S.; Avrova, A.O.; Holeva, M.C.; Cardle, L.; Morris, W.L.; De Jong, W.; Toth, I.K.; Waugh, R.; Bryan, G.J.; Birch, P.R.J. (2001) Sample sequencing of large, overlapping DNA fragments from Erwinia carotovora subsp. atroseptica reveals novel putative phytopathogenicity genes and allows comparison with the model animal pathogen Escherichia coli., Agricultural Microbes Genomes II. San Diego, USA, 17-19 January 2001.
- May, S.; Bradnam, K.; Cardle, L.; Cartinhour, S.; Couchman, M.; Davenport, G.; Devos, K.; Dicks, J.; Gale, M.; Huang, L.; Marshall, D.F.; McWilliam, H.; Ougham, H.; Trick, M.; Waugh, R. (2000) UK CropNet 99 - the second phase., Journal of Experimental Botany, 51, 22-23.
- Waugh, R.; Ramsay, L.; Macaulay, M.; McLean, K.; Thomas, W.T.B.; Ellis, R.P.; Swanston, J.S.; Russell, J.R.; Cardle, L.; Harrower, B.E.; Hedley, P.E.; Powell, W.; Machray, G.C. (1999) Identification and improvement of components of barley malting quality., Proceedings of the 9th Australian Barley Technical Symposium, Melbourne, 12-16 September 1999, pp98-112.
- Cardle, L.; Waugh, R.; Marshall, D.F. (1998) UK CROPNET Barley Db., BBSRC PAGA/GAIT Workshop, Edinburgh, April 1998.
