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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Liu, H.; Hedley, P.E.; Cardle, L.; Wright, K.M.; Hein, I.; Marshall, D.F.; Waugh, R. (2005) Characterisation and functional analysis of two barley caleosins expressed during barley caryopsis development., Planta, 221, 513-522.
- 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.
