• West Mains Road, Kings Buildings

    EH9 3JG Edinburgh

    United Kingdom

1980 …2020

Research output per year

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Research Output

2020

Genomics of Rubber Biosynthesis in Hevea brasiliensis

Chow, K-S., Bahari, A., Taylor, M. A. & Marshall, D., 31 May 2020, The Rubber Tree Genome.. Chow, KS. & Matsui, M. (eds.). Springer, p. 93-115 22 p. (Compendium of Plant Genomes).

Research output: Chapter in Book/Report/Conference proceedingChapter

2019

BrAPI - an application programming interface for plant breeding applications

Selby, P., Abbeloos, R., Backlund, J. E., Basterrechea Salido, M., Bauchet, G., Benites-Alfaro, O., Birkett, C., Calaminos, V. C., Carceller, P., Cornut, G., Vasques Costa, B., Edwards, J. D., Finkers, R., Gao, S. Y., Ghaffar, M., Glaser, P., Guignon, V., Hok, P., Kilian, A., König, P. & 30 others, Lagare, J. E. B., Lange, M., Laporte, M-A., Larmande, P., LeBauer, D., Lyon, D., Marshall, D., Matthews, D., Milne, I., Mistry, N., Morales, N., Mueller, L., Neveu, P., Papoutsoglou, E., Pearce, B., Perez-Masias, I., Pommier, C., Ramirez-Gonzalez, R. H., Rathore, A., Raquel, A. M., Raubach, S., Rife, T., Robbins, K., Rouard, M., Sarma, C., Scholz, U., Sempéré, G., Shaw, P., Simon, R. & Soldevilla, N., 15 Oct 2019, In : Bioinformatics (Oxford, England). 35, 20, p. 4147-4155 9 p., btz190.

Research output: Contribution to journalArticle

Open Access
File
8 Citations (Scopus)
4 Downloads (Pure)

RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family

Daly, P., McClellan, C., Maluk, M., Oakey, H., Lapierre, C., Waugh, R., Stephens, J., Marshall, D., Barakate, A., Tsuji, Y., Goeminne, G., Vanholme, R., Boerjan, W., Ralph, J. & Halpin, C., Mar 2019, In : Plant Biotechnology Journal. 17, 3, p. 594-607 14 p.

Research output: Contribution to journalArticle

Open Access
File
3 Citations (Scopus)
1 Downloads (Pure)
2017

Germinate 3: Development of a common platform to support the distribution of experimental data on crop wild relatives

Shaw, P. D., Raubach, S., Hearne, S. J., Dreher, K., Bryan, G., McKenzie, G., Milne, I., Stephen, G. & Marshall, D. F., 16 Jun 2017, In : Crop Science. 57, 3, p. 1259-1273 15 p.

Research output: Contribution to journalArticle

Open Access
9 Citations (Scopus)
2016

Analytical and decision support tools for genomics-assisted breeding

Varshney, R. K., Singh, V. K., Hickey, J. M., Xun, X., Marshall, D. F., Wang, J., Edwards, D. & Ribaut, J. M., 1 Apr 2016, In : Trends in Plant Science. 21, 4, p. 354-363 10 p.

Research output: Contribution to journalReview article

Open Access
23 Citations (Scopus)

An ultra-high density genetic linkage map of perennial ryegrass (Lolium perenne) using genotyping by sequencing (GBS) based on a reference shotgun genome assembly

Velmurugan, J., Mollison, E., Barth, S., Marshall, D., Milne, L., Creevey, C. J., Lynch, B., Meally, H., McCabe, M. & Milbourne, D., 1 Jul 2016, In : Annals of Botany. 118, 1, p. 71-87 17 p.

Research output: Contribution to journalArticle

8 Citations (Scopus)

Tablet: Visualizing Next-Generation Sequence Assemblies and Mappings

Milne, I., Bayer, M., Stephen, G., Cardle, L. & Marshall, D., 2016, Plant Bioinformatics: Methods and Protocols. Edwards, D. (ed.). Springer, Vol. 1374. p. 253-68 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

12 Citations (Scopus)
2015

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

Ribeiro, A., Golicz, A., Hackett, C. A., Milne, I., Stephen, G., Marshall, D., Flavell, A. J. & Bayer, M., 11 Nov 2015, In : BMC Bioinformatics. 16, 382.

Research output: Contribution to journalArticle

Open Access
19 Citations (Scopus)

Evolutionary dynamics of the cellulose synthase gene superfamily in grasses

Schwerdt, J. G., MacKenzie, K., Wright, F., Oehme, D., Wagner, J. M., Harvey, A. J., Shirley, N. J., Burton, R. A., Schreiber, M., Halpin, C., Zimmer, J., Marshall, D. F., Waugh, R. & Fincher, G. B., Jul 2015, In : Plant Physiology. 168, p. 968-983

Research output: Contribution to journalArticle

Open Access
24 Citations (Scopus)
2014

Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing

Ho, T., Cardle, L., Xu, X., Bayer, M., Prince, K. S. J., Mutava, R. N., Marshall, D. F. & Syed, N., Apr 2014, In : Plant Breeding. 34, 3, p. 977-988

Research output: Contribution to journalArticle

3 Citations (Scopus)

Helium: visualization of large scale plant pedigrees

Shaw, P. D., Graham, M., Kennedy, J., Milne, I. & Marshall, D. F., 1 Aug 2014, In : BMC Bioinformatics. 15, 259.

Research output: Contribution to journalArticle

Open Access
18 Citations (Scopus)

In silico identification and characterization of conserved plant microRNAs in barley

Wu, X., Hornyik, C., Bayer, M., Marshall, D., Waugh, R. & Zhang, R., 2014, In : Central European Journal of Biology. 9, 9, p. 841-852 12 p.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

The barley genome sequence assembly reveals three additional members of the CslF (1,3;1,4)-β-glucan synthase gene family

Schreiber, M., Wright, F., MacKenzie, K., Hedley, P. E., Schwerdt, J. G., Little, A., Burton, R. A., Fincher, G. B., Marshall, D., Waugh, R. & Halpin, C., 2014, In : PLoS ONE. 9, 3, e90888.

Research output: Contribution to journalArticle

Open Access
27 Citations (Scopus)

The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression

Baker, K., Bayer, M., Cook, N., Dreißig, 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., Sep 2014, In : Plant Journal. 79, 6, p. 981-992

Research output: Contribution to journalArticle

Open Access
17 Citations (Scopus)

The use of genotyping by sequencing in blackcurrant (Ribes nigrum): developing high-resolution linkage maps in species without reference genome sequences

Russell, J., Hackett, C., Hedley, P., Liu, H., Milne, L., Bayer, M., Marshall, D., Jorgensen, L., Gordon, S. & Brennan, R., Apr 2014, In : Molecular Breeding. 33, 4, p. 835-849

Research output: Contribution to journalArticle

35 Citations (Scopus)
2013

Construction of reference chromosome-scale pseudomolecules for potato: integrating the potato genome with genetic and physical maps

Sharma, S. K., Bolser, D., de Boer, J., Sønderkær, 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., Li, Y., Lozano, R., Maass, A., Marshall, D. & 25 others, Martinez, D., McLean, K., Mejía, N., Milne, L., Munive, S., Nagy, I., Ponce, O., Ramirez, M., Simon, R., Thomson, S. J., Torres, Y., Waugh, R., Zhang, Z., Huang, S., 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., 6 Nov 2013, In : G3: Genes, Genomes, Genetics. 3, 11, p. 2031-47 17 p.

Research output: Contribution to journalArticle

Open Access
File
123 Citations (Scopus)
10 Downloads (Pure)

Identification and characterization of miRNA transcriptome in potato by high-throughput sequencing

Zhang, R., Marshall, D., Bryan, G. J. & Hornyik, C., 21 Feb 2013, In : PLoS ONE. 8, 2, e57233.

Research output: Contribution to journalArticle

Open Access
76 Citations (Scopus)

Using Tablet for visual exploration of second-generation sequencing data

Milne, I., Stephen, G., Bayer, M., Cock, P. J. A., Pritchard, L., Cardle, L., Shaw, P. D. & Marshall, D., Mar 2013, In : Briefings in Bioinformatics. 14, 2, p. 193-202 10 p.

Research output: Contribution to journalArticle

425 Citations (Scopus)
2012

Natural variation in a homolog of Antirrhinum CENTRORADIALIS contributed to spring growth habit and environmental adaptation in cultivated barley

Comadran, J., Kilian, B., Russell, J., Ramsay, L., Stein, N., Ganal, M., Shaw, P., Bayer, M., Thomas, W., Marshall, D., Hedley, P., Tondelli, A., Pecchioni, N., Francia, E., Korzun, V., Walther, A. & Waugh, R., Nov 2012, In : Nature Genetics. 44, p. 1388-1392

Research output: Contribution to journalArticle

258 Citations (Scopus)
2011

A robust statistical method for association-based eQTL analysis

Jiang, N., Wang, M., Jia, T., Wang, L., Leach, L., Hackett, C., Marshall, D. & Luo, Z., 2011, In : PLoS ONE. 6, 8, e23192.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Comparative visualization of genetic and physical maps with Strudel

Bayer, M., Milne, I., Stephen, G., Shaw, P., Cardle, L., Wright, F. & Marshall, D., 1 May 2011, In : Bioinformatics (Oxford, England). 27, 9, p. 1307-8 2 p.

Research output: Contribution to journalArticle

Open Access
24 Citations (Scopus)

Genome sequence and analysis of the tuber crop potato

Potato Genome Sequencing Consortium, 10 Jul 2011, In : Nature. 475, 7355, p. 189-95 7 p.

Research output: Contribution to journalArticle

Open Access
1086 Citations (Scopus)

Highly parallel gene-to-BAC addressing using microarrays

Liu, H., McNicol, J., Bayer, M., Morris, J. A., Cardle, L., Marshall, D. F., Schulte, D., Stein, N., Shi, B-J., Taudien, S., Waugh, R. & Hedley, P. E., Mar 2011, In : BioTechniques. 50, 3, p. 165-74 10 p.

Research output: Contribution to journalArticle

Open Access
7 Citations (Scopus)

INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1

Ramsay, L., Comadran, J., Druka, A., Marshall, D. F., Thomas, W. T. B., Macaulay, M., MacKenzie, K., Simpson, C., Fuller, J., Bonar, N., Hayes, P. M., Lundqvist, U., Franckowiak, J. D., Close, T. J., Muehlbauer, G. J. & Waugh, R., 9 Jan 2011, In : European Journal of Medical Genetics. 43, p. 169-172

Research output: Contribution to journalArticle

169 Citations (Scopus)

Syringyl lignin is unaltered by severe sinapyl alcohol dehydrogenase suppression in tobacco

Barakate, A., Stephens, J., Goldie, A., Hunter, W. N., Marshall, D., Hancock, R. D., Lapierre, C., Morreel, K., Boerjan, W. & Halpin, C., Dec 2011, In : Plant Cell. 23, 12, p. 4492-506 15 p.

Research output: Contribution to journalArticle

21 Citations (Scopus)
2010

An eQTL analysis of partial resistance to Puccinia hordei in barley

Chen, X., Hackett, C. A., Niks, R. E., Hedley, P. E., Booth, C., Druka, A., Marcel, T. C., Vels, A., Bayer, M., Milne, I., Morris, J., Ramsay, L., Marshall, D., Cardle, L. & Waugh, R., 6 Jan 2010, In : PLoS ONE. 5, 1, e8598.

Research output: Contribution to journalArticle

Open Access
57 Citations (Scopus)

Cereal variety identification using MALDI-TOF mass spectrometry SNP genotyping

Pattemore, J. A., Rice, N., Marshall, D. F., Waugh, R. & Henry, R. J., Nov 2010, In : Journal of Cereal Science. 52, 3, p. 356-361 6 p.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Exploiting induced variation to dissect quantitative traits in barley

Druka, A., Franckowiak, J., 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., Morgante, M., Stein, N. & Waugh, R., Apr 2010, In : Biochemical Society Transactions. 38, 2, p. 683-8 6 p.

Research output: Contribution to journalReview article

7 Citations (Scopus)

Flapjack--graphical genotype visualization

Milne, I., Shaw, P., Stephen, G., Bayer, M., Cardle, L., Thomas, W. T. B., Flavell, A. J. & Marshall, D., 15 Dec 2010, In : Bioinformatics (Oxford, England). 26, 24, p. 3133-4 2 p.

Research output: Contribution to journalArticle

Open Access
106 Citations (Scopus)

Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

Cockram, J., White, J., Zuluaga, DL., Smith, D., Comadran, J., Macaulay, M., Lou, Z., Kearsey, MJ., Werner, P., Harrap, D., Tapsell, C., H, L., Hedley, PE., Stein, N., Schulte, DE., Steuernagel, B., Marshall, D., Thomas, WBT., L, R., Mackay, I. & 1 others, Balding, D., 14 Dec 2010, In : Proceedings of the National Academy of Sciences of the United States of America. 107, 50, p. 21611-21616 6 p.

Research output: Contribution to journalArticle

Tablet--next generation sequence assembly visualization

Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F. & Marshall, D., 1 Feb 2010, In : Bioinformatics (Oxford, England). 26, 3, p. 401-2 2 p.

Research output: Contribution to journalArticle

Open Access
429 Citations (Scopus)

The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis

Jing, R., Vershinin, A., Grzebyta, J., Shaw, P., Smýkal, P., Marshall, D., Ambrose, M. J., Ellis, T. H. N. & Flavell, A. J., 15 Feb 2010, In : BMC Evolutionary Biology. 10, 44.

Research output: Contribution to journalArticle

Open Access
105 Citations (Scopus)

Whole-genome association mapping in elite inbred crop varietiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Francki, M., Waugh, R., Marshall, D., Thomas, B., Comadran, J., Russell, J., Close, T., Stein, N., Hayes, P., Muehlbauer, G., Cockram, J., O’Sullivan, D., Mackay, I., Flavell, A. & Ramsay, L., Nov 2010, In : Genome. 53, 11, p. 967-972

Research output: Contribution to journalArticle

18 Citations (Scopus)
2009

Development and implementation of high-throughput SNP genotyping in barley

Close, T. J., Bhat, P. R., Lonardi, S., Wu, Y., Rostoks, N., Ramsay, L., Druka, A., Stein, N., Svensson, J. T., Wanamaker, S., Bozdag, S., Roose, M. L., Moscou, M. J., Chao, S., Varshney, R. K., Szűcs, P., Sato, K., Hayes, P. M., Matthews, D. E., Kleinhofs, A. & 8 others, Muehlbauer, G. J., DeYoung, J., Marshall, D. F., Madishetty, K., Fenton, R. D., Condamine, P., Graner, A. & Waugh, R., 4 Dec 2009, In : BMC Genomics. 10, 582.

Research output: Contribution to journalArticle

Open Access
441 Citations (Scopus)

TOPALi v2: A rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

Milne, I., Lindner, D., Bayer, M., Husmeier, D., Mcguire, G., Marshall, D. F. & Wright, F., Jan 2009, In : Bioinformatics. 25, 1, p. 126-127 2 p.

Research output: Contribution to journalArticle

Open Access
447 Citations (Scopus)
2008

Exploiting regulatory variation to identify genes underlying quantitative resistance to the wheat stem rust pathogen Puccinia graminis f. sp. tritici in barley

Druka, A., Potokina, E., Luo, Z., Bonar, N., Druka, I., Zhang, L., Marshall, D. F., Steffenson, B. J., Close, T. J., Wise, R. P., Kleinhofs, A., Williams, R. W., Kearsey, M. J. & Waugh, R., Jul 2008, In : Theoretical And Applied Genetics. 117, 2, p. 261-272

Research output: Contribution to journalArticle

39 Citations (Scopus)

Intronic noncoding RNAs and splicing

Brown, J. W. S., Marshall, D. F. & Echeverria, M., Jul 2008, In : Trends in Plant Science. 13, 7, p. 335-342 8 p.

Research output: Contribution to journalReview article

99 Citations (Scopus)

The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

Song, B-K., Hein, I., Druka, A., Waugh, R., Marshall, D., Nadarajah, K., Yap, S-J. & Ratnam, W., Jul 2008, In : Funct Integr Genomics. 9, 1, p. 97-108

Research output: Contribution to journalArticle

3 Citations (Scopus)

The generation challenge programme platform: semantic standards and workbench for crop science

Bruskiewich, R., Senger, M., Davenport, G., Ruiz, M., Rouard, M., Hazekamp, T., Takeya, M., Doi, K., Satoh, K., Costa, M., Simon, R., Balaji, J., Akintunde, A., Mauleon, R., Wanchana, S., Shah, T., Anacleto, M., Portugal, A., Ulat, V. J., Thongjuea, S. & 37 others, Braak, K., Ritter, S., Dereeper, A., Skofic, M., Rojas, E., Martins, N., Pappas, G., Alamban, R., Almodiel, R., Barboza, L. H., Detras, J., Manansala, K., Mendoza, M. J., Morales, J., Peralta, B., Valerio, R., Zhang, Y., Gregorio, S., Hermocilla, J., Echavez, M., Yap, J. M., Farmer, A., Schiltz, G., Lee, J., Casstevens, T., Jaiswal, P., Meintjes, A., Wilkinson, M., Good, B., Wagner, J., Morris, J., Marshall, D., Collins, A., Kikuchi, S., Metz, T., McLaren, G. & Van Hintum, T., 2008, In : International Journal of Plant Genomics. 2008, 6 p., 369601.

Research output: Contribution to journalArticle

Open Access
File
7 Citations (Scopus)
14 Downloads (Pure)

Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

Druka, A., Druka, I., Centeno, A. G., Li, H., Sun, Z., Thomas, W. TB., Bonar, N., Steffenson, B. J., Ullrich, S. E., Kleinhofs, A., Wise, R. P., Close, T. J., Potokina, E., Luo, Z., Wagner, C., Schweizer, G. F., Marshall, D. F., Kearsey, M. J., Williams, R. W. & Waugh, R., 2008, In : BMC Genetics. 9, 1

Research output: Contribution to journalArticle

Open Access
22 Citations (Scopus)
2007

Molecular barley breeding

Rae, S. J., Macaulay, M., Ramsay, L., Leigh, F., Matthews, D., O'Sullivan, D. M., Donini, P., Morris, P. C., Powell, W., Marshall, D. F., Waugh, R. & Thomas, W. T. B., 2007, In : Euphytica. 158, 3, p. 295-303 9 p.

Research output: Contribution to journalArticle

25 Citations (Scopus)
2006

A hAT superfamily transposase recruited by the cereal grass genome

Muehlbauer, G. J., Bhau, B. S., Syed, N. H., Heinen, S., Cho, S., Marshall, D., Pateyron, S., Buisine, N., Chalhoub, B. & Flavell, A. J., Jun 2006, In : Molecular Genetics and Genomics. 275, 6, p. 553-563 11 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

An atlas of gene expression from seed to seed through barley development

Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., McNicol, J., Marshall, D. & Waugh, R., Mar 2006, In : Functional and Integrative Genomics. 6, 3, p. 202-211

Research output: Contribution to journalArticle

110 Citations (Scopus)

Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties

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., 5 Dec 2006, In : Proceedings of the National Academy of Sciences of the United States of America. 103, 49, p. 18656-18661 6 p.

Research output: Contribution to journalArticle

245 Citations (Scopus)
2005

A comparative analysis of transcript abundance using SAGE and Affymetrix arrays

Ibrahim, A. F. M., Hedley, P. E., Cardle, L., Kruger, W., Marshall, D. F., Muehlbauer, G. J. & Waugh, R., Jul 2005, In : Functional and Integrative Genomics. 5, 3, p. 163-174 12 p.

Research output: Contribution to journalArticle

33 Citations (Scopus)

Arabidopsis nucleolar protein database (AtNoPDB)

Brown, J. W. S., Shaw, P. J., Shaw, P. & Marshall, D. F., 1 Jan 2005, In : Nucleic Acids Research. 33, DATABASE ISS.

Research output: Contribution to journalArticle

Open Access
58 Citations (Scopus)

Characterisation and functional analysis of two barley caleosins expressed during barley caryopsis development

Liu, H., Hedley, P., Cardle, L., Wright, K. M., Hein, I., Marshall, D. & Waugh, R., Jun 2005, In : Planta. 221, 4, p. 513-522 10 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress

Rostoks, N., Mudie, S., Cardle, L., Russell, J., 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., Dec 2005, In : Molecular Genetics and Genomics. 274, 5, p. 515-527 13 p.

Research output: Contribution to journalArticle

219 Citations (Scopus)

GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections

Lee, J. M., Davenport, G. F., Marshall, D., Ellis, T. H. N., Ambrose, M. J., Dicks, J., van Hintum, T. J. L. & Flavell, A. J., Oct 2005, In : Plant Physiology. 139, 2, p. 619-31 13 p.

Research output: Contribution to journalArticle

27 Citations (Scopus)