Publications

February 2012

Bioinformatics

Raoul JP Bonnal, Jan Aerts, George Githinji, Naohisa Goto, Dan MacLean, Chase A Miller, Hiroyuki Mishima, Massimiliano Pagani, Ricardo Ramirez-Gonzalez, Geert Smant, et al. (2012)

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics, 28(7):1035–1037

May 2012

Bioinformatics

Ricardo Ramirez-Gonzalez, Raoul JP Bonnal, Mario Caccamo, Daniel MacLean, et al. (2012)

Bio-samtools: Ruby bindings for samtools, a library for accessing bam files containing high-throughput sequence alignments. Source Code for Biology and Medicine, 7(6),

July 2012

Bioinformatics

GJ Etherington and D MacLean. (2012)

Bioinformatik-analyse von next generation-sequenzierungsdaten. BIOforum-Forschung und Entwicklung, 35(1):34

October 2012

Bioinformatics, Sophien Kamoun Group

Cooke, D.E.L., Cano, L.M., Raffaele, S., Bain, R.A., Cooke, L.R., Etherington, G.J., Deahl, K.L., Farrer, R.A., Gilroy, E.M., Goss, E.M., Grunwald, N.J., Hein, I., MacLean, D., McNicol, J.W., Randall, E., Oliva, R.F., Pel, M.A., Shaw, D.S., Squires, J.N., Taylor, M.C., Vleeshouwers, V.G.A.A., Birch, P.R.J., Lees, A.K., and Kamoun, S. 2012.

Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen. PLoS Pathogens, 8:e1002940.

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October 2012

Bioinformatics

Beck, M., Zhou, J., Faulkner, C., MacLean, D. and Robatzek, S. (2012)

Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting. Plant Cell. 24: 4205-4219.

March 2013

Bioinformatics

Rhys A Farrer, Daniel A Henk, Dan MacLean, David J Studholme, and Matthew C Fisher. (2013)

Using false discovery rates to benchmark snp-callers in next-generation sequencing projects. Scientific Reports, 3

March 2013

Bioinformatics, Jonathan Jones Group

Richard M Leggett, Ricardo H Ramirez-Gonzalez, Walter Verweij, Cintia G Kawashima, Zamin Iqbal, Jonathan DG Jones, Mario Caccamo, and Daniel MacLean. (2013)

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs. PloS ONE, 8(3):e60058

April 2013

Bioinformatics, Sophien Kamoun Group

MacLean, D., Yoshida, K., Edwards, A., Crossman, L., Clavijo, B., Clark, M., Swarbreck, D., Bashton, M., Chapman, P., Gijzen, M., Caccamo, M., Downie, A., Kamoun, S., and Saunders, D. 2013.

Crowdsourcing genomic analyses of ash and ash dieback — power to the people. GigaScience, 2:2.

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April 2013

Bioinformatics, Sophien Kamoun Group

Cantu, D., Segovia, V., Maclean, D., Bayles, R., Chen, X., Kamoun, S., Dubcovsky, J., Saunders, D.G., and Uauy, C. 2013.

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors. BMC Genomics, 14:270.

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June 2013

Bioinformatics

Graham J Etherington and Daniel MacLean. (2013)

Svgenes: a library for ren- dering genomic features in scalable vector graphic format. Bioinformatics, 29(15):1890–1892