Publications

July 2010

Bioinformatics, Jonathan Jones Group

David J Studholme, Eric Kemen, Daniel MacLean, Sebastian Schornack, Valente Aritua, Richard Thwaites, Murray Grant, Julian Smith, and Jonathan DG Jones. (2010)

Genome-wide sequencing data reveals virulence factors implicated in banana xanthomonas wilt. FEMS Microbiology Letters, 310(2):182–192.

May 2009

Bioinformatics

Vladimir T Valkov, Nunzia Scotti, Sabine Kahlau, Daniel MacLean, Ste- fania Grillo, John C Gray, Ralph Bock, and Teodoro Cardi. (2009)

Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and posttranscriptional control. Plant Physi- ology, 150(4):2030–2044.

August 2009

Bioinformatics, Jonathan Jones Group, Sophien Kamoun Group

Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grunwald, N.J., Horn, K., Horner, N.R., Hu, C.-H., Huitema, E., Jeong, D.-H., Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., MacLean, D., Chibucos, M.C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O'Neill, K., Ospina-Giraldo, M., Pinzon, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Phuntumart, V., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S., and Nusbaum, C. 2009.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461:393-398.

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December 2010

Bioinformatics, Sophien Kamoun Group

Raffaele, S., Farrer, R.A., Cano, L.M., Studholme, D.J., MacLean, D., Thines, M., Jiang, R.H.Y., Zody, M.C., Kunjeti, S.G., Donofrio, N.M., Meyers, B.C., Nusbaum, C., and Kamoun, S. 2010.

Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science, 330:1540-1543.

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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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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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July 2011

Bioinformatics, Jonathan Jones Group

Eric Kemen, Anastasia Gardiner, Torsten Schultz-Larsen, Ariane C Ke- men, Alexi L Balmuth, Alexandre Robert-Seilaniantz, Kate Bailey, Eric Holub, David J Studholme, Dan MacLean, et al. (2011)

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of arabidopsis thaliana. PLoS Biology, 9(7):e1001094

July 2011

Bioinformatics

Ricardo Ramirez-Gonzalez, Mario Caccamo, and Daniel MacLean (2011)

Gee fu: a sequence version and web-services database tool for genomic assembly, genome feature and ngs data. Bioinformatics, 27(19):2754–2755

February 2010

Bioinformatics

Daniel MacLean, Vincent Moulton, and David J Studholme. (2010)

Finding srna generative locales from high-throughput sequencing data with nibls. BMC Bioinformatics, 11(1):93,

May 2014

Bioinformatics, Jonathan Jones Group

Ghanasyam Rallapalli, Eric Kemen, Alexandre Robert-Seilaniantz, Cecile Segonzac, Graham Etherington, Kee Sohn, Daniel MacLean, and Jonathan Jones. (2014)

Exprss: an illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. BMC Genomics, 15(1):341

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