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.

March 2010

Bioinformatics

Daniel MacLean, Nataliya Elina, Ericka R Havecker, Susanne B Heim- staedt, David J Studholme, and David C Baulcombe. (2010)

Evidence for large complex networks of plant short silencing rnas. PLoS One, 5(3):e9901

March 2010

Cyril Zipfel Group, Jonathan Jones Group, Tissue Culture & Transformation

Lacombe S, Rougon-Cardoso A, Sherwood E, Peeters N, Dahlbeck D, van Esse HP, Smoker M, Rallapalli G, Thomma BPHJ, Staskawicz B, Jones JDG and Zipfel C (2010)

Inter-family transfer of a plant pattern recognition receptor confers broad-spectrum bacterial resistance. Nature Biotechnology, 4 :365-369.

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,

February 2010

Bioinformatics

Daniel MacLean and David J Studholme. (2010)

A boolean model of the pseudomonas syringae hrp regulon predicts a tightly regulated system. PloS ONE, 5(2):e9101.

January 2010

Bioinformatics

Pawel Durek, Robert Schmidt, Joshua L Heazlewood, Alexandra Jones, Daniel MacLean, Axel Nagel, Birgit Kersten, and Waltraud X Schulze. (2010)

Phosphat: the arabidopsis thaliana phosphorylation site database. an up- date. Nucleic Acids Research, 38(suppl 1):D828–D834

August 2009

Bioinformatics

Nalvo F Almeida, Shuangchun Yan, Magdalen Lindeberg, David J Studholme, David J Schneider, Bradford Condon, Haijie Liu, Carlos J Viana, Andrew Warren, Clive Evans, et al. (2009)

A draft genome sequence of pseudomonas syringae pv. tomato t1 reveals a type iii effector repertoire sig-nificantly divergent from that of pseudomonas syringae pv. tomato dc3000. Molecular Plant-Microbe Interactions, 22(1):52–62

August 2009

Bioinformatics

David J Studholme, Selena G Ibanez, Daniel MacLean, Jeffery L Dangl, Jeff H Chang, and John P Rathjen (2009)

A draft genome sequence and functional screen reveals the repertoire of type iii secreted proteins of pseudomonas syringae pathovar tabaci 11528. BMC Genomics, 10(1):395

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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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.