Publications

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.

March 2009

Bioinformatics

Alexandra ME Jones, Daniel MacLean, David J Studholme, Antonio Serna-Sanz, Erik Andreasson, John P Rathjen, and Scott C Peck. (2009)

Phosphoproteomic analysis of nuclei-enriched fractions from arabidopsis thaliana. Journal of Proteomics, 72(3):439–451

February 2009

Bioinformatics, Jonathan Jones Group

Daniel MacLean, Jonathan DG Jones, and David J Studholme. (2009)

Application of ’next-generation’ sequencing technologies to microbial genetics. Nature Reviews Microbiology, 7(4):287–296

January 2009

Bioinformatics

Dan MacLean and David J Studholme (2009)

Bioinformatics aspects of high-throughput sequencing technology. In Plant Pathogenic Bacteria: Genomics and Molecular Biology, page 311. Horizon Scientific Press

August 2008

Bioinformatics

Simon Moxon, Frank Schwach, Tamas Dalmay, Dan MacLean, David J Studholme, and Vincent Moulton (2008)

A toolkit for analysing large-scale plant small rna datasets. Bioinformatics, 24(19):2252–2253,

July 2008

Bioinformatics

Amanda J Cottage, Ellie K Mott, Jun-Hui Wang, James A Sullivan, Dan MacLean, Linh Tran, Mun-Kit Choy, Christine Newell, Tony A Kavanagh, Sue Aspinall, et al. (2008)

Gun1 (genomes uncoupled1) encodes a pentatricopep- tide repeat (ppr) protein involved in plastid protein synthesis-responsive retrograde signaling to the nucleus. In Photosynthesis. Energy from the Sun, pages 1201–1205. Springer Netherlands.

June 2008

Bioinformatics

Daniel MacLean, Michael A Burrell, David J Studholme, and Alexandra ME Jones. (2008)

Phoscalc: a tool for evaluating the sites of peptide phos- phorylation from mass spectrometer data. BMC Research Notes, 1(1):30, 2008.

March 2008

Bioinformatics

Daniel MacLean, Cheryl A Jerome, Anthony PC Brown, and John C Gray. (2008)

Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and arabidopsis. Plant Molecular Biology, 66(5):475–490