Brown, John
Professor
所属大学: University of Dundee
所属学院: School of Life Sciences
近期论文
Zhang, R., Calixto, C. P. G., Marquez, Y., Venhuizen, P., Tzioutziou, N. A., Guo, W., Spensley, M., Lewandowska, D., ten Have, S., Frei dit Frey, N., Hirt, H., James, A. B., Nimmo, H. G., Barta, A., Kalyna, M., Brown, J.W.S. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research (under revision) Calixto CPG, Simpson CG, Waugh R, Brown JWS (2016) Alternative Splicing of Barley Clock Genes in Response to Low Temperature. PLoS One 11:e0168028. Brown JWS, Calixto CPG, Zhang R. (2016) High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants. New Phytol. 213: 525-530. Simpson CG, Fuller J, Calixto CPG, McNicol J, Booth C, Brown JWS, Staiger D. (2016) Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes. Methods Mol Biol. 1398:119-132. Russell, J., Mascher, M., Dawson, I. K., Kyriakidis, S., Calixto, C. P. G., Freund, F., Bayer, M., Milne, I., Marshall-Griffiths, T., Heinen, S., Hofstad, A., Sharma, R., Himmelbach, A., Knauft, M., van Zonneveld, M., Brown, J. W. S., Schmid, K., Kilian, B., Muehlbauer, G. J., Stein, N. and Waugh, R. (2016) Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nature Genet. Sep;48(9):1024-30. Zhang, R., Calixto, C.P.G., Marquez, Y., Venhuizen, P., Tzioutziou, N.A., Guo, W., Spensley, M., Frei dit Frey, N., Hirt, H., James, A.B., Nimmo, H.G., Barta, A., Kalyna, M. and Brown, J.W.S. (2016) AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data. bioRxiv Carvalho, R.F., Simpson, C. G., Szakonyi, D., Crozet, P., Barbosa, I. C. R., Brown, J. W. S., Baena-González, E. and Duque, P. (2015) The Arabidopsis SR45 splicing factor, a negative regulator of sugar signaling, modulates Snf1-related protein kinase1 stability. Plant Cell Aug;28(8):1910-25. Brown, J. W. S., Simpson, C. G., Marquez, Y., Gadd, G. M., Barta, A. and Kalyna, M. (2015) Lost in translation: pitfalls in deciphering plant alternative splicing transcripts. Plant Cell 27, 2083-2087 Schlaen, R.G., Mancini, E., Sanchez, S.E., Santangelo, S.P., Rugnone, M.L., Simpson, C.G., Brown, J.W.S., Zhang, X., Chernomoretz, A. and Yanovsky, M. J. (2015) A splicing factor modulates temperature compensation of circadian rhythms in Arabidopsis. Proc Natl Acad Sci U S A. 112, 9382-9387. Zhang, R., Calixto, C.P.G., Tzioutziou, N.A., James, A.B., Simpson, C.G., Gou, W., Marquez, Y., Kalyna, M., Patro, R., Eyras, E., Barta, A., Nimmo, H.G. and Brown, J.W.S. (2015) AtRTD - A comprehensive Reference Transcript Dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. New Phytologist 208, 96-101. Shin, K. H., Yang, S. H., Lee, J. Y., Lim, C. W., Lee, S. C., Brown, J. W. S. and Kim, S. H. (2015) Alternative splicing of mini-exons in the Arabidopsis leaf rust receptor-like kinase LRK10 genes affects subcellular localisation. Plant Cell Rep. 34, 495-505. Calixto, C.P.G., Waugh, R. and Brown, J.W.S. (2015) Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes. J. Mol. Evol. 80:108-19. Bardou, F., Ariel, F., Simpson, C. G., Romero, N., Laporte, P., Balzergue, S., Brown, J. W. S. and Crespi, M. (2014) Long non-coding RNA modulates alternative splicing regulators in Arabidopsis. Developmental Cell 30, 166–176. Raczynska, K. D., Stepien, A., Kierzkowski, D., Kalak, M., Bajczyk, M., McNicol, J., Simpson, C. G., Szweykowska-Kulinska, Z., Brown, J. W. S. and Jarmolowski, A. (2014) The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana. Nucleic Acids Research 42, 1224-1244. Petrillo, E., Godoy Herz, M.A., Simpson, C.G., Fuller, J., Fuchs, A., Brown, J.W.S., Barta, A., Kalyna, M. & Kornblihtt, A.R. 2013. Regulation of plant alternative splicing by the photosynthesis electron transfer chain. Science 344, 427-430.. Simpson, C.G., Lewandowska, D., Liney, M., Davidson, D., Chapman, S., Fuller, J., McNicol, J.W., Shaw, P.J. & Brown, J.W.S. 2013. Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini-exon splicing reporter and can affect alternative splicing of endogenous genes differentially. New Phytologist 203:424-436.. Staiger, D. & Brown, J.W.S. 2013. Alternative splicing at the intersection of biological timing, development and stress responses (Review). The Plant Cell 25, 3640-56.. Streitner, C., Simpson, C.G., Shaw, P., Danisman, S., Brown, J.W.S. & Staiger, D. 2013. Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana. Plant Signaling & Behavior 8, e24638. Lewandowska D, ten Have S, Hodge K, Tillemans V, Lamond AI, et al. (2013) Plant SILAC: Stable-Isotope Labelling with Amino Acids of Arabidopsis Seedlings for Quantitative Proteomics. PLoS ONE 8(8): e72207. James, A., Syed, N.H., Bordage, S., Marshall, J., Nimmo, G.A., Jenkins, G.I., Herzyk, P., Brown, J.W.S. & Nimmo, H.G. 2012. Alternative splicing mediates responses of the Arabidopsis thaliana circadian clock to temperature changes. The Plant Cell 24, 961-981. James, A.B., Syed, N.H., Brown, J.W.S. & Nimmo, H.G. 2012. Thermoplasticity in the plant circadian clock: how plants tell the time-perature. Plant Signaling & Behavior 7, 1219-1223. Jones, M.A., Williams, B.A., McNicol, J.W., Simpson, C.G., Brown, J.W.S. & Harmer, S.L. 2012. Mutation of Arabidopsis spliceosomal timekeeper locus 1 causes circadian clock defects. The Plant Cell 24, 4066-4082. Kalyna, M., Simpson, C.G., Syed, N.H., Lewandowska, D., Marquez, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J.W., Dihn, H., Barta, A. & Brown, J.W.S. 2012. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Research 40, 2454-2469. Marquez, Y., Brown, J.W.S., Simpson, C.G., Barta, A. & Kalyna, M. 2012. Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Research 22, 1184-1195. Shaw, P.J. & Brown, J.W.S. 2012. Nucleoli: composition, function and dynamics (Review). Plant Physiology 158, 44-51.