Brown, John

Professor

  • Professor & Personal Chair of Molecular Plant Sciences, Plant Sciences
1989 …2020

Research output per year

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Research Output

2019

Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane

Dantas, L. L. B., Calixto, C. P. G., Dourado, M. M., Carneiro, M. S., Brown, J. W. S. & Hotta, C. T., 23 Dec 2019, In : Frontiers in Plant Science. 10, p. 1-15 15 p., 1614.

Research output: Contribution to journalArticle

Open Access
File
66 Downloads (Pure)

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs

Calixto, C., Tzioutziou, N., James, A. B., Hornyik, C., Guo, W., Zhang, R., Nimmo, H. G. & Brown, J., 28 Feb 2019, In : Frontiers in Plant Science. 10, p. 1-16 16 p., 235.

Research output: Contribution to journalArticle

Open Access
File
4 Citations (Scopus)
68 Downloads (Pure)

Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation

Godoy Herz, M. A., Kubaczka, M. G., Brzyżek, G., Servi, L., Krzyszton, M., Simpson, C., Brown, J., Swiezewski, S., Petrillo, E. & Kornblihtt, A. R., 7 Mar 2019, In : Molecular Cell. 73, 5, p. 1066-1074.e3 13 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)
2018

How does temperature affect splicing events? Isoform switching of splicing factors regulates splicing of LATE ELONGATED HYPOCOTYL (LHY)

James, A. B., Calixto, C. P. G., Tzioutziou, N. A., Guo, W., Zhang, R., Simpson, C. G., Jiang, W., Nimmo, G. A., Brown, J. W. S. & Nimmo, H. G., 1 Jul 2018, In : Plant, Cell & Environment. 41, 7, p. 1539-1550 12 p.

Research output: Contribution to journalArticle

Open Access
File
6 Citations (Scopus)
121 Downloads (Pure)

Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome

Calixto, C. P. G., Guo, W., James, A. B., Tzioutziou, N. A., Entizne, J. C., Panter, P. E., Knight, H., Nimmo, H., Zhang, R. & Brown, J. W. S., 1 Jul 2018, In : Plant Cell. 30, 7, p. 1424-1444 21 p.

Research output: Contribution to journalArticle

Open Access
File
31 Citations (Scopus)
115 Downloads (Pure)
2017

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

Zhang, R., Calixto, C. P. G., Marquez, Y., Venhuizen, P., Tzioutziou, N. A., Guo, W., Spensley, M., Entizne, J. C., 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., 19 May 2017, In : Nucleic Acids Research. 45, 9, p. 5061-5073 13 p.

Research output: Contribution to journalArticle

Open Access
File
52 Citations (Scopus)
178 Downloads (Pure)

Evaluation and improvement of the regulatory inference for large co-expression networks with limited sample size

Guo, W., Calixto, C. P. G., Tzioutziou, N., Lin, P., Waugh, R., Brown, J. W. S. & Zhang, R., 19 Jun 2017, In : BMC Systems Biology. 11, p. 1-12 12 p., 62.

Research output: Contribution to journalArticle

Open Access
File
5 Citations (Scopus)
123 Downloads (Pure)

High-quality reference transcript datasets hold the key to transcript-specific RNA-sequencing analysis in plants

Brown, J. W. S., Calixto, C. P. G. & Zhang, R., Jan 2017, In : New Phytologist. 213, 2, p. 525-530 6 p.

Research output: Contribution to journalReview article

5 Citations (Scopus)

TSIS: an R package to infer alternative splicing isoform switches for time-series data

Guo, W., Calixto, C. P. G., Brown, J. W. S. & Zhang, R., 15 Oct 2017, In : Bioinformatics. 33, 20, p. 3308-3310 3 p.

Research output: Contribution to journalArticle

Open Access
File
7 Citations (Scopus)
149 Downloads (Pure)
2016

Alternative splicing of barley clock genes in response to low temperature: evidence for alternative splicing conservation

Calixto, C. P. G., Simpson, C. G., Waugh, R. & Brown, J. W. S., 13 Dec 2016, In : PLoS ONE. 11, 12, p. 1-24 24 p., e0168028.

Research output: Contribution to journalArticle

Open Access
File
9 Citations (Scopus)
133 Downloads (Pure)

Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

Russell, J., Mascher, M., Dawson, I. K., Kyriakidis, S., Calixto, C., Freund, F., Bayer, M., Milne, I., Marshall-Griffiths, T., Heinen, S., Hofstad, A., Sharma, R., Himmelbach, A., Knauft, M., van Zonneveld, M., Brown, J., Schmid, K., Kilian, B., Muehlbauer, G. J., Stein, N. & 1 others, Waugh, R., 18 Jul 2016, In : Nature Genetics. 48, p. 1024-1030 7 p.

Research output: Contribution to journalArticle

Open Access
File
73 Citations (Scopus)
490 Downloads (Pure)

Monitoring alternative splicing changes in Arabidopsis circadian clock genes

Simpson, C. G., Fuller, J., Calixto, C. P. G., McNicol, J., Booth, C., Brown, J. W. S. & Staiger, D., 2016, Environmental responses in plants: methods and protocols. Duque, P. (ed.). New York: Springer , p. 119-132 14 p. (Methods in molecular biology; vol. 1398).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

7 Citations (Scopus)

The Arabidopsis SR45 splicing factor, a negative regulator of sugar signaling, modulates SNF1-related protein kinase 1 (SnRK1) stability

Carvalho, R. F., Szakonyi, D., Simpson, C. G., Barbosa, I. C. R., Brown, J. W. S., Baena-González, E. & Duque, P., 19 Jul 2016, In : Plant Cell. 28, 8, p. 1910-1925 16 p.

Research output: Contribution to journalArticle

Open Access
File
25 Citations (Scopus)
176 Downloads (Pure)
2015

Alternative splicing of mini-exons in the Arabidopsis leaf rust receptor-like kinase LRK10 genes affects subcellular localisation

Shin, K. H., Yang, S. H., Lee, J. Y., Lim, C. W., Lee, S. C., Brown, J. W. S. & Kim, S. H., Mar 2015, In : Plant Cell Reports. 34, 3, p. 495-505 11 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript - specific expression in Arabidopsis thaliana

Zhang, R., Calixto, C. P. G., Tzioutziou, N. A., James, A. B., Simpson, C. G., Guo, W., Marquez, Y., Kalyna, M., Patro, R., Eyras, E., Barta, A., Nimmo, H. G. & Brown, J. W. S., Oct 2015, In : New Phytologist. 208, 1, p. 96-101 6 p.

Research output: Contribution to journalArticle

Open Access
File
18 Citations (Scopus)
100 Downloads (Pure)

Evolutionary relationships among barley and Arabidopsis core circadian clock and clock-associated genes

Calixto, C. P. G., Waugh, R. & Brown, J. W. S., Feb 2015, In : Journal of Molecular Evolution. 80, 2, p. 108-119 12 p.

Research output: Contribution to journalArticle

Open Access
File
21 Citations (Scopus)
216 Downloads (Pure)

Lost in translation: pitfalls in deciphering plant alternative splicing transcripts

Brown, J. W. S., Simpson, C. G., Marquez, Y., Gadd, G. M., Barta, A. & Kalyna, M., Aug 2015, In : Plant Cell. 27, 8, p. 2083-2087 5 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)

The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms

Schlaen, R. G., Mancini, E., Sanchez, S. E., Perez-Santángelo, S., Rugnone, M. L., Simpson, C. G., Brown, J. W. S., Zhang, X., Chernomoretz, A. & Yanovsky, M. J., 28 Jul 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 30, p. 9382-7 6 p.

Research output: Contribution to journalArticle

34 Citations (Scopus)
2014

A chloroplast retrograde signal regulates nuclear alternative splicing

Petrillo, E., Godoy Herz, M. A., Fuchs, A., Reifer, D., Fuller, J., Yanovsky, M. J., Simpson, C., Brown, J. W. S., Barta, A., Kalyna, M. & Kornblihtt, A. R., 25 Apr 2014, In : Science. 344, 6182, p. 427-30 4 p.

Research output: Contribution to journalArticle

81 Citations (Scopus)

Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially

Simpson, C. G., Lewandowska, D., Liney, M., Davidson, D., Chapman, S., Fuller, J., McNicol, J., Shaw, P. & Brown, J. W. S., Jul 2014, In : New Phytologist. 203, 2, p. 424-436 13 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Long noncoding RNA modulates alternative splicing regulators in Arabidopsis

Bardou, F., Ariel, F., Simpson, C. G., Romero-Barrios, N., Laporte, P., Balzergue, S., Brown, J. W. S. & Crespi, M., 2014, In : Developmental Cell. 30, 2, p. 166-176 11 p.

Research output: Contribution to journalArticle

118 Citations (Scopus)

The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana

Raczynska, K. D., Stepien, A., Kierzkowski, D., Kalak, M., Bajczyk, M., McNicol, J., Simpson, C. G., Szweykowska-Kulinska, Z., Brown, J. W. S. & Jarmolowski, A., 1 Jan 2014, In : Nucleic Acids Research. 42, 2, p. 1224-1244 21 p.

Research output: Contribution to journalArticle

Open Access
File
41 Citations (Scopus)
153 Downloads (Pure)
2013

Alternative splicing at the intersection of biological timing, development, and stress responses

Staiger, D. & Brown, J. W. S., Oct 2013, In : Plant Cell. 25, 10, p. 3640-56 17 p.

Research output: Contribution to journalArticle

254 Citations (Scopus)

Plant SILAC: stable-isotope labelling with amino acids of Arabidopsis seedlings for quantitative proteomics

Lewandowska, D., ten Have, S., Hodge, K., Tillemans, V., Lamond, A. I. & Brown, J. W. S., 20 Aug 2013, In : PLoS ONE. 8, 8, e72207.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Small changes in ambient temperature affect alternative splicing in Arabidopsis thaliana

Streitner, C., Simpson, C. G., Shaw, P., Danisman, S., Brown, J. W. S. & Staiger, D., Jul 2013, In : Plant Signaling and Behavior. 8, 7, p. e24638.1-e24638.7 7 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)
2012

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

Kalyna, M., Simpson, C. G., Syed, N. H., Lewandowska, D., Marquez, Y., Kusenda, B., Marshall, J., Fuller, J., Cardle, L., McNicol, J., Dinh, H. Q., Barta, A. & Brown, J. W. S., Mar 2012, In : Nucleic Acids Research. 40, 6, p. 2454-2469 16 p.

Research output: Contribution to journalArticle

226 Citations (Scopus)

Alternative splicing in plants-coming of age

Hasan-Syed, N., Kalyna, M., Marquez, Y., Barta, A. & Brown, J. W. S., 2012, In : Trends in Plant Science. 17, 10, p. 616-623 8 p.

Research output: Contribution to journalArticle

219 Citations (Scopus)

Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes

James, A. B., Syed, N. H., Bordage, S., Marshall, J., Nimmo, G. A., Jenkins, G. I., Herzyk, P., Brown, J. W. S. & Nimmo, H. G., 2012, In : Plant Cell. 24, 3, p. 961-981 21 p.

Research output: Contribution to journalArticle

186 Citations (Scopus)

An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana

Streitner, C., Köster, T., Simpson, C. G., Shaw, P., Danisman, S., Brown, J. W. S. & Staiger, D., Dec 2012, In : Nucleic Acids Research. 40, 22, p. 11240-11255 16 p.

Research output: Contribution to journalArticle

68 Citations (Scopus)

A physical, genetic and functional sequence assembly of the barley genome

Mayer, K. F. X., Waugh, R., Brown, J. W. S., Schulman, A., Langridge, P., Platzer, M., Fincher, G. B., Muehlbauer, G. J., Sato, K., Close, T. J., Wise, R. P., Stein, N. & International Barley Genome Sequencing Consortium, 29 Nov 2012, In : Nature. 491, 7426, p. 711-716 6 p.

Research output: Contribution to journalArticle

914 Citations (Scopus)

Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 causes Circadian clock defects

Jones, M. A., Williams, B. A., McNicol, J., Simpson, C. G., Brown, J. W. S. & Harmer, S. L., Oct 2012, In : Plant Cell. 24, 10, p. 4066-82 17 p.

Research output: Contribution to journalArticle

60 Citations (Scopus)

Nucleoli: composition, function, and dynamics

Shaw, P. & Brown, J., Jan 2012, In : Plant Physiology. 158, 1, p. 44-51 8 p.

Research output: Contribution to journalArticle

69 Citations (Scopus)

Thermoplasticity in the plant circadian clock: how plants tell the time-perature

James, A. B., Hasan-Syed, N., Brown, J. W. S. & Nimmo, H. G., Oct 2012, In : Plant Signaling and Behavior. 7, 10, p. 1219-23 5 p.

Research output: Contribution to journalArticle

20 Citations (Scopus)

Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

Marquez, Y., Brown, J. W. S., Simpson, C., Barta, A. & Kalyna, M., 2012, In : Genome Research. 22, 6, p. 1184-1195 12 p.

Research output: Contribution to journalArticle

377 Citations (Scopus)
2011

Two RNA-binding sites in plant fibrillarin provide interactions with various RNA substrates

Rakitina, D. V., Taliansky, M., Brown, J. W. S. & Kalinina, N. O., Nov 2011, In : Nucleic Acids Research. 39, 20, p. 8869-8880

Research output: Contribution to journalArticle

15 Citations (Scopus)
2010

A methyl transferase links the circadian clock to the regulation of alternative splicing

Sanchez, S. E., Petrillo, E., Beckwith, E. J., Zhang, X., Rugnone, M. L., Hernando, C. E., Cuevas, J. C., Godoy Herz, M. A., Depetris-Chauvin, A., Simpson, C. G., Brown, J. W. S., Cerdán, P. D., Borevitz, J. O., Mas, P., Ceriani, M. F., Kornblihtt, A. R. & Yanovsky, M. J., 2010, In : Nature. 468, 7320, p. 112-116 5 p.

Research output: Contribution to journalArticle

188 Citations (Scopus)

Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana

Raczynska, K. D., Simpson, C. G., Ciesiolka, A., Szewc, L., Lewandowska, D., McNicol, J., Szweykowska-Kulinska, Z., Brown, J. W. S. & Jarmolowski, A., 2010, In : Nucleic Acids Research. 38, 1, p. 265-278 14 p.

Research output: Contribution to journalArticle

60 Citations (Scopus)

Plant U13 orthologues and orphan snoRNAs identified by RNomics of RNA from Arabidopsis nucleoli

Kim, S. H., Spensley, M., Choi, S. K., Calixto, C. P. G., Pendle, A. F., Koroleva, O., Shaw, P. J. & Brown, J. W. S., May 2010, In : Nucleic Acids Research. 38, 9, p. 3054-3067 14 p.

Research output: Contribution to journalArticle

23 Citations (Scopus)

Regulation of plant gene expression by alternative splicing

Simpson, C. G., Manthri, S., Raczynska, K. D., Kalyna, M., Lewandowska, D., Kusenda, B., Maronova, M., Szweykowska-Kulinska, Z., Jarmolowski, A., Barta, A. & Brown, J. W. S., Apr 2010, In : Biochemical Society Transactions. 38, 2, p. 667-671 5 p.

Research output: Contribution to journalArticle

28 Citations (Scopus)
2009

Aberrant mRNA Transcripts and the Nonsense-Mediated Decay Proteins UPF2 and UPF3 Are Enriched in the Arabidopsis Nucleolus

Kim, S. H., Koroleva, O. A., Lewandowska, D., Pendle, A. F., Clark, G. P., Simpson, C. G., Shaw, P. J. & Brown, J. W. S., Jul 2009, In : Plant Cell. 21, 7, p. 2045-2057 13 p.

Research output: Contribution to journalArticle

71 Citations (Scopus)

Dynamic behavior of Arabidopsis eIF4A-III, putative core protein of exon junction complex: fast relocation to nucleolus and splicing speckles under hypoxia

Koroleva, O. A., Calder, G., Pendle, A. F., Kim, S. H., Lewandowska, D., Simpson, C. G., Jones, I. M., Brown, J. W. S. & Shaw, P. J., 2009, In : Plant Cell. 21, 5, p. 1592-1606 15 p.

Research output: Contribution to journalArticle

69 Citations (Scopus)

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

Cole, C., Sobala, A., Lu, C., Thatcher, S. R., Bowman, A., Brown, J. W. S., Green, P. J., Barton, G. J. & Hutvagner, G., Dec 2009, In : RNA: a Publication of the RNA Society. 15, 12, p. 2147-2160 14 p.

Research output: Contribution to journalArticle

329 Citations (Scopus)

Localization of eIF4A-III in the nucleolus and splicing speckles is an indicator of plant stress

Koroleva, O. A., Brown, J. W. S. & Shaw, P. J., Dec 2009, In : Plant Signaling and Behavior. 4, 12, p. 1148-1151

Research output: Contribution to journalArticle

15 Citations (Scopus)
2008

Alternative splicing in plants

Simpson, C. G., Lewandowska, D., Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J., Raczynska, D., Jarmolowski, A., Barta, A. & Brown, J. W. S., 2008, In : Biochemical Society Transactions. 36, 3, p. 508-10 3 p.

Research output: Contribution to journalArticle

29 Citations (Scopus)

A plant virus movement protein forms ringlike complexes with the major nucleolar protein, fibrillarin, in vitro

Canetta, E., Kim, S. H., Kalinina, N. O., Shaw, J., Adya, A. K., Gillespie, T., Brown, J. W. S. & Taliansky, M., 29 Feb 2008, In : Journal of Molecular Biology. 376, 4, p. 932-937 6 p.

Research output: Contribution to journalArticle

37 Citations (Scopus)

Intronic noncoding RNAs and splicing

Brown, J. W. S., Marshall, D. F. & Echeverria, M., 2008, In : Trends in Plant Science. 13, 7, p. 335-342 8 p.

Research output: Contribution to journalArticle

99 Citations (Scopus)

Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts

Simpson, C. G., Fuller, J., Maronova, M., Kalyna, M., Davidson, D., McNicol, J., Barta, A. & Brown, J. W. S., Mar 2008, In : Plant Journal. 53, 6, p. 1035-1048 14 p.

Research output: Contribution to journalArticle

69 Citations (Scopus)

The role of the plant nucleolus in pre-mRNA processing

Brown, J. W. S. & Shaw, P. J., 2008, Nuclear pre-mRNA processing in plants. Reddy, A. S. N. & Golovkin, M. (eds.). Berlin: Springer , p. 291-311 21 p. (Current topics in microbiology and immunology; vol. 326).

Research output: Chapter in Book/Report/Conference proceedingChapter

21 Citations (Scopus)

U12-dependent intron splicing in plants

Simpson, C. G. & Brown, J. W. S., 2008, Nuclear pre-mRNA processing in plants. Reddy, A. S. N. & Golovkin, M. (eds.). Berlin: Springer , p. 61-82 22 p. (Current topics in microbiology and immunology; vol. 326).

Research output: Chapter in Book/Report/Conference proceedingOther chapter contribution

7 Citations (Scopus)
2007

Cajal bodies and the nucleolus are required for a plant virus systemic infection

Kim, S. H., Ryabov, E. V., Kalinina, N. O., Rakitina, D. V., Gillespie, T., Macfarlane, S., Haupt, S., Brown, J. W. S. & Taliansky, M., Apr 2007, In : The EMBO Journal. 26, 8, p. 2169-2179 11 p.

Research output: Contribution to journalArticle

95 Citations (Scopus)