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• 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 journal › Article › peer-review

  Open Access

  File

  • alternative splicing
  • circadian clocks
  • sugarcane
  • temperature
  • genes
  1 Citation (Scopus)

  111 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 journal › Article › peer-review

  Open Access

  File

  • non-coding RNA
  • alternative splicing
  • Arabidopsis
  • small interfering RNA
  • time series analysis
  14 Citations (Scopus)

  111 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 journal › Article › peer-review

  • Alternative Splicing
  • Light
  • Chloroplasts
  • Arabidopsis
  • transcription factor S-II
  31 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 journal › Article › peer-review

  Open Access

  File

  • Hypocotyl
  • RNA Splicing Factors
  • hypocotyls
  • Protein Isoforms
  • Temperature
  8 Citations (Scopus)

  163 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 journal › Article › peer-review

  Open Access

  File

  • Arabidopsis
  • alternative splicing
  • Alternative Splicing
  • Transcriptome
  • transcriptome
  65 Citations (Scopus)

  158 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 journal › Article › peer-review

  Open Access

  File

  • Arabidopsis
  • Alternative Splicing
  • Transcriptome
  • Protein Isoforms
  • RNA
  86 Citations (Scopus)

  214 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 journal › Article › peer-review

  Open Access

  File

  • Correlation methods
  • Partial Correlation
  • Electric network analysis
  • Genes
  • Sample Size
  8 Citations (Scopus)

  174 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 journal › Review article › peer-review

  • plant analysis
  • RNA Sequence Analysis
  • alternative splicing
  • Alternative Splicing
  • Datasets
  7 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 journal › Article › peer-review

  Open Access

  File

  • Alternative Splicing
  • Time Series Data
  • Switch
  • Time series
  • Protein Isoforms
  8 Citations (Scopus)

  209 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 journal › Article › peer-review

  Open Access

  File

  • Hordeum
  • alternative splicing
  • Alternative Splicing
  • Conservation
  • Genes
  10 Citations (Scopus)

  167 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 journal › Article › peer-review

  Open Access

  File

  • Hordeum
  • Exome
  • Domestication
  • Gardens
  • Genome
  97 Citations (Scopus)

  706 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 proceeding › Chapter (peer-reviewed) › peer-review

  • Arabidopsis
  • Circadian Clocks
  • Alternative Splicing
  • Ecotype
  • Physiological Stress
  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 journal › Article › peer-review

  Open Access

  File

  • protein kinases
  • Arabidopsis
  • sugars
  • alternative splicing
  • glucose
  31 Citations (Scopus)

  269 Downloads (Pure)