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Items: 13

1.

Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome.

Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo H, Zhang R, Brown JWS.

Plant Cell. 2018 May 15. pii: tpc.00177.2018. doi: 10.1105/tpc.18.00177. [Epub ahead of print]

2.

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

James AB, Calixto CPG, Tzioutziou NA, Guo W, Zhang R, Simpson CG, Jiang W, Nimmo GA, Brown JWS, Nimmo HG.

Plant Cell Environ. 2018 Jul;41(7):1539-1550. doi: 10.1111/pce.13193. Epub 2018 May 2.

3.

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

Guo W, Calixto CPG, Brown JWS, Zhang R.

Bioinformatics. 2017 Oct 15;33(20):3308-3310. doi: 10.1093/bioinformatics/btx411.

4.

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

Guo W, Calixto CPG, Tzioutziou N, Lin P, Waugh R, Brown JWS, Zhang R.

BMC Syst Biol. 2017 Jun 19;11(1):62. doi: 10.1186/s12918-017-0440-2.

5.

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

Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JWS.

Nucleic Acids Res. 2017 May 19;45(9):5061-5073. doi: 10.1093/nar/gkx267.

6.

Ectopic ovary with torsion: uncommon diagnosis made by ultrasound.

Castro AD, Morandini F, Calixto CP, Barros WH, Nakatani ET, Castro AD.

Radiol Bras. 2017 Jan-Feb;50(1):60-61. doi: 10.1590/0100-3984.2014.0031.

7.

Alternative Splicing of Barley Clock Genes in Response to Low Temperature.

Calixto CP, Simpson CG, Waugh R, Brown JW.

PLoS One. 2016 Dec 13;11(12):e0168028. doi: 10.1371/journal.pone.0168028. eCollection 2016.

8.

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

Brown JW, Calixto CP, Zhang R.

New Phytol. 2017 Jan;213(2):525-530. doi: 10.1111/nph.14208. Epub 2016 Sep 23. Review.

9.

Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes.

Simpson CG, Fuller J, Calixto CP, McNicol J, Booth C, Brown JW, Staiger D.

Methods Mol Biol. 2016;1398:119-32. doi: 10.1007/978-1-4939-3356-3_11.

PMID:
26867620
10.

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

Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW.

New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.

11.

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

Calixto CP, Waugh R, Brown JW.

J Mol Evol. 2015 Feb;80(2):108-19. doi: 10.1007/s00239-015-9665-0. Epub 2015 Jan 22.

12.

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

Kim SH, Spensley M, Choi SK, Calixto CP, Pendle AF, Koroleva O, Shaw PJ, Brown JW.

Nucleic Acids Res. 2010 May;38(9):3054-67. doi: 10.1093/nar/gkp1241. Epub 2010 Jan 16.

13.

Analyses of sexual reproductive success in transgenic and/or mutant plants.

Calixto CP, Goldman GH, Goldman MH.

J Integr Plant Biol. 2009 Aug;51(8):719-26. doi: 10.1111/j.1744-7909.2009.00845.x. Review.

PMID:
19686369

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