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Items: 26

1.

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Jabre I, Reddy ASN, Kalyna M, Chaudhary S, Khokhar W, Byrne LJ, Wilson CM, Syed NH.

Nucleic Acids Res. 2019 Apr 8;47(6):2716-2726. doi: 10.1093/nar/gkz121. Review.

2.

PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in Arabidopsis thaliana.

Kanno T, Venhuizen P, Wen TN, Lin WD, Chiou P, Kalyna M, Matzke AJM, Matzke M.

Genetics. 2018 Dec;210(4):1267-1285. doi: 10.1534/genetics.118.301515. Epub 2018 Oct 8.

3.

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.

4.

Generating Targeted Gene Knockout Lines in Physcomitrella patens to Study Evolution of Stress-Responsive Mechanisms.

Maronova M, Kalyna M.

Methods Mol Biol. 2016;1398:221-34. doi: 10.1007/978-1-4939-3356-3_18.

5.

Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.

Brown JW, Simpson CG, Marquez Y, Gadd GM, Barta A, Kalyna M.

Plant Cell. 2015 Aug;27(8):2083-7. doi: 10.1105/tpc.15.00572. Epub 2015 Aug 18.

6.

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.

7.

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.

Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M.

Genome Res. 2015 Jul;25(7):995-1007. doi: 10.1101/gr.186585.114. Epub 2015 May 1.

8.

Let there be light: regulation of gene expression in plants.

Petrillo E, Godoy Herz MA, Barta A, Kalyna M, Kornblihtt AR.

RNA Biol. 2014;11(10):1215-20. doi: 10.4161/15476286.2014.972852.

9.

Shedding light on the chloroplast as a remote control of nuclear gene expression.

Godoy Herz MA, Kornblihtt AR, Barta A, Kalyna M, Petrillo E.

Plant Signal Behav. 2014;9(11):e976150. doi: 10.4161/15592324.2014.976150. Review.

10.

A chloroplast retrograde signal regulates nuclear alternative splicing.

Petrillo E, Godoy Herz MA, Fuchs A, Reifer D, Fuller J, Yanovsky MJ, Simpson C, Brown JW, Barta A, Kalyna M, Kornblihtt AR.

Science. 2014 Apr 25;344(6182):427-30. doi: 10.1126/science.1250322. Epub 2014 Apr 10.

11.

Complexity of the alternative splicing landscape in plants.

Reddy AS, Marquez Y, Kalyna M, Barta A.

Plant Cell. 2013 Oct;25(10):3657-83. doi: 10.1105/tpc.113.117523. Epub 2013 Oct 31. Review.

12.

Introns of plant pri-miRNAs enhance miRNA biogenesis.

Bielewicz D, Kalak M, Kalyna M, Windels D, Barta A, Vazquez F, Szweykowska-Kulinska Z, Jarmolowski A.

EMBO Rep. 2013 Jul;14(7):622-8. doi: 10.1038/embor.2013.62. Epub 2013 May 17.

13.

Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity.

Bannikova O, Zywicki M, Marquez Y, Skrahina T, Kalyna M, Barta A.

Nucleic Acids Res. 2013 Feb 1;41(3):1783-96. doi: 10.1093/nar/gks1252. Epub 2012 Dec 16.

14.

Alternative splicing in plants--coming of age.

Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW.

Trends Plant Sci. 2012 Oct;17(10):616-23. doi: 10.1016/j.tplants.2012.06.001. Epub 2012 Jun 27. Review.

15.

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

Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M.

Genome Res. 2012 Jun;22(6):1184-95. doi: 10.1101/gr.134106.111. Epub 2012 Mar 5.

16.

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

Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JW.

Nucleic Acids Res. 2012 Mar;40(6):2454-69. doi: 10.1093/nar/gkr932. Epub 2011 Nov 29.

17.

Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants.

Barta A, Kalyna M, Reddy AS.

Plant Cell. 2010 Sep;22(9):2926-9. doi: 10.1105/tpc.110.078352. Epub 2010 Sep 30.

18.

Regulation of plant gene expression by alternative splicing.

Simpson CG, Manthri S, Raczynska KD, Kalyna M, Lewandowska D, Kusenda B, Maronova M, Szweykowska-Kulinska Z, Jarmolowski A, Barta A, Brown JW.

Biochem Soc Trans. 2010 Apr;38(2):667-71. doi: 10.1042/BST0380667. Review.

PMID:
20298240
19.

Plant SR proteins and their functions.

Barta A, Kalyna M, Lorković ZJ.

Curr Top Microbiol Immunol. 2008;326:83-102. Review.

PMID:
18630748
20.

Alternative splicing in plants.

Simpson CG, Lewandowska D, Fuller J, Maronova M, Kalyna M, Davidson D, McNicol J, Raczynska D, Jarmolowski A, Barta A, Brown JW.

Biochem Soc Trans. 2008 Jun;36(Pt 3):508-10. doi: 10.1042/BST0360508. Review.

PMID:
18481991
21.

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

Simpson CG, Fuller J, Maronova M, Kalyna M, Davidson D, McNicol J, Barta A, Brown JW.

Plant J. 2008 Mar;53(6):1035-48. Epub 2007 Dec 15.

22.

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins.

Kalyna M, Lopato S, Voronin V, Barta A.

Nucleic Acids Res. 2006;34(16):4395-405. Epub 2006 Aug 26.

23.
24.

Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development.

Kalyna M, Lopato S, Barta A.

Mol Biol Cell. 2003 Sep;14(9):3565-77. Epub 2003 Jun 13.

25.

Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors.

Lopato S, Forstner C, Kalyna M, Hilscher J, Langhammer U, Indrapichate K, Lorković ZJ, Barta A.

J Biol Chem. 2002 Oct 18;277(42):39989-98. Epub 2002 Aug 9.

26.

atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.

Lopato S, Kalyna M, Dorner S, Kobayashi R, Krainer AR, Barta A.

Genes Dev. 1999 Apr 15;13(8):987-1001.

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