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Kalyna Mariya

Scientific publications from BOKU scientists, especially those which are published in SCI / SSCI journals, or in other refereed journals, proceedings, monographs as well as articles in collected volumes are listed under PUBLICATIONS.

Publications with special focus on transfer of knowledge ("social impact") to practitioners as well as the interested public can be found under the menu item:

>> Transfer of Knowledge


** = Publications listed in SCI/SSCI - Journals (published in Web of Science)
* = peer-reviewed publication (not listed in SCI/SSCI)
Only: Full paper/article, Review, Proceedings Paper

= Open Access - Publications

 

2022

Journal Articles

** Zhang, RX; Kuo, R; Coulter, M; Calixto, CPG; Entizne, JC; Guo, WB; Marquez, Y; Milne, L; Riegler, S; Matsui, A; Tanaka, M; Harvey, S; Gao, YB; Wiessner-Kroh, T; Paniagua, A; Crespi, M; Denby, K; Ben Hur, A; Huq, E; Jantsch, M; Jarmolowski, A; Koester, T; Laubinger, S; Li, QQ; Gu, LF; Seki, M; Staiger, D; Sunkar, R; Szweykowska-Kulinska, Z; Tu, SL; Wachter, A; Waugh, R; Xiong, LM; Zhang, XN; Conesa, A; Reddy, ASN; Barta, A; Kalyna, M; Brown, JWS A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.

GENOME BIOL. 2022; 23(1), 149 WoS PubMed FullText FullText_BOKU

2021

** Fuchs, A; Riegler, S; Ayatollahi, Z; Cavallari, N; Giono, LE; Nimeth, BA; Mutanwad, KV; Schweighofer, A; Lucyshyn, D; Barta, A; Petrillo, E; Kalyna, M; Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing..

Nucleic Acids Res. 2021; 49(2):1133-1151 WoS PubMed FullText FullText_BOKU

** Jabre, I; Chaudhary, S; Guo, W; Kalyna, M; Reddy, ASN; Chen, W; Zhang, R; Wilson, C; Syed, NH; Differential nucleosome occupancy modulates alternative splicing in Arabidopsis thaliana..

New Phytol. 2021; 229(4):1937-1945 WoS PubMed FullText FullText_BOKU

** Riegler, S; Servi, L; Scarpin, MR; Herz, MAG; Kubaczka, MG; Venhuizen, P; Meyer, C; Brunkard, JO; Kalyna, M; Barta, A; Petrillo, E Light regulates alternative splicing outcomes via the TOR kinase pathway.

CELL REP. 2021; 36(10), 109676 WoS PubMed FullText FullText_BOKU

** Velasquez, SM; Guo, XY; Gallemi, M; Aryal, B; Venhuizen, P; Barbez, E; Dunser, KA; Darino, M; Pencik, A; Novak, O; Kalyna, M; Mouille, G; Benkova, E; Bhalerao, R; Mravec, J; Kleine-Vehn, J Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.

INT J MOL SCI. 2021; 22(17), 9222 WoS PubMed FullText FullText_BOKU

2020

** Führer, M; Gaidora, A; Venhuizen, P; Dobrogojski, J; Béziat, C; Feraru, MI; Kleine-Vehn, J; Kalyna, M; Barbez, E; FRUITFULL Is a Repressor of Apical Hook Opening in .

Int J Mol Sci. 2020; 21(17): WoS PubMed FullText FullText_BOKU

** Kanno, T; Venhuizen, P; Wu, MT; Chiou, P; Chang, CL; Kalyna, M; Matzke, AJM; Matzke, M; A Collection of Pre-mRNA Splicing Mutants in .

G3 (Bethesda). 2020; 10(6):1983-1996 WoS PubMed FullText FullText_BOKU

** Melo, JP; Kalyna, M; Duque, P; Current Challenges in Studying Alternative Splicing in Plants: The Case of .

Front Plant Sci. 2020; 11:286 WoS PubMed PUBMED Central FullText FullText_BOKU

** Nimeth, BA; Riegler, S; Kalyna, M; Alternative Splicing and DNA Damage Response in Plants..

Front Plant Sci. 2020; 11:91 WoS PubMed PUBMED Central FullText FullText_BOKU

** Petrillo, E; Kalyna, M; Mandadi, KK; Tu, SL; Simpson, CG Editorial: Alternative Splicing Regulation in Plants.

FRONT PLANT SCI. 2020; 11, 913 WoS PubMed FullText FullText_BOKU

Editorial

Petrillo, E; Kalyna, M; Simpson, CG; Tu, S-L; Mandadi, KK. Eds. (2020): Alternative Splicing Regulation in Plants .

; Frontiers Media SA , Lausanne FullText

2019

Journal Articles

** Jabre, I; Reddy, ASN; Kalyna, M; Chaudhary, S; Khokhar, W; Byrne, LJ; Wilson, CM; Syed, NH; Does co-transcriptional regulation of alternative splicing mediate plant stress responses?.

Nucleic Acids Res. 2019; 47(6):2716-2726 WoS PubMed FullText FullText_BOKU

Prototyp

Velasquez, SM; Gallemi, M; Aryal, B; Venhuizen, P; Barbez, E; Dünser, K; Kalyna, M; Mouille, G; Benkova, E; Bhalerao, R; Kleine-Vehn, J (2019): Auxin-dependent xyloglucan remodelling defines differential tissue expansion in Arabidopsis thaliana.

bioRxiv 808964 FullText

2018

Journal Articles

** Kanno, T; Venhuizen, P; Wen, TN; Lin, WD; Chiou, P; Kalyna, M; Matzke, AJM; Matzke, M; PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in .

Genetics. 2018; 210(4):1267-1285 WoS PubMed FullText FullText_BOKU

Prototyp

Petrillo, E; Riegler, S; Fuchs, A; Servi, L; Godoy Herz, MA; Kubaczka, MG; Venhuizen, P; Schweighofer, A; Kornblihtt, AR; Simpson, C; Brown, JWS; Meyer, C; Kalyna, M; Barta A (2018): Remote control of alternative splicing in roots through TOR kinase.

bioRxiv doi: https://doi.org/10.1101/472126 FullText

2017

Journal Articles

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

Nucleic Acids Res. 2017; 45(9):5061-5073 WoS PubMed PUBMED Central FullText FullText_BOKU

2016

* Maronova, M; Kalyna, M; (2016): Generating Targeted Gene Knockout Lines in Physcomitrella patens to Study Evolution of Stress-Responsive Mechanisms..

Methods Mol Biol. 2016; 1398:221-234 PubMed FullText FullText_BOKU

Prototyp

Runxuan Zhang, Cristiane P G Calixto, Yamile Marquez, Peter Venhuizen, Nikoleta A Tzioutziou, Wenbin Guo, Mark Spensley, Nicolas Frei dit Frey, Heribert Hirt, Allan B James, Hugh G Nimmo, Andrea Barta, Maria Kalyna, John W S Brown (2016): AtRTD2: A Reference Transcript Dataset for accurate quantification of alternative splicing and expression changes in Arabidopsis thaliana RNA-seq data.

bioRxiv doi: http://dx.doi.org/10.1101/051938 FullText

2015

Journal Articles

** Brown, JW; Simpson, CG; Marquez, Y; Gadd, GM; Barta, A; Kalyna, M; Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts..

Plant Cell. 2015; 27(8):2083-2087 WoS PubMed PUBMED Central FullText FullText_BOKU

** Marquez, Y; Höpfler, M; Ayatollahi, Z; Barta, A; Kalyna, M; Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity..

Genome Res. 2015; 25(7):995-1007 WoS PubMed PUBMED Central FullText FullText_BOKU

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

New Phytol. 2015; 208(1):96-101 WoS PubMed FullText FullText_BOKU

2014

** Petrillo, E; Godoy Herz, MA; Barta, A; Kalyna, M; Kornblihtt, AR; Let there be light: Regulation of gene expression in plants..

RNA Biol. 2014; 11(10):1215-1220 WoS PubMed FullText FullText_BOKU

** Petrillo, E; Godoy Herz, MA; Fuchs, A; Reifer, D; Fuller, J; Yanovsky, MJ; Simpson, C; Brown, JW; Barta, A; Kalyna, M; Kornblihtt, AR; A chloroplast retrograde signal regulates nuclear alternative splicing..

Science. 2014; 344(6182):427-430 WoS PubMed PUBMED Central FullText FullText_BOKU

* Godoy Herz, MA; Kornblihtt, AR; Barta, A; Kalyna, M; Petrillo, E; (2014): Shedding light on the chloroplast as a remote control of nuclear gene expression..

Plant Signal Behav. 2014; 9(11):e976150 PubMed FullText FullText_BOKU

2013

** Bannikova, O; Zywicki, M; Marquez, Y; Skrahina, T; Kalyna, M; Barta, A; Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity..

Nucleic Acids Res. 2013; 41(3):1783-1796 WoS PubMed PUBMED Central FullText FullText_BOKU

** Bielewicz, D; Kalak, M; Kalyna, M; Windels, D; Barta, A; Vazquez, F; Szweykowska-Kulinska, Z; Jarmolowski, A; Introns of plant pri-miRNAs enhance miRNA biogenesis..

EMBO Rep. 2013; 14(7):622-628 WoS PubMed PUBMED Central FullText FullText_BOKU

** Reddy, AS; Marquez, Y; Kalyna, M; Barta, A; Complexity of the alternative splicing landscape in plants..

Plant Cell. 2013; 25(10):3657-3683 WoS PubMed PUBMED Central FullText FullText_BOKU

Bielewicz, D; Kalak, M; Kalyna, M; Windels, D; Barta, A; Vazquez, F; Szweykowska-Kulinska, Z;; Jarmolowski, A (2013): Introns of plant pri-miRNAs are required for proper biogenesis and function of miRNAs.

Biotechnologia, 94, 59-59; ISSN 0860-7796 FullText

2012

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

Nucleic Acids Res. 2012; 40(6):2454-2469 WoS PubMed PUBMED Central FullText FullText_BOKU

** Marquez, Y; Brown, JW; Simpson, C; Barta, A; Kalyna, M; Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis..

Genome Res. 2012; 22(6):1184-1195 WoS PubMed PUBMED Central FullText FullText_BOKU

** Syed, NH; Kalyna, M; Marquez, Y; Barta, A; Brown, JW; Alternative splicing in plants--coming of age..

Trends Plant Sci. 2012; 17(10):616-623 WoS PubMed PUBMED Central FullText FullText_BOKU

Chapter in Collected Volumes

Bannikova, O; Kalyna, M; Barta A (2012): Genomic SELEX to Identify RNA Targets of Plant RNA-Binding Proteins.

In: Stamm, S; Smith, C; Luehrmann, R (Eds.), Alternative pre-mRNA Splicing: Theory and Protocols , 218-226; Wiley-VCH, Weinheim; ISBN 9783527326068 FullText

Simpson, CG; Liney, M; Davidson, D; Lewandowska, D; Kalyna, M; Chapman, S; Barta A; Brown, JWS (2012): In vivo analysis of plant intron splicing .

In: Stamm, S; Smith, C; Lührmann, R (Eds.), Alternative pre-mRNA Splicing. Theory and Protocols, 450-462; Wiley-VCH, Weinheim; ISBN 9783527326068 FullText

Simpson, CG; Syed, NH; Manthri, S; Fuller, JD; Maronova, M; Kusenda, B; Kalyna, M; Barta, A; Brown, JWS (2012): Monitoring changes in plant alternative splicing events.

In: Stamm, S; Smith, C; Luehrmann, R (Eds.), Alternative pre-mRNA Splicing: Theory and Protocols , 248-259; Wiley-VCH, Weinheim; ISBN 9783527326068 FullText

2010

Journal Articles

** Barta, A; Kalyna, M; Reddy, AS; Implementing a rational and consistent nomenclature for serine/arginine-rich protein splicing factors (SR proteins) in plants..

Plant Cell. 2010; 22(9):2926-2929 WoS PubMed PUBMED Central FullText FullText_BOKU

** Simpson, CG; Manthri, S; Raczynska, KD; Kalyna, M; Lewandowska, D; Kusenda, B; Maronova, M; Szweykowska-Kulinska, Z; Jarmolowski, A; Barta, A; Brown, JW; Regulation of plant gene expression by alternative splicing..

Biochem Soc Trans. 2010; 38(2):66-71 WoS PubMed FullText FullText_BOKU

2008

** Barta, A; Kalyna, M; Lorković, ZJ; Plant SR proteins and their functions..

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

** Simpson, CG; Fuller, J; Maronova, M; Kalyna, M; Davidson, D; McNicol, J; Barta, A; Brown, JW; Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts..

Plant J. 2008; 53(6):1035-1048 WoS PubMed FullText FullText_BOKU

** Simpson, CG; Lewandowska, D; Fuller, J; Maronova, M; Kalyna, M; Davidson, D; McNicol, J; Raczynska, D; Jarmolowski, A; Barta, A; Brown, JW; Alternative splicing in plants..

Biochem Soc Trans. 2008; 36(Pt 3):508-510 WoS PubMed FullText FullText_BOKU

2007

Conference & Workshop Proceedings, Paper, Abstract

** Maronova, M; Kalyna, M; Simpson, CG; Brown, JW; Barta, A Role of Arabidopsis SR protein atRSp31 in plant growth and development..
[32nd Congress of the Federation of European Biochemical Societies FEBS 2007 - Molecular Machines, Vienna, Austria, 07.07.2007 - 12.07.2007]

FEBS J. 2007; 274: 346-346. WoS

2006

Journal Articles

** Kalyna, M; Lopato, S; Voronin, V; Barta, A; Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins..

Nucleic Acids Res. 2006; 34(16):439-405 WoS PubMed PUBMED Central FullText FullText_BOKU

2004

** Kalyna, M; Barta, A; A plethora of plant serine/arginine-rich proteins: redundancy or evolution of novel gene functions?.

Biochem Soc Trans. 2004; 32(Pt 4):561-564 WoS PubMed FullText FullText_BOKU

2003

** Kalyna, M; Lopato, S; Barta, A; Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development..

Mol Biol Cell. 2003; 14(9):3565-3577 WoS PubMed PUBMED Central FullText FullText_BOKU

2002

** Lopato, S; Forstner, C; Kalyna, M; Hilscher, J; Langhammer, U; Indrapichate, K; Lorković, ZJ; Barta, A; Network of interactions of a novel plant-specific Arg/Ser-rich protein, atRSZ33, with atSC35-like splicing factors..

J Biol Chem. 2002; 277(42):3-98 WoS PubMed FullText FullText_BOKU

1999

** Lopato, S; Kalyna, M; Dorner, S; Kobayashi, R; Krainer, AR; Barta, A; atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes..

Genes Dev. 1999; 13(8):987-1001 WoS PubMed PUBMED Central FullText FullText_BOKU

1997

Conference & Workshop Proceedings, Paper, Abstract

** Barta, A; Kalyna, M; Lopato, S Arg/Ser-rich plant splicing factors and their tissue specific expression in Arabidopsis thaliana.

FASEB J. 1997; 11(9): A998-A998. WoS

1995

** KALYNA, MP PETAL PROTOPLAST CULTURE SYSTEM - A NOVEL-APPROACH TO STUDY PLASTID BIOGENESIS.

J CELL BIOCHEM. 1995; 451-451. WoS

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