Search Results

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.

2022 GENOME BIOL;23(1):149.
PMID: 35799267

Zhang, Runxuan; Kuo, Richard; Coulter, Max; Calixto, Cristiane P G; Entizne, Juan Carlos; Guo, Wenbin; Marquez, Yamile; Milne, Linda; Riegler, Stefan; Matsui, Akihiro; Tanaka, Maho; Harvey, Sarah; Gao, Yubang; Wießner-Kroh, Theresa; Paniagua, Alejandro; Crespi, Martin; Denby, Katherine; Hur, Asa Ben; Huq, Enamul; Jantsch, Michael; Jarmolowski, Artur; Koester, Tino; Laubinger, Sascha; Li, Qingshun Quinn; Gu, Lianfeng; Seki, Motoaki; Staiger, Dorothee; Sunkar, Ramanjulu; Szweykowska-Kulinska, Zofia; Tu, Shih-Long; Wachter, Andreas; Waugh, Robbie; Xiong, Liming; Zhang, Xiao-Ning; Conesa, Ana; Reddy, Anireddy S N; Barta, Andrea; Kalyna, Maria; Brown, John W S

Light regulates alternative splicing outcomes via the TOR kinase pathway.

2021 Cell Rep;36(10):109676.
PMID: 34496244

Riegler, Stefan; Servi, Lucas; Scarpin, M Regina; Godoy Herz, Micaela A; Kubaczka, María G; Venhuizen, Peter; Meyer, Christian; Brunkard, Jacob O; Kalyna, Maria; Barta, Andrea; Petrillo, Ezequiel

Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing.

2021 NUCLEIC ACIDS RES;49(2):1133-1151.
PMID: 33406240

Fuchs, Armin; Riegler, Stefan; Ayatollahi, Zahra; Cavallari, Nicola; Giono, Luciana E; Nimeth, Barbara A; Mutanwad, Krishna V; Schweighofer, Alois; Lucyshyn, Doris; Barta, Andrea; Petrillo, Ezequiel; Kalyna, Maria

The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A.

2018 PLANT J
PMID: 29602264

Cavallari, Nicola; Nibau, Candida; Fuchs, Armin; Dadarou, Despoina; Barta, Andrea; Doonan, John H

RNA in Disease and development

2017 RNA BIOL;14(5):457-459.
PMID: 28402218

Barta, Andrea; Jantsch, Michael F

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

2017 NUCLEIC ACIDS RES;9(45)
PMID: 28402429

Zhang, Runxuan; Calixto, Cristiane P G; Marquez, Yamile; Venhuizen, Peter; Tzioutziou, Nikoleta A; Guo, Wenbin; Spensley, Mark; Entizne, Juan Carlos; Lewandowska, Dominika; Ten Have, Sara; Frei Dit Frey, Nicolas; Hirt, Heribert; James, Allan B; Nimmo, Hugh G; Barta, Andrea; Kalyna, Maria; Brown, John W S

The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast.

2016 NUCLEIC ACIDS RES;44(4):1703-17..
PMID: 26682798

Aronica, Lucia; Kasparek, Torben; Ruchman, David; Marquez, Yamile; Cipak, Lubos; Cipakova, Ingrid; Anrather, Dorothea; Mikolaskova, Barbora; Radtke, Maximilian; Sarkar, Sovan; Pai, Chen-Chun; Blaikley, Elizabeth; Walker, Carol; Shen, Kuo-Fang; Schroeder, Renee; Barta, Andrea; Forsburg, Susan L; Humphrey, Timothy C

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

2015 GENOME RES;25(7):995-1007.
PMID: 25934563

Marquez, Yamile; Höpfler, Markus; Ayatollahi, Zahra; Barta, Andrea; Kalyna, Maria

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

2015 New Phytologist;208(1):96-101.
PMID: 26111100

Zhang, Runxuan; Calixto, Cristiane P G; Tzioutziou, Nikoleta A; James, Allan B; Simpson, Craig G; Guo, Wenbin; Marquez, Yamile; Kalyna, Maria; Patro, Rob; Eyras, Eduardo; Barta, Andrea; Nimmo, Hugh G; Brown, John W S

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

2015 PLANT CELL;27(8):2083-7.
PMID: 26286536

Brown, John W S; Simpson, Craig G; Marquez, Yamile; Gadd, Geoffrey M; Barta, Andrea; Kalyna, Maria

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

2014 Plant Signal Behav;9(11):e976150.
PMID: 25482785

Godoy Herz, Micaela A; Kornblihtt, Alberto R; Barta, Andrea; Kalyna, Maria; Petrillo, Ezequiel

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

2014 RNA BIOL;11(10):1215-20.
PMID: 25590224

Petrillo, Ezequiel; Godoy Herz, Micaela A; Barta, Andrea; Kalyna, Maria; Kornblihtt, Alberto R

Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis.

2014 PLANT CELL;26(2):754-64.
PMID: 24532591

Göhring, Janett; Jacak, Jaroslaw; Barta, Andrea

Suitable transfection methods for single particle tracing in plant suspension cells.

2014 Plant methods;10:15.
PMID: 24991230

Göhring, Janett; Fulcher, Nick; Schilcher, Kurt; Barta, Andrea; Jacak, Jaroslaw

A chloroplast retrograde signal regulates nuclear alternative splicing.

2014 SCIENCE;344(6182):427-30.
PMID: 24763593

Petrillo, Ezequiel; Herz, Micaela A Godoy; Fuchs, Armin; Reifer, Dominik; Fuller, John; Yanovsky, Marcelo J; Simpson, Craig; Brown, John W S; Barta, Andrea; Kalyna, Maria; Kornblihtt, Alberto R

Complexity of the alternative splicing landscape in plants.

2013 PLANT CELL;25(10):3657-83.
PMID: 24179125

Reddy, Anireddy S N; Marquez, Yamile; Kalyna, Maria; Barta, Andrea

Introns of plant pri-miRNAs enhance miRNA biogenesis.

2013 EMBO REP;14(7):622-8.
PMID: 23681439

Bielewicz, Dawid; Kalak, Malgorzata; Kalyna, Maria; Windels, David; Barta, Andrea; Vazquez, Franck; Szweykowska-Kulinska, Zofia; Jarmolowski, Artur

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

2013 NUCLEIC ACIDS RES;41(3):1783-96.
PMID: 23248006

Bannikova, Olga; Zywicki, Marek; Marquez, Yamile; Skrahina, Tatsiana; Kalyna, Maria; Barta, Andrea

Alternative splicing in plants - coming of age.

2012 TRENDS PLANT SCI
PMID: 22743067

Syed, Naeem H; Kalyna, Maria; Marquez, Yamile; Barta, Andrea; Brown, John W S

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

2012 GENOME RES
PMID: 22391557

Yamile Marquez, John W.S. Brown, Craig Simpson, Andrea Barta, Maria Kalyna

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