Illuminating the dark side of the human transcriptome with long read transcript sequencing
Kuo, Richard I, Cheng, Yuanyuan, Zhang, Runxuan, Brown, John W S, Smith, Jacqueline, Archibald, Alan L, Burt, David W
Published in BMC genomics (30.10.2020)
Published in BMC genomics (30.10.2020)
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A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
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
Published in Nucleic acids research (19.05.2017)
Published in Nucleic acids research (19.05.2017)
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Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis
Kalyna, Maria, Simpson, Craig G, Syed, Naeem H, Lewandowska, Dominika, Marquez, Yamile, Kusenda, Branislav, Marshall, Jacqueline, Fuller, John, Cardle, Linda, McNicol, Jim, Dinh, Huy Q, Barta, Andrea, Brown, John W S
Published in Nucleic acids research (01.03.2012)
Published in Nucleic acids research (01.03.2012)
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Journal Article
A methyl transferase links the circadian clock to the regulation of alternative splicing
Yanovsky, Marcelo J, Sanchez, Sabrina E, Petrillo, Ezequiel, Beckwith, Esteban J, Zhang, Xu, Rugnone, Matias L, Hernando, C. Esteban, Cuevas, Juan C, Godoy Herz, Micaela A, Depetris-Chauvin, Ana, Simpson, Craig G, Brown, John W. S, Cerdán, Pablo D, Borevitz, Justin O, Mas, Paloma, Ceriani, M. Fernanda, Kornblihtt, Alberto R
Published in Nature (London) (04.11.2010)
Published in Nature (London) (04.11.2010)
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Journal Article
BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq
Rapazote-Flores, Paulo, Bayer, Micha, Milne, Linda, Mayer, Claus-Dieter, Fuller, John, Guo, Wenbin, Hedley, Pete E, Morris, Jenny, Halpin, Claire, Kam, Jason, McKim, Sarah M, Zwirek, Monika, Casao, M Cristina, Barakate, Abdellah, Schreiber, Miriam, Stephen, Gordon, Zhang, Runxuan, Brown, John W S, Waugh, Robbie, Simpson, Craig G
Published in BMC genomics (11.12.2019)
Published in BMC genomics (11.12.2019)
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Journal Article
Alternative Splicing of Barley Clock Genes in Response to Low Temperature
Calixto, Cristiane P G, Simpson, Craig G, Waugh, Robbie, Brown, John W S
Published in PloS one (13.12.2016)
Published in PloS one (13.12.2016)
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Journal Article
spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms
Schlaen, RubeÌn Gustavo, EstefaneÌiÌa Mancini, Sabrina Elena Sanchez, Soledad Perez-SanteÌiÌaÌngelo, MateÌiÌaÌiÌas L. Rugnone, Craig G. Simpson, John W. S. Brown, Xu Zhang, Ariel Chernomoretz, Marcelo J. Yanovsky
Published in Proceedings of the National Academy of Sciences - PNAS (28.07.2015)
Published in Proceedings of the National Academy of Sciences - PNAS (28.07.2015)
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Journal Article
AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
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.
Published in The New phytologist (01.10.2015)
Published in The New phytologist (01.10.2015)
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Journal Article
Monitoring changes in alternative precursor messenger RNA splicing in multiple gene transcripts
Simpson, Craig G, Fuller, John, Maronova, Monika, Kalyna, Maria, Davidson, Diane, McNicol, Jim, Barta, Andrea, Brown, John W.S
Published in The Plant journal : for cell and molecular biology (01.03.2008)
Published in The Plant journal : for cell and molecular biology (01.03.2008)
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Journal Article
Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini‐exon splicing reporter and affect alternative splicing of endogenous genes differentially
Simpson, Craig G, Lewandowska, Dominika, Liney, Michele, Davidson, Diane, Chapman, Sean, Fuller, John, McNicol, Jim, Shaw, Paul, Brown, John W. S
Published in The New phytologist (01.07.2014)
Published in The New phytologist (01.07.2014)
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Journal Article
Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions
Pendle, Alison F, Clark, Gillian P, Boon, Reinier, Lewandowska, Dominika, Lam, Yun Wah, Andersen, Jens, Mann, Matthias, Lamond, Angus I, Brown, John W S, Shaw, Peter J
Published in Molecular biology of the cell (01.01.2005)
Published in Molecular biology of the cell (01.01.2005)
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Journal Article
Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana
Raczynska, Katarzyna Dorota, Simpson, Craig G, Ciesiolka, Adam, Szewc, Lukasz, Lewandowska, Dominika, McNicol, Jim, Szweykowska-Kulinska, Zofia, Brown, John W S, Jarmolowski, Artur
Published in Nucleic acids research (01.01.2010)
Published in Nucleic acids research (01.01.2010)
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Journal Article
Interaction of a Plant Virus-Encoded Protein with the Major Nucleolar Protein Fibrillarin Is Required for Systemic Virus Infection
Kim, Sang Hyon, MacFarlane, Stuart, Kalinina, Natalia O., Rakitina, Daria V., Ryabov, Eugene V., Gillespie, Trudi, Haupt, Sophie, Brown, John W. S., Taliansky, Michael
Published in Proceedings of the National Academy of Sciences - PNAS (26.06.2007)
Published in Proceedings of the National Academy of Sciences - PNAS (26.06.2007)
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Journal Article
Alternative splicing in plants – coming of age
Syed, Naeem H, Kalyna, Maria, Marquez, Yamile, Barta, Andrea, Brown, John W.S
Published in Trends in plant science (01.10.2012)
Published in Trends in plant science (01.10.2012)
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Journal Article
Alternative splicing of mini-exons in the Arabidopsis leaf rust receptor-like kinase LRK10 genes affects subcellular localisation
Shin, Ki Hun, Yang, Seung Hwan, Lee, Jun Yong, Lim, Che Woo, Lee, Sung Chul, Brown, John W. S, Kim, Sang Hyon
Published in Plant cell reports (01.03.2015)
Published in Plant cell reports (01.03.2015)
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Journal Article
Cajal bodies and the nucleolus are required for a plant virus systemic infection
Kim, Sang Hyon, Ryabov, Eugene V, Kalinina, Natalia O, Rakitina, Daria V, Gillespie, Trudi, MacFarlane, Stuart, Haupt, Sophie, Brown, John WS, Taliansky, Michael
Published in The EMBO journal (18.04.2007)
Published in The EMBO journal (18.04.2007)
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Journal Article
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis
Marquez, Yamile, Brown, John W S, Simpson, Craig, Barta, Andrea, Kalyna, Maria
Published in Genome research (01.06.2012)
Published in Genome research (01.06.2012)
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