The Arabidopsis Epitranscriptome (Joint with University of Nottingham)

Barton, Geoffrey (Investigator)
Simpson, Gordon (Investigator)

12 Article

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2022
m⁶A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site
Parker, M. T., Soanes, B. K., Kusakina, J., Larrieu, A., Knop, K., Joy, N., Breidenbach, F., Sherwood, A. V., Barton, G. J., Fica, S. M., Davies, B. H. (Lead / Corresponding author) & Simpson, G. G. (Lead / Corresponding author), 30 Dec 2022, In: eLife. 11, 34 p., e78808.
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Two zinc finger proteins with functions in m6A writing interact with HAKAI
Zhang, M., Bodi, Z., Mackinnon, K., Zhong, S., Archer, N., Mongan, N. P., Simpson, G. G. & Fray, R. G. (Lead / Corresponding author), 2 Mar 2022, In: Nature Communications. 13, 15 p., 1127.
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2021
2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
Parker, M. T. (Lead / Corresponding author), Knop, K., Barton, G. J. & Simpson, G. G. (Lead / Corresponding author), 1 Mar 2021, In: Genome Biology. 22, 1, 24 p., 72.
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Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA
Parker, M., Knop, K., Zacharaki, V., Sherwood, A., Tomé, D., Yu, X., Martin, P., Beynon, J., Michaels, S., Barton, G. J. & Simpson, G. G. (Lead / Corresponding author), 12 May 2021, In: eLife. 10, 36 p., e65537.
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2020
Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification
Parker, M. T., Knop, K., Sherwood, A. V., Schurch, N. J., Mackinnon, K., Gould, P. D., Hall, A. J. W., Barton, G. J. (Lead / Corresponding author) & Simpson, G. G. (Lead / Corresponding author), 14 Jan 2020, In: eLife. 9, 35 p., e49658.
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2019
Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA
Mourão, K., Schurch, N. J., Lukoszek, R., Froussios, K., Mackinnon, K., Duc, C., Simpson, G. (Lead / Corresponding author) & Barton, G. (Lead / Corresponding author), 7 Jun 2019, In: F1000 Research. 8, p. 1-7 7 p., 819.
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How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in Arabidopsis thaliana
Froussios, K., Schurch, N., Mackinnon, K., Gierlinski, M., Duc, C., Simpson, G. G. (Lead / Corresponding author) & Barton, G. J. (Lead / Corresponding author), 15 Sept 2019, In: Bioinformatics. 35, 18, p. 3372-3377 6 p.
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Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq [version 1; referees: 1 approved, 2 approved with reservations]
Froussios, K., Mourao, K., Simpson, G., Barton, G. & Schurch, N. (Lead / Corresponding author), 24 Feb 2019, In: F1000 Research. 8, p. 1-20 20 p., 213.
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2016
How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?
Schurch, N. J., Schofield, P., Gierliński, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G. G. (Lead / Corresponding author), Owen-Hughes, T. (Lead / Corresponding author), Blaxter, M. (Lead / Corresponding author) & Barton, G. J. (Lead / Corresponding author), Jun 2016, In: RNA: a Publication of the RNA Society. 22, 6, p. 839-851 13 p.
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2015
Enter exitrons
Staiger, D. (Lead / Corresponding author) & Simpson, G. G., 7 Jul 2015, In: Genome Biology. 16, 1, p. 1-3 3 p., 136.
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Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment
Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., 15 Nov 2015, In: Bioinformatics. 31, 22, p. 3625-3630 6 p.
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The Arabidopsis epitranscriptome
Fray, R. G. (Lead / Corresponding author) & Simpson, G. G. (Lead / Corresponding author), Oct 2015, In: Current Opinion in Plant Biology. 27, p. 17-21 5 p.
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The Arabidopsis Epitranscriptome (Joint with University of Nottingham)

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2022

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2015