Evaluation of tools for differential gene expression analysis by RNA-seq on a 48 biological replicate experiment

Authors: Schurch, Nicholas J., Schofield, Pieta, Gierliński, Marek, Cole, Christian, Sherstnev, Alexander, Singh, Vijender, Wrobel, Nicola, Gharbi, Karim, Simpson, Gordon G., Owen-Hughes, Tom, Blaxter, Mark, Barton, Geoffrey J.

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1505.02017

Improved annotation of 3-prime untranslated regions and complex loci by combination of strand-specific Direct RNA Sequencing, RNA-seq and ESTs

Authors: Schurch, Nick, Cole, Christian, Sherstnev, Alexander, Song, Junfang, Duc, Céline, Storey, Kate G., McLean, W. H. Irwin, Brown, Sara J., Simpson, Gordon G., Barton, Geoffrey J.

Source: PLoS ONE 9(4) (2014): e94270

Subject Terms: Quantitative Biology - Genomics

Access URL: http://arxiv.org/abs/1311.2494

Arabidopsis, the Rosetta Stone of Flowering Time?

Authors: Simpson, Gordon G., Dean, Caroline

Source: Science, 2002 Apr 01. 296(5566), 285-289.

Access URL: https://www.jstor.org/stable/3076508

U6 snRNA m6A modification is required for accurate and efficient splicing of C. elegans and human pre-mRNAs.

Authors: Shen, Aykut, Hencel, Katarzyna, Parker, Matthew T, Scott, Robyn, Skukan, Roberta, Adesina, Aduragbemi S, Metheringham, Carey L, Miska, Eric A, Nam, Yunsun, Haerty, Wilfried, Simpson, Gordon G, Akay, Alper

Source: Nucleic Acids Research; 8/27/2024, Vol. 52 Issue 15, p9139-9160, 22p

The Arabidopsis epitranscriptome

Authors: Fray, Rupert G, Simpson, Gordon G

Source: In Current Opinion in Plant Biology October 2015 27:17-21

Message ends: RNA 3′ processing and flowering time control

Authors: Rataj, Katarzyna, Simpson, Gordon G.

Source: Journal of Experimental Botany, 2014 Jan 01. 65(2), 353-363.

Access URL: http://dx.doi.org/10.1093/jxb/ert439

Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis

Authors: Vanholme, Ruben, Cesarino, Igor, Rataj, Katarzyna, Xiao, Yuguo, Sundin, Lisa, Goeminne, Geert, Kim, Hoon, Cross, Joanna, Morreel, Kris, Araujo, Pedro, Welsh, Lydia, Haustraete, Jurgen, McClellan, Christopher, Vanholme, Bartel, Ralph, John, Simpson, Gordon G., Halpin, Claire, Boerjan, Wout

Source: Science, 2013 Sep 01. 341(6150), 1103-1106.

Access URL: http://dx.doi.org/10.1126/science.1241602

Inter-species association mapping links splice site evolution to METTL16 and SNRNP27K.

Authors: Parker, Matthew T., Fica, Sebastian M., Barton, Geoffrey J., Simpson, Gordon G.

Source: eLife; 10/17/2023, p1-25, 25p

Noncanonical Translation Initiation of the Arabidopsis Flowering Time and Alternative Polyadenylation Regulator FCA

Authors: Simpson, Gordon G., Laurie, Rebecca E., Dijkwel, Paul P., Quesada, Victor, Stockwell, Peter A., Dean, Caroline, Macknight, Richard C.

Source: The Plant Cell, 2010 Nov 01. 22(11), 3764-3777.

Access URL: https://www.jstor.org/stable/41059388

The Spen Family Protein FPA Controls Alternative Cleavage and Polyadenylation of RNA

Authors: Hornyik, Csaba, Terzi, Lionel C., Simpson, Gordon G.

Source: In Developmental Cell 16 February 2010 18(2):203-213

Plant pre-mRNA Splicing and Splicing Components

Authors: Simpson, Craig G., Simpson, Gordon G., Turnbull-Ross, Andrew D., Clark, Gillian P.

Source: Philosophical Transactions: Biological Sciences, 1993 Nov . 342(1301), 217-224.

Access URL: https://www.jstor.org/stable/55662

m⁶A modification of U6 snRNA modulates usage of two major classes of pre-mRNA 5' splice site.

Authors: Parker, Matthew T., Soanes, Beth K., Kusakina, Jelena, Larrieu, Antoine, Knop, Katarzyna, Joy, Nisha, Breidenbach, Friedrich, Sherwood, Anna V., Barton, Geoffrey J., Fica, Sebastian M., Davies, Brendan H., Simpson, Gordon G.

Source: eLife; 12/30/2022, p1-34, 34p

FY Is an RNA 3′ End-Processing Factor that Interacts with FCA to Control the Arabidopsis Floral Transition.

Authors: Simpson, Gordon G., Dijkwel, Paul P., Quesada, Victor

Source: Cell; June 13 2003, Vol. 113 Issue 6, p777-787, 11p

The autonomous pathway: epigenetic and post-transcriptional gene regulation in the control of Arabidopsis flowering time

Authors: Simpson, Gordon G

Source: In Current Opinion in Plant Biology 2004 7(5):570-574

Two zinc finger proteins with functions in m⁶A writing interact with HAKAI.

Authors: Zhang, Mi, Bodi, Zsuzsanna, Mackinnon, Katarzyna, Zhong, Silin, Archer, Nathan, Mongan, Nigel P., Simpson, Gordon G., Fray, Rupert G.

Source: Nature Communications; 3/2/2022, Vol. 13 Issue 1, p1-15, 15p

Subject Terms: ZINC-finger proteins, ROOT formation

Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA.

Authors: Parker, Matthew T., Knop, Katarzyna, Zacharaki, Vasiliki, Sherwood, Anna V., Tomé, Daniel, Xuhong Yu, Martin, Pascal G. P., Beynon, Jim, Michaels, Scott D., Barton, Geoffrey J., Simpson, Gordon G.

Source: eLife; 5/12/2021, p1-36, 36p

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.

Authors: Parker, Matthew T., Knop, Katarzyna, Barton, Geoffrey J., Simpson, Gordon G.

Source: Genome Biology; 3/1/2021, Vol. 22 Issue 1, p1-24, 24p

New frontiers in plant development: from genes to phenotype.

Alternate Title: 17th Long Ashton International Symposium, 15-17th April 2002, Bristol, UK

Authors: Hedden, Peter, Holdsworth, Michael J., Simpson, Gordon G.

Source: Trends in Plant Science; September 2002, Vol. 7 Issue 9, p381-383, 3p

WHEN TO SWITCH TO FLOWERING.

Authors: Simpson, Gordon G., Gendall, Anthony R., Dean, Caroline

Source: Annual Review of Cell & Developmental Biology. 1999, Vol. 15 Issue 1, p519. 32p.

Subject Terms: *FLOWERING time, *ARABIDOPSIS

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.

Authors: Parker, Matthew T., Knop, Katarzyna, Sherwood, Anna V., Schurch, Nicholas J., Mackinnon, Katarzyna, Gould, Peter D., Hall, Anthony J. W., Barton, Geoffrey J., Simpson, Gordon G.

Source: eLife; 2020, p1-35, 35p, 7 Graphs