Publications

August 2020

Bioinformatics, Cyril Zipfel Group, Proteomics

Thor K, Jiang S, Michard E, George J, Scherzer S, Huang S, Dindas J, Derbyshire P, Leitão N, DeFalco TA, Köster P, Hunter K, Kimura S, Gronnier J, Stransfeld L, Kadota Y, Bücherl CA, Charpentier M, Wrzaczek M, MacLean D, Oldroyd GED, Menke FLH, M. Roelfsema MRG, Hedrich R, Feijó J, Zipfel C (2020)

The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity. Nature. 25 August 2020. DOI: 10.1038/s41586-020-2702-1

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July 2020

Bioinformatics

Kristianingsih R, MacLean D (2020)

Accurate plant pathogen effector protein classification ab initio with deepredeff, an ensemble of convolutional neural networks. bioRxiv preprint July 09, 2020 doi: https://doi.org/10.1101/2020.07.08.193250

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June 2020

Bioinformatics, Jonathan Jones Group

Ding P, Sakai T, Shrestha RK, Perez NM, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG (2020)

Chromatin accessibility landscapes activated by cell surface and intracellular immune receptors. bioRxiv preprint June 18, 2020 doi: https://doi.org/10.1101/2020.06.17.157040

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February 2020

Bioinformatics, Nick Talbot Group

Oses-Ruiz M, Martin-Urdiroz M, Soanes DM, Kershaw MJ, Cruz-Mireles N, Valdovinos-Ponce G, Molinari C, Littlejohn GR, Derbyshire P, Menke F, Valent B, Talbot NJ (2020)

A hierarchical transcriptional network controls appressorium-mediated plant infection by the rice blast fungus Magnaporthe oryzae. bioRxiv preprint Feb 06, 2020 doi: https://doi.org/10.1101/2020.02.05.936203

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January 2020

Bioinformatics, Sophien Kamoun Group

Langner T, Harant A, Gómez-Luciano LB, Shrestha RK, Win J, Kamoun S (2020)

Genomic rearrangements generate hypervariable mini-chromosomes in host-specific lineages of the blast fungus. bioRxiv preprint Jan 11, 2020 doi: https://doi.org/10.1101/2020.01.10.901983

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January 2020

Bioinformatics, Jonathan Jones Group

Ding P, Ngou BPM, Furzer OJ, Sakai T, Shrestha RK, MacLean D, Jones JDG (2020)

High-resolution Expression Profiling of Selected Gene Sets during Plant Immune Activation. Plant Biotechnol J. 2020 Jan 8. doi: 10.1111/pbi.13327.

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October 2019

Bioinformatics

MacLean D (2019)

R Bioinformatics Cookbook: Use R and Bioconductor to perform RNAseq, genomics, data visualization, and bioinformatic analysis. Packt Publishing.

September 2019

Bioinformatics, Jonathan Jones Group

Ding P, Ngou BPM, Oliver J. Furzer OJ, Sakai T, Shrestha RK, MacLean D, Jones JDG (2019)

High-resolution Expression Profiling of Selected Gene Sets during Plant Immune Activation. bioRxiv preprint Sep 23, 2019 doi: https://doi.org/10.1101/775973

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September 2019

Bioinformatics, Sophien Kamoun Group

De la Concepcion JC, Franceschetti M, MacLean D, Terauchi R, Kamoun S, Banfield MJ (2019)

Protein engineering expands the effector recognition profile of a rice NLR immune receptor. Elife. 2019 Sep 19;8. pii: e47713. doi: 10.7554/eLife.47713.

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May 2019

Bioinformatics

MacLean D (2019)

A convolutional neural network for predicting transcriptional regulators of genes in Arabidopsis transcriptome data reveals classification based on positive regulatory interactions. bioRxiv preprint Apr 28, 2019 doi: https://doi.org/10.1101/618926

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