Publications

October 2019

Bioinformatics

MacLean D (2019)

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

October 2019

Proteomics, Sophien Kamoun Group

Ryder LS, Dagdas YF, Kershaw MJ, Venkataraman C, Madzvamuse A, Yan, X Cruz-Mireles N, Soanes DM, Oses-Ruiz M, Styles V, Sklenar J, Menke FLH, Talbot NJ (2019)

A sensor kinase controls turgor-driven plant infection by the rice blast fungus. Nature 09 Oct 2019. doi: https://doi.org/10.1038/s41586-019-1637-x

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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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September 2019

Proteomics

Liu Y, Maierhofer T, Rybak K, Sklenar J, Breakspear A, Johnston MG, Fliegmann J, Huang S, Roelfsema MRG, Felix G, Faulkner C, Menke FL, Geiger D, Hedrich R, Robatzek S (2019)

Anion channel SLAH3 is a regulatory target of chitin receptor-associated kinase PBL27 in microbial stomatal closure. Elife. 2019 Sep 16;8. pii: e44474. doi: 10.7554/eLife.44474.

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July 2019

Proteomics, Sophien Kamoun Group

Zess EK, Jensen C, Cruz-Mireles N, De la Concepcion JC, Sklenar J, Stephani M, Imre R, Roitinger E, Hughes R, Belhaj K, Mechtler K, Menke FLH, Bozkurt T, Banfield MJ, Kamoun S, Maqbool A, Dagdas YF (2019)

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform. PLoS Biol. 2019 Jul 22;17(7):e3000373. doi: 10.1371/journal.pbio.3000373.

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July 2019

Jonathan Jones Group, Synthetic Biology

Ngou BPM, Ahn HK, Ding P, Redkar A, Brown H, Ma Y, Youles M, Tomlinson L, Jones JDG (2019)

Estradiol-inducible AvrRps4 expression reveals distinct properties of TIR-NLR-mediated effector-triggered immunity. bioRxiv preprint Jul 14, 2019 doi: https://doi.org/10.1101/701359

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June 2019

Cyril Zipfel Group, Proteomics

Wong JEMM, Nadzieja M, Madsen LH, Bücherl CA, Dam S, Sandal NN, Couto D, Derbyshire P, Uldum-Berentsen M, Schroeder S, Schwämmle V, Nogueira FCS, Asmussen MH, Thirup S, Radutoiu S, Blaise M, Andersen KR, Menke FLH, Zipfel C, Stougaard J (2019)

A Lotus japonicus cytoplasmic kinase connects Nod factor perception by the NFR5 LysM receptor to nodulation. Proc Natl Acad Sci U S A. 2019 Jun 25. pii: 201815425. doi: 10.1073/pnas.1815425116.

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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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January 2019

Bioinformatics

Rallapalli G, Corredor-Moreno P, Chalstrey E, Page M, MacLean D (2019)

Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence. BMC Bioinformatics. 2019 Jan 7;20(1):9. doi: 10.1186/s12859-018-2515-5.

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