Publications

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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August 2017

Bioinformatics

Faulkner C, Zhou J, Evrard A, Bourdais G, MacLean D, Häweker H, Eckes P, Robatzek S (2017)

An automated quantitative image analysis tool for the identification of microtubule patterns in plants. Traffic. 2017 Jul 26. doi: 10.1111/tra.12505.

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March 2021

Bioinformatics, Jonathan Jones Group

Furzer OJ, Cevik V, Fairhead S, Bailey K, Redkar A, Schudoma C, MacLean D, Holub EB, Jones JDG (2021)

An improved assembly of the Albugo candida Ac2V genome reveals the expansion of the “CCG” class of effectors. bioRxiv preprint Mar 29, 2021 doi: https://doi.org/10.1101/2021.03.29.437041

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May 2017

Bioinformatics, Jonathan Jones Group, Proteomics

Wirthmueller L, Asai S, Rallapalli G, Sklenar J, Fabro G, Kim DS, Lintermann R, Jaspers P, Wrzaczek M, Kangasjärvi L, MacLean D, Menke FLH, Banfield MJ, JDG (2017)

An Oomycete Effector Protein Induces Shade Avoidance In Arabidopsis And Attenuates Salicylate Signaling By Binding To Host Proteins Of The RADICAL-INDUCED CELL DEATH1 Family. bioRxiv preprint May 14, 2017 doi: https://doi.org/10.1101/137844

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January 2015

Bioinformatics

Aleksic J, Alexa A, Attwood TK, Chue Hong N, Dahlö M, Davey R, Dinkel H, Förstner KU, Grigorov I, Hériché JK, Lahti L, MacLean D, Markie ML, Molloy J, Schneider MV, Scott C, Smith-Unna R, Vieira BM (2015)

An open science peer review oath. [v2; ref status: indexed, http://f1000r.es/4wf] F1000Research 2015, 3:271 (doi: 10.12688/f1000research.5686.2)

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February 2009

Bioinformatics, Jonathan Jones Group

Daniel MacLean, Jonathan DG Jones, and David J Studholme. (2009)

Application of ’next-generation’ sequencing technologies to microbial genetics. Nature Reviews Microbiology, 7(4):287–296

September 2011

Bioinformatics

Dent Earl, Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Fass, Hung On Ken Yu, Vince Buffalo, Daniel R Zerbino, Mark Diekhans, et al.

Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21(12):2224–2241

March 2015

Bioinformatics

Etherington GJ, Ricardo H. Ramirez-Gonzalez RH, MacLean D (2015)

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby. Bioinformatics (2015) doi: 10.1093/bioinformatics/btv178

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May 2012

Bioinformatics

Ricardo Ramirez-Gonzalez, Raoul JP Bonnal, Mario Caccamo, Daniel MacLean, et al. (2012)

Bio-samtools: Ruby bindings for samtools, a library for accessing bam files containing high-throughput sequence alignments. Source Code for Biology and Medicine, 7(6),