List of works - Dan MacLean

A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system

scientific article

A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528.

scientific article

A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.

scientific article

A pigeonpea gene confers resistance to Asian soybean rust in soybean.

scientific article published on 25 April 2016

A putative phosphatase, LSF1, is required for normal starch turnover in Arabidopsis leaves.

scientific article published on 16 December 2009

A toolkit for analysing large-scale plant small RNA datasets

scientific article

Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks

scientific article published on 17 July 2021

An Open Science Peer Review Oath

scientific article published on 9 January 2015

An automated quantitative image analysis tool for the identification of microtubule patterns in plants.

scientific article

Assemblathon 1: a competitive assessment of de novo short read assembly methods

scientific article

Big data in small places

scientific article published on 9 January 2012

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

scientific article

Changing the rules of the game

scientific article (publication date: 13 August 2013)

Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors

scientific article published in 2021

Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and Arabidopsis

scientific article published on 10 January 2008

Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling

scientific article published in December 2007

Coordination of plastid and nuclear gene expression.

scientific article

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

scientific article

Crowdsourcing genomic analyses of ash and ash dieback - power to the people

scientific article

Disruption of essential plastid gene expression caused by T7 RNA polymerase-mediated transcription of plastid transgenes during early seedling development

scientific article published on 14 November 2006

Disruption of two defensive signaling pathways by a viral RNA silencing suppressor

scientific article published in July 2010

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.

scientific article

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.

scientific article

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana

scientific article

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors.

scientific article

Genome evolution following host jumps in the Irish potato famine pathogen lineage

scientific article published in December 2010

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

scientific article

High-resolution expression profiling of selected gene sets during plant immune activation

scientific article published on 08 January 2020

High-throughput confocal imaging of intact live tissue enables quantification of membrane trafficking in Arabidopsis.

scientific article

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

scientific article

Lessons from Fraxinus, a crowd-sourced citizen science game in genomics

scientific article published on 29 July 2015

Major transcriptome reprogramming underlies floral mimicry induced by the rust fungus Puccinia monoica in Boechera stricta

scientific article

Mapping mutations in plant genomes with the user-friendly web application CandiSNP.

scientific article published on 30 December 2014

Out of the woods. Ash dieback and the future of emergent pathogenomics.

scientific article

Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana.

scientific article published on 24 February 2009

Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains.

scientific article published on 6 March 2017

Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network

scientific article published on 23 August 2021

Publisher Correction: The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity

scientific article published on 17 November 2020

Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence

scientific article published on 07 January 2019

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

scientific article published on 08 October 2013

SVGenes: a library for rendering genomic features in scalable vector graphic format

scientific article

Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting

article

The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1.

scientific article

The F-box protein ACRE189/ACIF1 regulates cell death and defense responses activated during pathogen recognition in tobacco and tomato.

scientific article

The calcium-dependent protein kinase CPK28 buffers plant immunity and regulates BIK1 turnover

scientific article published on 12 November 2014

The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity

scientific article published on 26 August 2020

The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates

article

Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs

scientific article published on 24 October 2014

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

scientific article published on January 2013

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby.

scientific article published on 29 March 2015

blastjs: a BLAST+ wrapper for Node.js

scientific article

List of works by Dan MacLean

A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system

A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528.

A draft genome sequence of Pseudomonas syringae pv. tomato T1 reveals a type III effector repertoire significantly divergent from that of Pseudomonas syringae pv. tomato DC3000.

A pigeonpea gene confers resistance to Asian soybean rust in soybean.

A putative phosphatase, LSF1, is required for normal starch turnover in Arabidopsis leaves.

A toolkit for analysing large-scale plant small RNA datasets

Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks

An Open Science Peer Review Oath

An automated quantitative image analysis tool for the identification of microtubule patterns in plants.

Assemblathon 1: a competitive assessment of de novo short read assembly methods

Big data in small places

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics

Changing the rules of the game

Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors

Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and Arabidopsis

Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling

Coordination of plastid and nuclear gene expression.

Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data.

Crowdsourcing genomic analyses of ash and ash dieback - power to the people

Disruption of essential plastid gene expression caused by T7 RNA polymerase-mediated transcription of plastid transgenes during early seedling development

Disruption of two defensive signaling pathways by a viral RNA silencing suppressor

EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics.

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors.

Genome evolution following host jumps in the Irish potato famine pathogen lineage

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

High-resolution expression profiling of selected gene sets during plant immune activation

High-throughput confocal imaging of intact live tissue enables quantification of membrane trafficking in Arabidopsis.

Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.

Lessons from Fraxinus, a crowd-sourced citizen science game in genomics

Major transcriptome reprogramming underlies floral mimicry induced by the rust fungus Puccinia monoica in Boechera stricta

Mapping mutations in plant genomes with the user-friendly web application CandiSNP.

Out of the woods. Ash dieback and the future of emergent pathogenomics.

Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana.

Plant immune and growth receptors share common signalling components but localise to distinct plasma membrane nanodomains.

Plant pathogens convergently evolved to counteract redundant nodes of an NLR immune receptor network

Publisher Correction: The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity

Rapid fine mapping of causative mutations from sets of unordered, contig-sized fragments of genome sequence

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

SVGenes: a library for rendering genomic features in scalable vector graphic format

Spatio-temporal cellular dynamics of the Arabidopsis flagellin receptor reveal activation status-dependent endosomal sorting

The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1.

The F-box protein ACRE189/ACIF1 regulates cell death and defense responses activated during pathogen recognition in tobacco and tomato.

The calcium-dependent protein kinase CPK28 buffers plant immunity and regulates BIK1 turnover

The calcium-permeable channel OSCA1.3 regulates plant stomatal immunity

The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates

Using 2k + 2 bubble searches to find single nucleotide polymorphisms in k-mer graphs

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby.

blastjs: a BLAST+ wrapper for Node.js