Dan MacLean

Publications

• Big data in small places DOI: 10.1038/nbt.2079
• Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments. DOI: 10.1186/1751-0473-7-6
• Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics DOI: 10.1093/bioinformatics/bts080
• Genome Analyses of an Aggressive and Invasive Lineage of the Irish Potato Famine Pathogen DOI: 10.1371/journal.ppat.1002940
• Spatio-Temporal Cellular Dynamics of the Arabidopsis Flagellin Receptor Reveal Activation Status-Dependent Endosomal Sorting DOI: 10.1105/tpc.112.100263
• Assemblathon 1: A competitive assessment of de novo short read assembly methods DOI: 10.1101/gr.126599.111
• Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data DOI: 10.1093/bioinformatics/btr442
• Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana DOI: 10.1371/journal.pbio.1001094
• Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. ISSN: 1545-7885
• The microRNA miR393 re-directs secondary metabolite biosynthesis away from camalexin and towards glucosinolates DOI: 10.1111/j.1365-313X.2011.04591.x
• A Boolean Model of the Pseudomonas syringae hrp Regulon Predicts a Tightly Regulated System DOI: 10.1371/journal.pone.0009101
• A Putative Phosphatase, LSF1, Is Required for Normal Starch Turnover in Arabidopsis Leaves DOI: 10.1104/pp.109.148981
• Disruption of Two Defensive Signaling Pathways by a Viral RNA Silencing Suppressor DOI: 10.1094/MPMI-23-7-0835
• Disruption of the salicylate and jasmonate signaling pathways by the cucumber mosaic virus 2b RNA silencing suppressor ISSN: 0031-949X
• Evidence for Large Complex Networks of Plant Short Silencing RNAs DOI: 10.1371/journal.pone.0009901
• Finding sRNA generative locales from high-throughput sequencing data with NiBLS DOI: 10.1186/1471-2105-11-93
• Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage DOI: 10.1126/science.1193070
• Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt DOI: 10.1111/j.1574-6968.2010.02065.x
• High-Throughput Confocal Imaging of Intact Live Tissue Enables Quantification of Membrane Trafficking in Arabidopsis DOI: 10.1104/pp.110.160325
• PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update DOI: 10.1093/nar/gkp810
• 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 DOI: 10.1094/MPMI-22-1-0052
• A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of pathovar 11528. ISSN: 1471-2164
• A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528 DOI: 10.1186/1471-2164-10-395
• A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528 (vol 10, pg 395, 2009) DOI: 10.1186/1471-2164-10-569
• Application of 'next-generation' sequencing technologies to microbial genetics DOI: 10.1038/nrmicro2088
• Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans DOI: 10.1038/nature08358
• Genome-Wide Analysis of Plastid Gene Expression in Potato Leaf Chloroplasts and Tuber Amyloplasts: Transcriptional and Posttranscriptional Control DOI: 10.1104/pp.109.140483
• Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana DOI: 10.1016/j.jprot.2009.02.004
• A toolkit for analysing large-scale plant small RNA datasets DOI: 10.1093/bioinformatics/btn428
• Biogenesis and function of plant viral small RNAs
• Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and Arabidopsis DOI: 10.1007/s11103-007-9279-z
• PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data. DOI: 10.1186/1756-0500-1-30
• The F-box protein ACRE189/ACIF1 regulates cell death and defense responses activated during pathogen recognition in tobacco and tomato DOI: 10.1105/tpc.107.056978
• The F-box protein ACRE189/ACIF1 regulates cell death and defense responses activated during pathogen recognition in tobacco and tomato. DOI: 10.1105/tpc.107.056978
• Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling DOI: 10.1016/j.devcel.2007.10.001
• Disruption of essential plastid gene expression caused by T7 RNA polymerase-mediated transcription of plastid transgenes during early seedling development DOI: 10.1007/s11248-006-9045-z
• GUNI (GENOMES UNCOUPLED1) encodes a pentatricopeptide repeat (PPR) protein involved in plastid protein synthesis-responsive retrograde signaling to the nucleus
• Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones DOI: 10.1111/j.1365-313X.2004.02007.x
• Coordination of plastid and nuclear gene expression DOI: 10.1098/rstb.2002.1180