Ramirez-Gonzalez R, Caccamo M, MacLean D. Gee Fu: a sequence version and web-services
database tool for genomic assembly, genome feature and NGS data (2011) Bioinformatics27,
2754-2755
Earl D et al. Assemblathon 1: A competitive assessment of de novo short read assembly methods. (2011). Genome Res. 21, 2224-2241
Eric Kemen, Anastasia Gardiner, Torsten Schultz-Larsen, Ariane C. Kemen, Alexi L. Balmuth,
Alexandre Robert-Seilaniantz, Kate Bailey, Eric Holub, David J. Studholme, Dan MacLean,
Jonathan D. G. Jones. (2011) Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis. PLoS Biol
Robert-Seilaniantz A, Maclean D, Jikumaru Y, Hill L, Yamaguchi S, Kamiya Y, Jones JD. (2011).
The microRNA miR393 redirects secondary metabolite biosynthesis away from camalexin and
towards glucosinolates. Plant J. 67, 218-231
Etherington G and MacLean D (2011) Next-Generation techniques for analysing Next-Generation sequence data (2011). GIT Laboratory Journal, 15, 11-12, pp 10-11
2010
MacLean D, Yelina N, Havecker E, Heimstadt S, Studholme DJ and Baulcombe DC (2010) Evidence for Large Complex Networks of Plant Short Silencing RNAs.
PLoS ONE, 5, e9901 PubMed
MacLean D and Studholme DJ (2010) A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system
PLoS ONE, 5, e9101 PubMed
MacLean D, Moulton V and Studholme DJ (2010) Identification of small RNA generative loci from high-throughput sequencing data using NiBLS.
BMC Bioinformatics 11, 93 PubMed
Lewsey MG, Murphy AM, MacLean D, Dalchaua N, Westwood JH, Macaulay K, Bennett MH, Moulin M, Hanke DE, Powell G, Smith AG and Carr JP. (2010) Disruption of two defensive signalling pathways bt a viral RNA silencing suppressor.
MPMI in pressPubMed
Durek P, Schmidt R, Heazlewood JL, Jones A, MacLean D, Nagel A, Kersten B and Schulze WX. (2010) PhosPhAt: the
arabidopsis thaliana phosphorylation site database. An update.
Nucleic Acids Res. 38, 828-384. PubMed
Comparot-Moss S, Kötting O, Stettler M, Edner C, Graf A, Weise SE, Streb S, Lue WL, MacLean D, Mahlow S, Ritte G, Steup M, Chen J, Zeeman SC, Smith AM. (2010) A putative phosphatase, LSF1, Is Required for normal starch turnover in
Arabidopsis Leaves.
Plant Physiol., 152, 685-697. PubMed
2009
MacLean D, Jones JD and Studholme D (2009) Application of 'Next Generation' sequencing technologies to microbial genetics,
Nature Reviews Microbiology, 7, 287-296 PubMed
Haas BJ, Kamoun S
et al (2009) Genome sequence and analysis of the Irish potato famine pathogen
Phytophthora infestans.
Nature 461, 393-398 PubMed
Almeida NF, Yan S, Lindeberg M
et al (2009) A draft genome sequence of Pseudomonas syringae pv. tomato strain T1 reveals a repertoire of type III related genes significantly divergent from that of Pseudomonas syringae pv tomato strain DC3000,
MPMI 22, 52-62 PubMed
Studholme DJ, Ibanez SG, MacLean D, Dangl JL, Chang JH and Rathjen JP.A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of
Pseudomonas syringae pathovar tabaci 11528.
BMC Genomics 24, 395PubMedJones AM, MacLean D, Studholme DJ, Serna-Sanz A, Andreasson E and Peck SC (2009) Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana
Journal of Proteomics, 72, 439-451
PubMed
Valkov VT, Scotti N, Kahlau S, MacLean D, Grillo MS, Gray JC, Bock R and Cardi T (2009) Genome-wide analysis of plastid gene expression in potato leaf chloroplasts and tuber amyloplasts: transcriptional and post-transcriptional control
Plant Phys. DOI: 10.1104/pp.109.140483 PubMed
2008
MacLean D, Burrell MA, Studholme DJ and Jones AMEJ (2008) PhosCalc: A tool for determining the likelihood of peptide phosphorylation from Mass Spectrometer data.
BMC Research Notes 1:30 PubMed
MacLean D, Jerome CA, Brown AP, Gray JC (2008) Co-regulation of nuclear genes encoding plastid ribosomal proteins by light and plastid signals during seedling development in tobacco and Arabidopsis.
Plant Mol Biol. 66, 475-490 PubMed
Moxon S, Schwach F, Dalmay T, MacLean D, Studholme DJ, Moulton V. (2008) A toolkit for analysing large-scale plant small RNA datasets.
Bioinformatics 24, 2252-2253 PubMed
van den Burg HA, Tsitsigiannis DI, Rowland O, Lo J, Rallapalli G, MacLean D, Takken FL, Jones JD (2008) The F-Box Protein ACRE189/ACIF1 Regulates Cell Death and Defense Responses Activated during Pathogen Recognition in Tobacco and Tomato.
Plant Cell. 20, 697-719 PubMed
2007
Cottage AJ, Mott AK, Wang JH, Sullivan JA, MacLean D, Tran L, Choy MK, Newell CA, Kavanagh TA, Aspinall S, Gray JC (2007) GUN1 (GENOMES UNCOUPLED1) encodes a pentatricopeptide repeat (PPR) protein involved in plastid protein synthesis-responsive retrograde signaling to the nucleus. In: Allen J, Gantt E, Golbeck J, Osmond B (eds)
Energy from the Sun Proceedings of the International Photosynthesis Congress. Springer, Berlin
Anastasiou E, Kenz S, Gerstung M, MacLean D, Timmer J, Fleck C, Lenhard M. (2007) Control of plant organ size by KLUH/CYP78A5-dependent intercellular signaling
Dev Cell. 13, 843-856 PubMed
Magee AM, MacLean D, Gray JC, Kavanagh TA. (2007) Disruption of essential plastid gene expression caused by T7 RNA polymerase-mediated transcription of plastid transgenes during early seedling development.
Transgenic Res. 4, 415-428 PubMed
2004
Chua YL, Mott E, Brown AP, MacLean D, Gray JC (2004) Microarray analysis of chromatin-immunoprecipitated DNA identifies specific regions of tobacco genes associated with acetylated histones.
Plant J. 37, 789-800 PubMed
2003
Gray JC, Sullivan JA, Wang J-H, Jerome CA and MacLean D (2003) Coordination of plastid and nuclear gene expression.
Phil Trans R Soc Lond B 358, 135-145 PubMed
MacLean D. Report on the Transcriptomics Session of the 2003 Main Meeting of the SEB.
SEB Bulletin, July 2003.
Book Chapters
- Daniel MacLean (2012) Big data in a small place. A case study in scalable lightweight core-support” Invited book chapterFree and Open Source Software in Applied Life Science and Industry: Practical Solutions to Common Problems Eds Lee Harland and Mark Forster, BioHealthcare Publishing.
- Walshaw J, Etherington G and MacLean D (2011) Next-Generation Sequencing Approaches to Metagenomics In D Marco (ed) Metagenomics,Caister Academic Press, UK
- MacLean D and Studholme DJ (2009) Bioinformatics aspects of high-throughput sequencing. In RW Jackson (ed),
Plant Pathogenic Bacteria: Genomics and Molecular Biology, Caister Academic Press, UK
Talks
- MacLean D, Big Data in Small Places, Bio-IT World, Hannover, Germany, 2011
- MacLean D, Squeezing Big Data into a Small Organization, Eagle Genomics Symposium,
Babraham, UK, 2011
- MacLean D, Finding Resistance-Linked SNPs in Potato with Illumina Data. ICRISAT, India, 2009
- MacLean D, Keystone Symposium on Plant Responses to Abiotic Stress. System Level Response to Abiotic Stresses in Arabidopsis Keystone Symposia, Copper Mountain, CO, USA, 2006
- MacLean D, Society for Experimental Biology Meeting 2003, Examining chloroplast genome gene expression with a custom microarray. Transcriptomics Session, Southampton, UK, 2003.
- MacLean D, Plastid Preview 2002. Microarray analysis of plastid transcripts. Leicester, UK, 2002
Posters
- MacLean D gee_fu: an extensible Ruby-on-Rails database and web-service application for delivering HTGS data
VizBi: Visualising Biological Information, EMBL, Heidelberg, Germany, 2010
- MacLean D and Jones AME. PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
Proteomics Day, John Innes Centre, UK, 2009
- MacLean D, Yelina N, Havecker E, Heimstadt S, Studholme DJ and Baulcombe DC. sRNAs regulate each other in large complex networks.
International Conference on Systems Biology, Gothenburg, Sweden, 2008.
- Kemen E, Studholme DJ, MacLean D and Jones DG. Identification of Novel Effectors from Albugo candida using Solexa sequencing technologies.
Keystone Symposia, Keystone, CO, USA, 2008.
- Lewsey M, MacLean D and Carr J. RNA silencing in SA induced defence.
Keystone Symposia, Keystone, CO, USA, 2008.
- MacLean D and Rhee SY. System Level Response to Abiotic Stresses in Arabidopsis
Keystone Symposia, Copper Mountain, CO, USA, 2006.
