Dan MacLean

Support Specialist

Contact details

+44 (0)1603 450166
Email: Dan.MacLean@sainsbury-laboratory.ac.uk

Research interests

My role is to provide The Sainsbury Laboratory with cutting edge bioinformatics expertise and resources. Particular areas of expertise include genomics in particular assembly and alignment with high-throughput sequencing data, genetic polymorphism detection, homology search and automatic sequence annotation, transcriptomics (microarray and RNA-seq), statistical analysis, mathematical and systems-biology approaches to modelling and visualising data and large scale phosphoproteomics analysis. I also provide extensive training in bioinformatics from basic computer use and scripting for the new user up to discussion of new techniques and algorithms for working bioinformaticians. I maintain a small library of print and digital training resources and a busy calendar of training events much of which may be viewed online here.

My research can be divided into two complementary streams; tool and resource development and systems biology of plant and pathogen interactions.

I have developed a range of tools that were inspired by the needs of the research groups at The Sainsbury Laboratory, including the creation of tools for the delivery and visualisation of next-generation sequencing data, detection of phosphorylated sites in peptides, identification of sRNA loci in genomes. Allied to this I have created a 'toolkit' of modules and objects that can be used by all groups across the laboratory. All of these can be seen on my github page here. Currently in collaboration with Mario Caccamo's group at TGAC we are developing tools and methods for the detection of genetic polymorphisms from high-throughput sequencing data without a reference genome and visualisation of these within a draft assembly.

I have a background in molecular biology and bioinformatics with particular expertise in microarray analysis and statistics and systems and mathematical approaches to biological analyses of large datasets from my Ph.D and Post-Doctoral work at the University of Cambridge and the Carnegie Institution Department of Plant Biology at Stanford University.

Selected Publications

2012

  • MacLean D and Kamoun S “Big Data in Small Places” Nat Biotech, 30, 33–34
  • Ruby Biogems: pluggable software modules for the next generation. Raoul J.P. Bonnal et al Bioinformatics in press

 

2011

  • 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). G enome 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
  • MacLean D and Studholme DJ (2010) A Boolean model of the \emph{Pseudomonas syringae} hrp regulon predicts a tightly regulated system PLoS ONE, 5, e9101
  • 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
  • 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 phosphorylation site database. An update. Nucleic Acids Res. 38, 828-384.
  • 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.
  • 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
  • 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, 395
  • Jones 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
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