Dan MacLean
Support Staff
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
2009
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
2008
