Dr Martin Swain PhD
An introduction to Linux and Bioinformatics for PGM1520; Study and Communication Skills, BR12410; Molecular Laboratory Skills, BR12210; Research Methods, Dissertation, and a few lectures to other modules.
I am interested in analysing large biological data sets from a variety of organisms, including plants, animals, parasites and microbes. Some recent and current projects include the sequencing of the tsetse fly and biomphalaria genomes, snake venom transcriptome analyses, methylation in flatworms, microRNAs, whole genome comparisons (of sheep and schistosomes), metagenomics of limpet guts and cryoconite, red clover transcriptomics, and the identification of neuropeptide receptors and functions in arthropods.
My other interests include the development of infrastructure and new software methodolgy for the handling and analysis of large data sets in bioinformatics. This involves high performance computing, technologies for data integration and data mining, and the development of new algorithms to analyse high-throughput sequencing data sets.
The Biomphalaria glabrata DNA methylation machinery displays spatial tissue expression, is differentially active in distinct snail populations and is modulated by interactions with Schistosoma mansoni. PLoS Neglected Tropical Diseases 11 (5) e0005246 10.1371/journal.pntd.0005246 Cadair2017.
DISMISS: MeDIP-seq: High-throughput sequencing. Other2016.
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports 5 17394 10.1038/srep173942015.
Epigenetic regulation of sex ratios may explain natural variation in self-fertilization rates. Proceedings of the Royal Society B: Biological Sciences 282 (1819) pp. 1900. 10.1098/rspb.2015.1900 Cadair2015.
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function. BMC Genomics 15 1074 10.1186/1471-2164-15-1074 Cadair2014.
Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract Microbiome. International Journal of Molecular Sciences 15 (10) pp. 18819-18839. 10.3390/ijms151018819 Cadair2014.
De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification. BMC Genomics 15 pp. 453. 10.1186/1471-2164-15-453 Cadair2014.
A metagenomic snapshot of taxonomic and functional diversity in an Alpine glacier cryoconite ecosystem: Alpine cryoconite metagenome. Environmental Research Letters 8 (3) 035003 10.1088/1748-9326/8/3/035003 Cadair2013.
Fast Comparison of Microbial Genomes Using the Chaos Games Representation for Metagenomic Applications. Procedia Computer Science 18 2013 International Conference on Computational Science. pp. 1372-1381. 10.1016/j.procs.2013.05.304 Other Cadair2013.
A Topology-Aware Evolutionary Algorithm for Reverse-Engineering Gene Regulatory Networks. Large-Scale Computing Techniques for Complex System Simulations. Large-Scale Computing Techniques for Complex System Simulations Wiley pp. 141-162. Cadair2011.
P-found: Grid-enabling distributed repositories of protein folding and unfolding simulations for data mining. Future Generation Computer Systems 26 (3) pp. 424-433. 10.1016/j.future.2009.08.008 Cadair2010.
Data Pre-Processing Using OGSA-DAI. In (ed) Data Mining in Grid Computing Environments. Data Mining Techniques in Grid Computing Environments Wiley pp. 247-261. Cadair2008.