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.

Mora-Ortiz, M., Swain, M., Vickers, M., Hegarty, M., Kelly, R., Smith, L., Skot, L. 2016. De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia. BMC Genomics 17 756 Cadair Niazi, U., Geyer, K.K., Vickers, M.J., Hoffmann, K., Swain, M. 2016. DISMISS: detection of stranded methylation in MeDIP-Seq data. BMC Bioinformatics 17 295 Cadair O'Grady, J.F., Hoelters, L.S., Swain, M., Wilcockson, D. 2016. Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator. PeerJ e2555 Cadair Kara, A., Vickers, M., Swain, M., Whitworth, D., Fernandez-Fuentes, N. 2016. MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins. Bioinformatics 32 (21) pp. 3339-3341. Mizeranschi, A.E., Swain, M.T., Scona, R., Fazilleau, Q., Bosak, B., Piontek, T., Kopta, P., Thompson, P., Dubitzky, W. 2016. MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks. Future Generation Computer Systems 63 pp. 1-14. Damas, J., O'connor, R., Farré, M., Lenis, V., Martell, H., Mandawala, A., Fowler, K., Joseph, S., Swain, M., Griffin, D., Larkin, D.M. 2016. Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set. Genome Research Cadair Ellison, A.R., Rodrigues Lopez, C.M., Morán, P., Breen, J., Swain, M., Megias, M., Hegarty, M., Wilkinson, M.J., Pawluk, R., Consuegra Del Olmo, S. 2015. 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. Hadfield, S.J., Pachebat, J.A., Swain, M.T., Robinson, G., Cameron, S.J.S., Alexander, J., Hegarty, M.J., Elwin, K., Chalmers, R.M. 2015. Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples. BMC Genomics 16 650 Cadair