Dr Martin Swain PhD

Dr Martin Swain

Senior Lecturer

Contact Details

Teaching

Module Coordinator
Tutor

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.

Research

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.

Publications

2017

Adema, C.M., Hillier, L.W., Jones, C.S., Loker, E.S., Knight, M., Minx, P., Oliveira, G., Raghavan, N., Shedlock, A., do Amaral, L.R., Arican-Goktas, H.D., Assis, J.G., Baba, E.H., Baron, O.L., Bayne, C.J., Bickham-Wright, U., Biggar, K.K., Blouin, M., Bonning, B.C., Botka, C., Bridger, J.M., Buckley, K.M., Buddenborg, S.K., Lima Caldeira, R., Carleton, J., Carvalho, O.S., Castillo, M.G., Chalmers, I.W., Christensens, M., Clifton, S., Cosseau, C., Coustau, C., Cripps, R.M., Cuesta-Astroz, Y., Cummins, S.F., Di Stephano, L., Dinguirard, N., Duval, D., Emrich, S., Feschotte, C., Feyereisen, R., Fitzgerald, P., Fronick, C., Fulton, L., Galinier, R., Gava, S.G., Geusz, M., Geyer, K.K., Giraldo-Calderón, G.I., de Souza Gomes, M., Gordy, M.A., Gourbal, B., Grunau, C., Hanington, P.C., Hoffmann, K.F., Hughes, D., Humphries, J., Jackson, D.J., Jannotti-Passos, L.K., De Jesus Jeremias, W., Jobling, S., Kamel, B., Kapusta, A., Kaur, S., Koene, J.M., Kohn, A.B., Lawson, D., Lawton, S.P., Liang, D., Limpanont, Y., Liu, S., Lockyer, A.E., Lovato, T.L., Ludolf, F., Magrini, V., Mcmanus, D.P., Medina, M., Misra, M., Mitta, G., Mkoji, G.M., Montague, M.J., Montelongo, C., Moroz, L.L., Munoz-Torres, M.C., Niazi, U., Noble, L.R., Oliveira, F.S., Pais, F.S., Papenfuss, A.T., Peace, R., Pena, J.J., Pila, E.A., Quelais, T., Raney, B.J., Rast, J.P., Rollinson, D., Rosse, I.C., Rotgans, B., Routledge, E.J., Ryan, K.M., Scholte, L.L.S., Storey, K.B., Swain, M., Tennessen, J.A., Tomlinson, C., Trujillo, D.L., Volpi, E.V., Walker, A.J., Wang, T., Wannaporn, I., Warren, W.C., Wu, X., Yoshino, T.P., Yusuf, M., Zhang, S., Zhao, M., Wilson, R.K. 2017. Whole genome analysis of a schistosomiasis-transmitting freshwater snail. Nature Communications 8 15451 (2017) pp. 15451. 10.1038/ncomms15451 Other Cadair

Geyer, K., Niazi, U., Duval, D., Cosseau, C., Tomlinson, C., Chalmers, I., Swain, M., Cutress, D., Bickham-Wright, U., Munshi, S.E., Grunau, C., Yoshino, T.P., Hoffmann, K. 2017. 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 Cadair

2016

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 27 pp. 875-884. 10.1101/gr.213660.116 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. 10.1093/bioinformatics/btw403 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 10.7717/peerj.2555 Cadair

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. 10.1016/j.future.2016.04.002 Cadair

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 10.1186/s12864-016-3083-6 Cadair

Niazi, U., Geyer, K., Vickers, M., Hoffmann, K., Swain, M. 2016. DISMISS: MeDIP-seq: High-throughput sequencing. Other

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 10.1186/s12859-016-1158-7 Cadair

2015

de Vega, J., Ayling, S., Hegarty, M.J., Kudrna, D., Goicoechea, J.L., Ergon, Å., Rognli, O., Jones, C., Swain, M.T., Geurts, R., Lang, C., Mayer, K.F.X., Rössner, S., Yates, S.A., Webb, K.J., Donnison, I.S., Oldroyd, G.E.D., Wing, R., Caccamo, M., Powell, W., Abberton, M.T., Skot, L. 2015. Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement. Scientific Reports 5 17394 10.1038/srep17394

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. 10.1098/rspb.2015.1900 Cadair

Nowacki, F.C., Swain, M.T., Klychnikov, O.I., Niazi, U., Ivens, A., Quintana, J.F., Hensbergen, P.J., Hokke, C.H., Buck, A.H., Hoffmann, K.F. 2015. Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni. Journal of Extracellular Vesicles 4 28665 10.3402/jev.v4.28665 Cadair

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 10.1186/s12864-015-1805-9 Cadair

Kara, A., Vickers, M., Swain, M., Whitworth, D.E., Fernandez-Fuentes, N. 2015. Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. BMC Bioinformatics 16 (1) 297 10.1186/s12859-015-0741-7 Cadair

2014

Brelsfoard, C., Tsiamis, G., Falchetto, M., Gomulski, L., Telleria, E., Alam, U., Doudoumis, V., Scolari, F., Benoit, J., Swain, M.T., Malacrida, A., Bourtzis, K., Aksoy, S.Takac, P. 2014. Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans. PLoS Neglected Tropical Diseases 8 (4) e2728 10.1371/journal.pntd.0002728 Cadair

Mully, J.F., Hargreaves, A., Hegarty, M., Heller, R.S., Swain, M. 2014. 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 Cadair

Dudek, M., Adams, J., Swain, M., Hegarty, M., Huws, S., Gallagher, J. 2014. 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 Cadair

Hargreaves, A., Swain, M.T., Darren, L., John, M. 2014. Testing the Toxicofera: Comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system. Toxicon 92 pp. 140-156. 10.1016/j.toxicon.2014.10.004 Cadair

Hargreaves, A., Swain, M.T., Hegarty, M.J., Darren, L., John, M. 2014. Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins. Genome Biology and Evolution 6 (8) pp. 2088-2095. 10.1093/gbe/evu166 Other Cadair

Yates, S.A., Swain, M.T., Hegarty, M.J., Chernukin, I., Lowe, M.J., Allison, G.G., Ruttlink, T., Abberton, M.T., Jenkins, G., Skøt, L. 2014. 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 Cadair

Swain, M.T. 2014. Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis. Science 345 (6193) pp. 380-386 . 10.1126/science.1249656 Cadair

2013

Domoney, C., Knox, M., Moreau, C., Ambrose, M., Palmer, S., Smith, P., Christodoulou, V., Isaac, P., Hegarty, M.J., Blackmore, T.M., Swain, M.T., Ellis, N. 2013. Exploiting a fast neutron mutant genetic resource in Pisum sativum L. (pea) for functional genomics. Functional Plant Biology 40 (12) pp. 1261-1270. 10.1071/FP13147 Cadair

Edwards, A., Pachebat, J.A., Swain, M.T., Hegarty, M.J., Hodson, A.J., Irvine-Fynn, T.D., Edwards Rassner, S.M., Sattler, B. 2013. 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 Cadair

Swain, M. 2013. 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 Cadair

2012

Swain, M.T., Tsai, I.J., Assefa, S.A., Newbold, C., Berriman, M., Otto, T.D. 2012. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nature Protocols 7 pp. 1260–1284. 10.1038/nprot.2012.068 Cadair

2011

Swain, M., Coti, C., Mandel, J., Dubtizky, W. 2011. 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. Cadair

Swain, M.T., Larkin, D.M., Caffrey, C.R., Davies, S.J., Loukas, A., Skelly, P.J., Hoffmann, K.F. 2011. Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery. Trends in Parasitology 27 (12) pp. 555-564. 10.1016/j.pt.2011.09.003 Cadair

2010

Swain, M.T., Mandel, J., Dubitzky, W. 2010. Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks. BMC Bioinformatics 11 459 10.1186/1471-2105-11-459 Cadair

Kravtsov, V., Bar, P., Carmeli, D., Schuster, A., Swain, M. 2010. A scheduling framework for large-scale, parallel, and topology-aware applications. Journal of Parallel and Distributed Computing 70 (9) pp. 983-992. 10.1016/j.jpdc.2010.05.001 Cadair

Swain, M.T., Silva, C.G., Loureiro-Ferreira, N., Ostropytskyy, V., Brito, J., Riche, O., Stahl, F., Dubitzky, W., Brito, R.M. 2010. 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 Cadair

2008

Stankovski, V., Swain, M., Kravtsov, V., Niessen, T., Wegener, D., Kindermann, J., Dubitzky, W. 2008. Digging deep into the data mine with DataMiningGrid. IEEE Internet Computing 12 (6) pp. 69-76. 10.1109/MIC.2008.122 Cadair

Swain, M.T., Hong, N.P.C. 2008. Data Pre-Processing Using OGSA-DAI. In W. Dubitzky. (ed) Data Mining in Grid Computing Environments. Data Mining Techniques in Grid Computing Environments Wiley pp. 247-261. Cadair

Stankovski, V., Swain, M.T., Kravtsov, V., Niessen, T., Wegener, D., Kindermann, J., Dubitzky, W. 2008. Grid-enabling data mining applications with DataMiningGrid: An architectural perspective. Future Generation Computer Systems 24 (4) pp. 259-279. 10.1016/j.future.2007.05.004 Cadair