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

G-Anchor: a novel approach for whole-genome comparative mapping utilising evolutionary conserved DNA sequencesLenis, V. P., Swain, M. & Larkin, D. M. 2018 In : GigaScience.
The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulation transcription, translation and stem cell activitiesGeyer, K., Munshi, S. E., Vickers, M., Squance, M., Wilkinson, T., Berrar, D., Chaparro, C., Swain, M. & Hoffmann, K. 2018 In : International Journal for Parasitology: Drugs and Drug Resistance.8, 2, p. 213-22210 p.
Transcriptional changes when Myxococcus xanthus preys on Escherichia coli suggest myxobacterial predators are consititutively toxic but regulate their feedingLivingstone, P., Millard, A., Swain, M. T. & Whitworth, D. E. 2018 In : Microbial Genomics. 152
Whole genome analysis of a schistosomiasis-transmitting freshwater snailAdema, 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-J., Yoshino, T. P., Yusuf, M., Zhang, S-M., Zhao, M. & Wilson, R. K. 2017 In : Nature Communications.8, p. 15451 15451 (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 mansoniGeyer, 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 In : PLoS Neglected Tropical Diseases.11, 5, e0005246
Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe setDamas, J., O'connor, R., Farré, M., Lenis, V., Martell, H., Mandawala, A., Fowler, K., Joseph, S., Swain, M., Griffin, D. & Larkin, D. M. 2016 In : Genome Research.27, p. 875-884
MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteinsKara, A., Vickers, M., Swain, M., Whitworth, D. & Fernandez-Fuentes, N. 2016 In : Bioinformatics.32, 21, p. 3339-33413 p.
Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltatorO'Grady, J. F., Hoelters, L. S., Swain, M. & Wilcockson, D. 2016 In : PeerJ. e2555
MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networksMizeranschi, A. E., Swain, M. T., Scona, R., Fazilleau, Q., Bosak, B., Piontek, T., Kopta, P., Thompson, P. & Dubitzky, W. 2016 In : Future Generation Computer Systems.63, p. 1-14
De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifoliaMora-Ortiz, M., Swain, M., Vickers, M., Hegarty, M., Kelly, R., Smith, L. & Skot, L. 2016 In : BMC Genomics.17, 13 p., 756
DISMISS: MeDIP-seq: High-throughput sequencingNiazi, U., Geyer, K., Vickers, M., Hoffmann, K. & Swain, M. 2016
DISMISS: detection of stranded methylation in MeDIP-Seq dataNiazi, U., Geyer, K. K., Vickers, M. J., Hoffmann, K. & Swain, M. 2016 In : BMC Bioinformatics.17, 295
Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvementde Vega, J., Ayling, S., Hegarty, M. J., Kudrna, D., Goicoechea, J. L., Ergon, Å., Rognli, O-A., 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 In : Scientific Reports.5, 17394
Epigenetic regulation of sex ratios may explain natural variation in self-fertilization ratesEllison, 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 In : Proceedings of the Royal Society B: Biological Sciences.282, 1819, p. 1900
Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoniNowacki, 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 In : Journal of Extracellular Vesicles.4, 28665
Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samplesHadfield, 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 In : BMC Genomics.16, 650
Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictorKara, A., Vickers, M., Swain, M., Whitworth, D. E. & Fernandez-Fuentes, N. 2015 In : BMC Bioinformatics.16, 1, 297
Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxinsHargreaves, A., Swain, M. T., Hegarty, M. J., Darren, L. & John, M. 2014 In : Genome Biology and Evolution.6, 8, p. 2088-20957 p.
De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identificationYates, 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 In : BMC Genomics.15, p. 45315 p.
Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasisSwain, M. T. 2014 In : Science.345, 6193, p. 380-386 7 p.
Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitansBrelsfoard, C., Tsiamis, G., Falchetto, M., Gomulski, L., Telleria, E., Alam, U., Doudoumis, V., Scolari, F., Benoit, J., Swain, M. T., Takac, P., Malacrida, A., Bourtzis, K. & Aksoy, S. 2014 In : PLoS Neglected Tropical Diseases.8, 4, e2728
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas functionMully, J. F., Hargreaves, A., Hegarty, M., Heller, R. S. & Swain, M. 2014 In : BMC Genomics.15, 1074
Metaphylogenomic and Potential Functionality of the Limpet Patella pellucida’s Gastrointestinal Tract MicrobiomeDudek, M., Adams, J., Swain, M., Hegarty, M., Huws, S. & Gallagher, J. 2014 In : International Journal of Molecular Sciences.15, 10, p. 18819-18839
Testing the Toxicofera: Comparative transcriptomics casts doubt on the single, early evolution of the reptile venom systemHargreaves, A., Swain, M. T., Darren, L. & John, M. 2014 In : Toxicon.92, p. 140-15617 p.
Exploiting a fast neutron mutant genetic resource in Pisum sativum L. (pea) for functional genomicsDomoney, 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 In : Functional Plant Biology.40, 12, p. 1261-12709 p.
A metagenomic snapshot of taxonomic and functional diversity in an Alpine glacier cryoconite ecosystem: Alpine cryoconite metagenomeEdwards, A., Pachebat, J. A., Swain, M. T., Hegarty, M. J., Hodson, A. J., Irvine-Fynn, T. D., Edwards Rassner, S. M. & Sattler, B. 2013 In : Environmental Research Letters.8, 3, 035003
Fast Comparison of Microbial Genomes Using the Chaos Games Representation for Metagenomic ApplicationsSwain, M. 2013 In : Procedia Computer Science.18, p. 1372-13819 p.
A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigsSwain, M. T., Tsai, I. J., Assefa, S. A., Newbold, C., Berriman, M. & Otto, T. D. 2012 In : Nature Protocols.7, p. 1260–1284
A Topology-Aware Evolutionary Algorithm for Reverse-Engineering Gene Regulatory NetworksSwain, M., Coti, C., Mandel, J. & Dubtizky, W. 2011 Large-Scale Computing Techniques for Complex System Simulations.Wiley, p. 141-16219 p. (Large-Scale Computing Techniques for Complex System Simulations)
Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discoverySwain, M. T., Larkin, D. M., Caffrey, C. R., Davies, S. J., Loukas, A., Skelly, P. J. & Hoffmann, K. F. 2011 In : Trends in Parasitology.27, 12, p. 555-56410 p.
Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networksSwain, M. T., Mandel, J. & Dubitzky, W. 2010 In : BMC Bioinformatics.11, 459
A scheduling framework for large-scale, parallel, and topology-aware applicationsKravtsov, V., Bar, P., Carmeli, D., Schuster, A. & Swain, M. 2010 In : Journal of Parallel and Distributed Computing.70, 9, p. 983-99210 p.
P-found: Grid-enabling distributed repositories of protein folding and unfolding simulations for data miningSwain, M. T., Silva, C. G., Loureiro-Ferreira, N., Ostropytskyy, V., Brito, J., Riche, O., Stahl, F., Dubitzky, W. & Brito, R. M. M. 2010 In : Future Generation Computer Systems.26, 3, p. 424-43310 p.
Digging deep into the data mine with DataMiningGridStankovski, V., Swain, M., Kravtsov, V., Niessen, T., Wegener, D., Kindermann, J. & Dubitzky, W. 2008 In : IEEE Internet Computing.12, 6, p. 69-768 p.
Data Pre-Processing Using OGSA-DAISwain, M. T. & Hong, N. P. C. 2008 Data Mining in Grid Computing Environments. Dubitzky, W. (ed.). Wiley, p. 247-26115 p. (Data Mining Techniques in Grid Computing Environments)
Grid-enabling data mining applications with DataMiningGrid: An architectural perspectiveStankovski, V., Swain, M. T., Kravtsov, V., Niessen, T., Wegener, D., Kindermann, J. & Dubitzky, W. 2008 In : Future Generation Computer Systems.24, 4, p. 259-27921 p.