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

Adema, CM, Hillier, LW, Jones, CS, Loker, ES, Knight, M, Minx, P, Oliveira, G, Raghavan, N, Shedlock, A, do Amaral, LR, Arican-Goktas, HD, Assis, JG, Baba, EH, Baron, OL, Bayne, CJ, Bickham-Wright, U, Biggar, KK, Blouin, M, Bonning, BC, Botka, C, Bridger, JM, Buckley, KM, Buddenborg, SK, Lima Caldeira, R, Carleton, J, Carvalho, OS, Castillo, MG, Chalmers, IW, Christensens, M, Clifton, S, Cosseau, C, Coustau, C, Cripps, RM, Cuesta-Astroz, Y, Cummins, SF, Di Stephano, L, Dinguirard, N, Duval, D, Emrich, S, Feschotte, C, Feyereisen, R, Fitzgerald, P, Fronick, C, Fulton, L, Galinier, R, Gava, SG, Geusz, M, Geyer, KK, Giraldo-Calderón, GI, de Souza Gomes, M, Gordy, MA, Gourbal, B, Grunau, C, Hanington, PC, Hoffmann, KF, Hughes, D, Humphries, J, Jackson, DJ, Jannotti-Passos, LK, De Jesus Jeremias, W, Jobling, S, Kamel, B, Kapusta, A, Kaur, S, Koene, JM, Kohn, AB, Lawson, D, Lawton, SP, Liang, D, Limpanont, Y, Liu, S, Lockyer, AE, Lovato, TL, Ludolf, F, Magrini, V, Mcmanus, DP, Medina, M, Misra, M, Mitta, G, Mkoji, GM, Montague, MJ, Montelongo, C, Moroz, LL, Munoz-Torres, MC, Niazi, U, Noble, LR, Oliveira, FS, Pais, FS, Papenfuss, AT, Peace, R, Pena, JJ, Pila, EA, Quelais, T, Raney, BJ, Rast, JP, Rollinson, D, Rosse, IC, Rotgans, B, Routledge, EJ, Ryan, KM, Scholte, LLS, Storey, KB, Swain, M, Tennessen, JA, Tomlinson, C, Trujillo, DL, Volpi, EV, Walker, AJ, Wang, T, Wannaporn, I, Warren, WC, Wu, X-J, Yoshino, TP, Yusuf, M, Zhang, S-M, Zhao, M & Wilson, RK 2017, 'Whole genome analysis of a schistosomiasis-transmitting freshwater snail' Nature Communications, vol 8, 15451 (2017), pp. 15451. DOI: 10.1038/ncomms15451
Geyer, K, Niazi, U, Duval, D, Cosseau, C, Tomlinson, C, Chalmers, I, Swain, M, Cutress, D, Bickham-Wright, U, Munshi, SE, Grunau, C, Yoshino, TP & 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, vol 11, no. 5, e0005246. DOI: 10.1371/journal.pntd.0005246
Damas, J, O'connor, R, Farré, M, Lenis, V, Martell, H, Mandawala, A, Fowler, K, Joseph, S, Swain, M, Griffin, D & Larkin, DM 2016, 'Upgrading short read animal genome assemblies to chromosome level using comparative genomics and a universal probe set' Genome Research, vol 27, pp. 875-884. DOI: 10.1101/gr.213660.116
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, vol 32, no. 21, pp. 3339-3341. DOI: 10.1093/bioinformatics/btw403
O'Grady, JF, Hoelters, LS, Swain, M & Wilcockson, D 2016, 'Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator' PeerJ. DOI: 10.7717/peerj.2555
Mizeranschi, AE, Swain, MT, 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, vol 63, pp. 1-14. DOI: 10.1016/j.future.2016.04.002
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, vol 17, 756. DOI: 10.1186/s12864-016-3083-6
Niazi, U, Geyer, K, Vickers, M, Hoffmann, K & Swain, M, DISMISS: MeDIP-seq: High-throughput sequencing, 2016, Software, OMICtools.
Niazi, U, Geyer, KK, Vickers, MJ, Hoffmann, K & Swain, M 2016, 'DISMISS: detection of stranded methylation in MeDIP-Seq data' BMC Bioinformatics, vol 17, 295. DOI: 10.1186/s12859-016-1158-7
de Vega, J, Ayling, S, Hegarty, MJ, Kudrna, D, Goicoechea, JL, Ergon, Å, Rognli, O-A, Jones, C, Swain, MT, Geurts, R, Lang, C, Mayer, KFX, Rössner, S, Yates, SA, Webb, KJ, Donnison, IS, Oldroyd, GED, Wing, R, Caccamo, M, Powell, W, Abberton, MT & Skot, L 2015, 'Red clover (Trifolium pratense L.) draft genome provides a platform for trait improvement' Scientific Reports, vol 5, 17394 . DOI: 10.1038/srep17394
Ellison, AR, Rodrigues Lopez, CM, Morán, P, Breen, J, Swain, M, Megias, M, Hegarty, M, Wilkinson, MJ, 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, vol 282, no. 1819, pp. 1900. DOI: 10.1098/rspb.2015.1900
Nowacki, FC, Swain, MT, Klychnikov, OI, Niazi, U, Ivens, A, Quintana, JF, Hensbergen, PJ, Hokke, CH, Buck, AH & Hoffmann, KF 2015, 'Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni' Journal of Extracellular Vesicles, vol 4, 28665. DOI: 10.3402/jev.v4.28665
Hadfield, SJ, Pachebat, JA, Swain, MT, Robinson, G, Cameron, SJS, Alexander, J, Hegarty, MJ, Elwin, K & Chalmers, RM 2015, 'Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples' BMC Genomics, vol 16, 650. DOI: 10.1186/s12864-015-1805-9
Kara, A, Vickers, M, Swain, M, Whitworth, DE & Fernandez-Fuentes, N 2015, 'Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor' BMC Bioinformatics, vol 16, no. 1, 297. DOI: 10.1186/s12859-015-0741-7
Mully, JF, Hargreaves, A, Hegarty, M, Heller, RS & 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, vol 15, 1074. DOI: 10.1186/1471-2164-15-1074
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, vol 15, no. 10, pp. 18819-18839. DOI: 10.3390/ijms151018819
Hargreaves, A, Swain, MT, Darren, L & John, M 2014, 'Testing the Toxicofera: Comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system' Toxicon, vol 92, pp. 140-156. DOI: 10.1016/j.toxicon.2014.10.004
Hargreaves, A, Swain, MT, Hegarty, MJ, Darren, L & John, M 2014, 'Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins' Genome Biology and Evolution, vol 6, no. 8, pp. 2088-2095. DOI: 10.1093/gbe/evu166
Yates, SA, Swain, MT, Hegarty, MJ, Chernukin, I, Lowe, MJ, Allison, GG, Ruttlink, T, Abberton, MT, 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, vol 15, pp. 453. DOI: 10.1186/1471-2164-15-453
Swain, MT 2014, 'Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis' Science, vol 345, no. 6193, pp. 380-386 . DOI: 10.1126/science.1249656
Brelsfoard, C, Tsiamis, G, Falchetto, M, Gomulski, L, Telleria, E, Alam, U, Doudoumis, V, Scolari, F, Benoit, J, Swain, MT, Takac, P, Malacrida, A, Bourtzis, K & Aksoy, S 2014, 'Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans' PLoS Neglected Tropical Diseases, vol 8, no. 4, e2728. DOI: 10.1371/journal.pntd.0002728
Domoney, C, Knox, M, Moreau, C, Ambrose, M, Palmer, S, Smith, P, Christodoulou, V, Isaac, P, Hegarty, MJ, Blackmore, TM, Swain, MT & Ellis, N 2013, 'Exploiting a fast neutron mutant genetic resource in Pisum sativum L. (pea) for functional genomics' Functional Plant Biology, vol 40, no. 12, pp. 1261-1270. DOI: 10.1071/FP13147
Edwards, A, Pachebat, JA, Swain, MT, Hegarty, MJ, Hodson, AJ, Irvine-Fynn, TD, Edwards Rassner, SM & Sattler, B 2013, 'A metagenomic snapshot of taxonomic and functional diversity in an Alpine glacier cryoconite ecosystem: Alpine cryoconite metagenome' Environmental Research Letters, vol 8, no. 3, 035003. DOI: 10.1088/1748-9326/8/3/035003
Swain, M 2013, 'Fast Comparison of Microbial Genomes Using the Chaos Games Representation for Metagenomic Applications' Procedia Computer Science, vol 18, pp. 1372-1381. DOI: 10.1016/j.procs.2013.05.304
Swain, MT, Tsai, IJ, Assefa, SA, Newbold, C, Berriman, M & Otto, TD 2012, 'A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs' Nature Protocols, vol 7, pp. 1260–1284. DOI: 10.1038/nprot.2012.068
Swain, M, Coti, C, Mandel, J & Dubtizky, W 2011, A Topology-Aware Evolutionary Algorithm for Reverse-Engineering Gene Regulatory Networks. in Large-Scale Computing Techniques for Complex System Simulations. Large-Scale Computing Techniques for Complex System Simulations, Wiley, pp. 141-162.
Swain, MT, Larkin, DM, Caffrey, CR, Davies, SJ, Loukas, A, Skelly, PJ & Hoffmann, KF 2011, 'Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery' Trends in Parasitology, vol 27, no. 12, pp. 555-564. DOI: 10.1016/j.pt.2011.09.003
Swain, MT, Mandel, J & Dubitzky, W 2010, 'Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks' BMC Bioinformatics, vol 11, 459. DOI: 10.1186/1471-2105-11-459
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, vol 70, no. 9, pp. 983-992. DOI: 10.1016/j.jpdc.2010.05.001
Swain, MT, Silva, CG, Loureiro-Ferreira, N, Ostropytskyy, V, Brito, J, Riche, O, Stahl, F, Dubitzky, W & Brito, RMM 2010, 'P-found: Grid-enabling distributed repositories of protein folding and unfolding simulations for data mining' Future Generation Computer Systems, vol 26, no. 3, pp. 424-433. DOI: 10.1016/j.future.2009.08.008
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, vol 12, no. 6, pp. 69-76. DOI: 10.1109/MIC.2008.122
Swain, MT & Hong, NPC 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.
Stankovski, V, Swain, MT, 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, vol 24, no. 4, pp. 259-279. DOI: 10.1016/j.future.2007.05.004