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Items: 21


Transcriptomic analysis of crustacean neuropeptide signaling during the moult cycle in the green shore crab, Carcinus maenas.

Oliphant A, Alexander JL, Swain MT, Webster SG, Wilcockson DC.

BMC Genomics. 2018 Sep 26;19(1):711. doi: 10.1186/s12864-018-5057-3.


Corrigendum to 'the anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities' [Int. J. Parasitol. Drugs and Drug Resist. 8 (2018) 213-222].

Geyer KK, Munshi SE, Vickers M, Squance M, Wilkinson TJ, Berrar D, Chaparro C, Swain MT, Hoffmann KF.

Int J Parasitol Drugs Drug Resist. 2018 Dec;8(3):493. doi: 10.1016/j.ijpddr.2018.07.002. Epub 2018 Jul 17. No abstract available.


The anti-fecundity effect of 5-azacytidine (5-AzaC) on Schistosoma mansoni is linked to dis-regulated transcription, translation and stem cell activities.

Geyer KK, Munshi SE, Vickers M, Squance M, Wilkinson TJ, Berrar D, Chaparro C, Swain MT, Hoffmann KF.

Int J Parasitol Drugs Drug Resist. 2018 Aug;8(2):213-222. doi: 10.1016/j.ijpddr.2018.03.006. Epub 2018 Apr 1. Erratum in: Int J Parasitol Drugs Drug Resist. 2018 Jul 17;:.


Transcriptional changes when Myxococcus xanthus preys on Escherichia coli suggest myxobacterial predators are constitutively toxic but regulate their feeding.

Livingstone PG, Millard AD, Swain MT, Whitworth DE.

Microb Genom. 2018 Jan 18. doi: 10.1099/mgen.0.000152. [Epub ahead of print]


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.

Geyer KK, Niazi UH, Duval D, Cosseau C, Tomlinson C, Chalmers IW, Swain MT, Cutress DJ, Bickham-Wright U, Munshi SE, Grunau C, Yoshino TP, Hoffmann KF.

PLoS Negl Trop Dis. 2017 May 16;11(5):e0005246. doi: 10.1371/journal.pntd.0005246. eCollection 2017 May.


Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set.

Damas J, O'Connor R, Farré M, Lenis VPE, Martell HJ, Mandawala A, Fowler K, Joseph S, Swain MT, Griffin DK, Larkin DM.

Genome Res. 2017 May;27(5):875-884. doi: 10.1101/gr.213660.116. Epub 2016 Nov 30.


Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator.

O'Grady JF, Hoelters LS, Swain MT, Wilcockson DC.

PeerJ. 2016 Oct 5;4:e2555. eCollection 2016.


De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia.

Mora-Ortiz M, Swain MT, Vickers MJ, Hegarty MJ, Kelly R, Smith LM, Skøt L.

BMC Genomics. 2016 Sep 26;17(1):756.


DISMISS: detection of stranded methylation in MeDIP-Seq data.

Niazi U, Geyer KK, Vickers MJ, Hoffmann KF, Swain MT.

BMC Bioinformatics. 2016 Jul 29;17(1):295. doi: 10.1186/s12859-016-1158-7.


Protein and small non-coding RNA-enriched extracellular vesicles are released by the pathogenic blood fluke Schistosoma mansoni.

Nowacki FC, Swain MT, Klychnikov OI, Niazi U, Ivens A, Quintana JF, Hensbergen PJ, Hokke CH, Buck AH, Hoffmann KF.

J Extracell Vesicles. 2015 Oct 5;4:28665. doi: 10.3402/jev.v4.28665. eCollection 2015.


Generation of whole genome sequences of new Cryptosporidium hominis and Cryptosporidium parvum isolates directly from stool samples.

Hadfield SJ, Pachebat JA, Swain MT, Robinson G, Cameron SJ, Alexander J, Hegarty MJ, Elwin K, Chalmers RM.

BMC Genomics. 2015 Aug 29;16:650. doi: 10.1186/s12864-015-1805-9.


Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function.

Mulley JF, Hargreaves AD, Hegarty MJ, Heller RS, Swain MT.

BMC Genomics. 2014 Dec 6;15:1074. doi: 10.1186/1471-2164-15-1074.


Testing the Toxicofera: comparative transcriptomics casts doubt on the single, early evolution of the reptile venom system.

Hargreaves AD, Swain MT, Logan DW, Mulley JF.

Toxicon. 2014 Dec 15;92:140-56. doi: 10.1016/j.toxicon.2014.10.004. Epub 2014 Oct 17.


Restriction and recruitment-gene duplication and the origin and evolution of snake venom toxins.

Hargreaves AD, Swain MT, Hegarty MJ, Logan DW, Mulley JF.

Genome Biol Evol. 2014 Aug;6(8):2088-95. doi: 10.1093/gbe/evu166.


De novo assembly of red clover transcriptome based on RNA-Seq data provides insight into drought response, gene discovery and marker identification.

Yates SA, Swain MT, Hegarty MJ, Chernukin I, Lowe M, Allison GG, Ruttink T, Abberton MT, Jenkins G, Skøt L.

BMC Genomics. 2014 Jun 9;15:453. doi: 10.1186/1471-2164-15-453.


A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD.

Nat Protoc. 2012 Jun 7;7(7):1260-84. doi: 10.1038/nprot.2012.068.


Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery.

Swain MT, Larkin DM, Caffrey CR, Davies SJ, Loukas A, Skelly PJ, Hoffmann KF.

Trends Parasitol. 2011 Dec;27(12):555-64. doi: 10.1016/ Epub 2011 Oct 23. Review.


Comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks.

Swain MT, Mandel JJ, Dubitzky W.

BMC Bioinformatics. 2010 Sep 14;11:459. doi: 10.1186/1471-2105-11-459.


Parametrization of Reversible Digitally Filtered Molecular Dynamics Simulations.

Wiley AP, Swain MT, Phillips SC, Essex JW, Edge CM.

J Chem Theory Comput. 2005 Jan;1(1):24-35. doi: 10.1021/ct049970t.


Modelling protein side-chain conformations using constraint logic programming.

Swain MT, Kemp GJ.

Comput Chem. 2001 Dec;26(1):85-95.


Self-concept and delinquency proneness.

Jones FR, Swain MT.

Adolescence. 1977 Winter;12(48):559-69.


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