Mathematics Department, NUI, Galway

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Seoighe C, Gehring C.
Heritability in the efficiency of nonsense-mediated mRNA decay in humans.
PLoS One. 2010 Jul 21;5(7):e11657.
Gaujoux R, Seoighe C.
A flexible R package for nonnegative matrix factorization.
BMC Bioinformatics. 2010 Jul 2;11:367.
de Wit E, Delport W, Rugamika CE, Meintjes A, Mör M, van Helden PD, Seoighe C, Hoal EG.
Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape.
Hum Genet. 2010 Aug;128(2):145-53.
Lacerda M, Scheffler K, Seoighe C.
Epitope discovery with phylogenetic hidden Markov models.
Mol Biol Evol. 2010 May;27(5):1212-20.
Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure.
Treurnicht FK, Seoighe C, Martin DP, Wood N, Abrahams MR, Rosa Dde A, Bredell H, Woodman Z, Hide W, Mlisana K, Karim SA, Gray CM, Williamson C.
Virology. 2010 Jan 20;396(2):213-25.
Ngandu NK, Seoighe C, Scheffler K.
Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission.
Virol J. 2009 Oct 10;6:164.
Illing N, Klak C, Johnson C, Brito D, Negrao N, Baine F, van Kets V, Ramchurn KR, Seoighe C, Roden L.
Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae.
Dev Genes Evol. 2009 Jun;219(6):331-8.
Wood N, Bhattacharya T, Keele BF, Giorgi E, Liu M, Gaschen B, Daniels M, Ferrari G, Haynes BF, McMichael A, Shaw GM, Hahn BH, Korber B, Seoighe C.
HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.
PLoS Pathog. 2009 May;5(5):e1000414.
Berman P, Collins M, Baumgarten I, Seoighe C, Jennings CL, Joffe Y, Lambert EV, Levitt NS, Faulenbach MV, Kahn SE, Goedecke JH.
Association between the 4 bp proinsulin gene insertion polymorphism (IVS-69) and body composition in black South African women.
Obesity (Silver Spring). 2009 Jun;17(6):1298-300.
Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C; CAPRISA Acute Infection Study Team; Center for HIV-AIDS Vaccine Immunology Consortium.
Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants.
J Virol. 2009 Apr;83(8):3556-67. Erratum in: J Virol. 2009 Jul;83(13):6974.
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences.
Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C.
Virol J. 2008 Dec 23;5(1):160
Delport W, Scheffler K, Seoighe C.
Frequent toggling between alternative amino acids is driven by selection in HIV-1
PLoS Pathog. 2008 Dec;4(12)
Delport W, Scheffler K, Seoighe C.
Models of coding sequence evolution.
Brief Bioinform. 2008 Oct 29
Gray CM, Mlotshwa M, Riou C, Mathebula T, de Assis Rosa D, Mashishi T, Seoighe C, Ngandu N, van Loggerenberg F, Morris L, Mlisana K, Williamson C, Karim SA; on behalf of the CAPRISA 002 Acute Infection Study Team.
Human Immunodeficiency Virus-Specific Gamma Interferon Enzyme-Linked Immunospot Assay Responses Targeting Specific Regions of the Proteome during Primary Subtype C Infection Are Poor Predictors of the Course of Viremia and Set Point.
J Virol. 2009 Jan;83(1):470-478
Nembaware V, Lupindo B, Schouest K, Spillane K, Scheffler K, Seoighe C
Genome-wide survey of allele-specific splicing in humans
BMC Genomics BMC Genomics. 2008 Jun 2;9(1):265.
Keele BF, Giorgi EE, Salazar-Gonzalez, JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping L, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA. Kilby M, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM (2008, in press)
Identification and Characterization of Transmitted and Early Founder Virus Envelopes in Primary HIV-1 Infection.
Proc Natl Acad Sci U S A. 2008 May 27;105(21):7552-7
D.R. Chopera, Z. Woodman, K. Mlisana, M. Mlotshwa, D.P. Martin, C. Seoighe,
F. Treurnicht, D. Assis de Rosa, W. Hide, S Abdool Karim, C.M. Gray, C.
Williamson and the CAPRISA 002 study team
Transmission of HIV-1 CTL escape variants provides HLA-mismatched
recipients with a survival advantage
PLoS Pathogens (In Press)
Poulter GL, Rubin DL, Altman RB, Seoighe C. MScanner: a classifier for retrieving Medline citations.
BMC Bioinformatics. 2008 Feb 19;9(1):108
Schwegmann A, Guler R, Cutler AJ, Arendse B, Horsnell WG, Flemming A, Kottmann AH, Ryan G, Hide W, Leitges M, Seoighe C, Brombacher F. Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes. Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16251-6.
Ngandu, N., Bredell, H., Gray, C.M., Williamson, C., Seoighe, C. & the HIVNET028 Study Team CTL response to HIV-1 subtype C is poorly predicted by known epitope motifs,
AIDS Research and Human Retroviruses 2007 Aug;23(8):1033-41.
Seoighe C, Ketwaroo F, Pillay V, Scheffler K, Wood N, Duffet R, Zvelebil M, Martinson N, McIntyre J, Morris L, Hide W. A Model of Directional Selection Applied to the Evolution of Drug Resistance in HIV-1.
Mol Biol Evol. 2007 Feb 14;
Bredenkamp N, Seoighe C, Illing N. (2007)
Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation.
Dev. Genes Evol. 2007 Jan 27;
Seoighe C, Nembaware V, Scheffler K. (2006)
Maximum likelihood inference of imprinting and allele-specific expression from EST data.
Bioinformatics. Dec 15;22(24):3032-9
Scheffler K, Martin DP, Seoighe C (2006)
Robust inference of positive selection from recombining coding sequences.
Bioinformatics. 2006 Oct 15;22(20):2493-9.
Scheffler K, Seoighe C. (2005)
A bayesian model comparison approach to inferring positive selection.
Molecular Biology & Evolution. 2005 Dec;22(12):2531-40.
Seoighe C., Scheffler, K. (2005)
Low power to detect asymmetric divergence of duplicated genes
In Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics Eds McLysaght, A. & Huson D.H.
Seoighe C, Gehring C, Hurst LD. (2005)
Gametophytic Selection in Arabidopsis thaliana Supports the Selective Model of Intron Length Reduction.
PLoS Genet. 2005 Aug 5;1(2):e13
Scheffler, K., Seoighe C. (2005) Detecting molecular evidence of positive Darwinian selection In Information Processing and Living Systems; Bajic, V & Tin Wee, T. (Eds); Imperial College Press
Nembaware V, Wolfe KH, Bettoni F, Kelso J, Seoighe C. Allele-specific transcript isoforms in human. FEBS Lett. 2004 Nov 5;577(1-2):233-8.
Seoighe, C., Gehring, C. Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome Trends in Genetics 2004 Oct;20(10):461-4.
Grobler, J., Gray, C.M., Rademeyer,C., Seoighe, C., Ramjee, G., Karim,S.A., Morris, L. Williamson, C. The incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of subtype C infected female sex-workers Journal of Infectious Disease, 2004: 190
Nembaware, V, Said, M, Seoighe, C., Gehring, C.A. Molecular mimicry of a plant signaling molecule enables pathogen control of plant homeostasis BMC Evolution Biol, 2004 Mar 24;4(1):10
Swart, E.C. , Hide, W.H., Seoighe, C. FRAGS: estimation of coding sequence substitution rates from fragmentary data (BMC Bioinformatics, 2004 Jan 29;5(1):8.
Seoighe, C. Turning the clock back on ancient genome duplication Curr Opin Genet Dev. 2003 Dec;13(6):636-43.
Seoighe, C. Johnston, C.R. Shields, D.C. Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation Mol Biol Evol. 2003 Apr;20(4):484-90.
Nembaware, V. Crum, K. Kelso, JF, Seoighe, C. Impact of the presence of paralogues on sequence divergence in a set of mouse-human orthologues Genome Res. 2002 Sep;12(9):1370-6.
Ludidi N.N., Heazlewood J.L., Seoighe C., Irving H.R. and Gehring C.A. Expansin-like molecules: Novel functions derived from common domains Journal of Molecular Evolution 2002 May;54(5):587-94.
Hide WA, Babenko VN, van Heusden PA, Seoighe C, Kelso JF. The contribution of exon-skipping events on chromosome 22 to protein coding diversity. Genome Res. 2001 Nov;11(11):1848-53.
Seoighe C, Federspiel N, Jones T, Hansen N, Bivolarovic V, Surzycki R, Tamse R, Komp C, Huizar L, Davis RW, Scherer S, Tait E, Shaw DJ, Harris D, Murphy L, Oliver K, Taylor K, Rajandream MA, Barrell BG, Wolfe KH. (2000) Prevalence of small inversions in yeast gene order evolution. Proc Natl Acad Sci U S A. Nov 21
McLysaght, A., Seoighe, C. and Wolfe, K.H. (2000) High Frequency of Inversions during Eukaryote Gene Order Evolution in Comparative Genomics Eds. D. Sankoff and J.H. Nadeau. Kluyver Academic Publishers pp 47-58
Seoighe, C. and Wolfe, K.H. (1999) Yeast genome evolution in the post genome era. Curr Opin Microbiol. Oct;2(5):548-54. Review.
Seoighe, C. and Wolfe, K.H. (1999) Updated map of duplicated regions in the yeast genome. Gene. Sep 30;238(1):253-61.
Bradnam, K.R., Seoighe, C., Sharp, P.M. and Wolfe, K.H. (1999) G+C content along and among Saccharomyces cerevisiae chromosomes. Mol. Biol. Evol.
Seoighe, C. and Wolfe, K.H. (1998) Extent of genomic rearrangement after genome duplication in yeast. Proc. Natl. Acad. Sci. USA 95, 4447-4452.
Keogh, R.S., Seoighe, C and Wolfe, K.H. (1998) Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast 14, 443-457.

Non-peer reviewed publications

Getz W, Gouws E, Hahne F, Kopp E, Mostert P, Muller C, Seioghe C, Williams B, Witten G. Mathematical models and the fight against diseases in Africa.
South African Journal of Science 2003: 99 (7/8) Hide W, Mizrahi V, Venkatesh B, Brenner S, Simpson A, Blatch G, Soodyall H, Denby K, Wingfield M, Wingfield B, van Helden P, Ramesar R, Dorrington R, Kelso J, Oppon E, Goyvaerts E, Ramsay M, de Villiers E, van Heerden C, Allsopp B, Seoighe C. (2001) A platform for genomics in South Africa. S Afr Med J. Dec;91(12):1006-7

Click here for a list of publications in pubmed

School of Mathematics, Statistics and Applied Mathematics
National University of Ireland, Galway, University Road, Galway, Ireland.
Phone: +353 (0)91 492332 (direct) , +353 (0)91 524411 x2332 (switchboard)
Fax: +353 (0)91 494542 Email: Mary.Kelly@nuigalway.ie
This page was last updated Friday, September 24