• Lacerda M, Moore PL, Ngandu NK, Seaman M, Gray ES, Murrell B, Krishnamoorthy M, Nonyane M, Madiga M, Wibmer CK, Sheward D, Bailer RT, Gao H, Greene KM, Karim SS, Mascola JR, Korber BT, Montefiori DC, Morris L, Williamson C, Seoighe C; CAVD-NSDP Consortium.
  Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models.
  Virol J. 2013 Dec 2;10(1):347. doi: 10.1186/1743-422X-10-347.
• Nguyen TT, Seoighe C.
  Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts. PLoS One. 2013 Nov 18;8(11):e79627. doi: 10.1371/journal.pone.0079627.
  
• Floutsakou I, Agrawal S, Nguyen TT, Seoighe C, Ganley AR, McStay B.
  The shared genomic architecture of human nucleolar organizer regions.
  Genome Res. 2013 Dec;23(12):2003-12. doi: 10.1101/gr.157941.113. Epub 2013 Aug 29.
• Gaujoux R, Seoighe C.
  CellMix: a comprehensive toolbox for gene expression deconvolution.
  Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3.
• Geeleher P, Hartnett L, Egan LJ, Golden A, Raja Ali RA, Seoighe C.
  Gene-set analysis is severely biased when applied to genome-wide methylation data.
  Bioinformatics. 2013 Aug 1;29(15):1851-7. doi: 10.1093/bioinformatics/btt311. Epub 2013 Jun 3.
• Ping LH, Joseph SB, Anderson JA, Abrahams MR, Salazar-Gonzalez JF, Kincer LP, Treurnicht FK, Arney L, Ojeda S, Zhang M, Keys J, Potter EL, Chu H, Moore P, Salazar MG, Iyer S, Jabara C, Kirchherr J, Mapanje C, Ngandu N, Seoighe C, Hoffman I, Gao F, Tang Y, Labranche C, Lee B, Saville A, Vermeulen M, Fiscus S, Morris L, Karim SA, Haynes BF, Shaw GM, Korber BT, Hahn BH, Cohen MS, Montefiori D, Williamson C, Swanstrom R; CAPRISA Acute Infection Study and the Center for HIV-AIDS Vaccine Immunology Consortium.
  Comparison of viral Env proteins from acute and chronic infections with subtype C human immunodeficiency virus type 1 identifies differences in glycosylation and CCR5 utilization and suggests a new strategy for immunogen design.
  J Virol. 2013 Jul;87(13):7218-33. doi: 10.1128/JVI.03577-12. Epub 2013 Apr 24.
• Abrahams MR, Treurnicht FK, Ngandu NK, Goodier SA, Marais JC, Bredell H, Thebus R, de Assis Rosa D, Mlisana K, Seoighe C, Karim SA, Gray CM, Williamson C.
  Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression.
  AIDS. 2013 Feb 20;27(4):507-18. doi: 10.1097/QAD.0b013e32835cab64. Erratum in: AIDS. 2013 Jun 1;27(9):1525.
• Geeleher P, Huang SR, Gamazon ER, Golden A, Seoighe C.
  The regulatory effect of miRNAs is a heritable genetic trait in humans.
  BMC Genomics. 2012 Aug 10;13:383. doi: 10.1186/1471-2164-13-383.
• Staff L, Hurd P, Reale L, Seoighe C, Rockwood A, Gehring C.
  The hidden geometries of the Arabidopsis thaliana epidermis.
  PLoS One. 2012;7(9):e43546. doi: 10.1371/journal.pone.0043546. Epub 2012 Sep 11.
• Seoighe C, Korir PK.
  Evidence for intron length conservation in a set of mammalian genes associated with embryonic development.
  BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S16. doi: 10.1186/1471-2105-12-S9-S16.
• Jankovic B, Seoighe C, Alqurashi M, Gehring C.
  Is there evidence of optimisation for carbon efficiency in plant proteomes?
  Plant Biol (Stuttg). 2011 Nov;13(6):831-4. doi: 10.1111/j.1438-8677.2011.00494.x. Epub 2011 Jul 25.
• Gaujoux R, Seoighe C.
  Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case study.
  Infect Genet Evol. 2012 Jul;12(5):913-21. doi: 10.1016/j.meegid.2011.08.014. Epub 2011 Sep 10.
• Millane RC, Kanska J, Duffy DJ, Seoighe C, Cunningham S, Plickert G, Frank U.
  Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor.
  Development. 2011 Jun;138(12):2429-39. doi: 10.1242/dev.064931.
• Letvin NL, Rao SS, Montefiori DC, Seaman MS, Sun Y, Lim SY, Yeh WW, Asmal M, Gelman RS, Shen L, Whitney JB, Seoighe C, Lacerda M, Keating S, Norris PJ, Hudgens MG, Gilbert PB, Buzby AP, Mach LV, Zhang J, Balachandran H, Shaw GM, Schmidt SD, Todd JP, Dodson A, Mascola JR, Nabel GJ.
  Immune and Genetic Correlates of Vaccine Protection Against Mucosal Infection by SIV in Monkeys.
  Sci Transl Med. 2011 May 4;3(81):81ra36. doi: 10.1126/scitranslmed.3002351.
• Tikhanovich I, Liang B, Seoighe C, Folk WR, Nasheuer HP.
  Inhibition of human BK polyomavirus replication by small noncoding RNAs.
  J Virol. 2011 Jul;85(14):6930-40. doi: 10.1128/JVI.00547-11. Epub 2011 May 4.
• Faure AJ, Seoighe C, Mulder NJ.
  Investigating the effect of paralogs on microarray gene-set analysis.
  BMC Bioinformatics. 2011 Jan 24;12:29. doi: 10.1186/1471-2105-12-29.
• 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

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