Research Interests

Modeling molecular biological data, including gene expression, alternative mRNA splicing and the evolution of viruses, in particular HIV-1.

 

     

Peer Reviewed Journals

Seoighe, C., Wolfe, K.H. (1998) 'Extent of genomic rearrangement after genome duplication in yeast'. Proc. Natl. Acad. Sci. USA 95, :4447-4452. [Details]

Keogh, R.S., Seoighe, C., Wolfe, K.H. (1998) 'Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi'. Yeast, 14 :443-457. [Details]

Bradnam, K.R., Seoighe, C., Sharp, P.M., Wolfe, K.H. (1999) 'G+C content along and among Saccharomyces cerevisiae chromosomes'. Mol. Biol. Evol, . [Details]

Seoighe, C., Wolfe, K.H. (1999) 'Yeast genome evolution in the post genome era'. Curr Opin Microbiol. Review, 2 (5):548-554. [Details]

Seoighe, C., Wolfe, K.H. (1999) 'Updated map of duplicated regions in the yeast genome'. Gene, 238 (1):253-261. [Details]

Seoighe, C., Federspiel, N., Jones, T., Hansen, N., Bivolarovic, V., Surzycki, R., Tamse, R., Komp, C., Huizar, L., Davis, R.W., Scherer, S., Tait, E., Shaw, D.J., Harris, D., Murphy, L., Oliver, K., Taylor, K., Rajandream, M.A., Barrell, B.G., Wolfe, K.H. (2000) 'Prevalence of small inversions in yeast gene order evolution'. Proc Natl Acad Sci U S A, . [Details]

Hide, W.A., Babenko, V.N., van Heusden, P.A., Seoighe, C., Kelso, J.F. (2001) 'The contribution of exon-skipping events on chromosome 22 to protein coding diversity'. Genome Res, 11 (11):1848-1853. [Details]

Nembaware, V., Crum, K., Kelso, J.F., Seoighe, C. (2002) 'Impact of the presence of paralogues on sequence divergence in a set of mouse-human orthologues'. Genome Res, 12 (9):1370-1376. [Details]

Ludidi N.N., Heazlewood J.L., Seoighe C., Irving H.R., Gehring C.A. (2002) 'Expansin-like molecules: Novel functions derived from common domains'. Journal of Molecular Evolution, 54 (5):587-594. [Details]

Seoighe, C., Johnston, C.R., Shields, D.C. (2003) 'Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation'. Mol Biol Evol, 20 (4):484-490. [Details]

Seoighe, C. (2003) 'Turning the clock back on ancient genome duplication'. Curr Opin Genet Dev, 13 (6):636-643. [Details]

Grobler, J., Gray, C.M., Rademeyer,C., Seoighe, C., Ramjee, G., Karim, S.A., Morris, L., Williamson, C. (2004) '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, 190 . [Details]

Seoighe, C., Gehring, C. (2004) 'Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome'. Trends in Genetics, 20 (10):461-464. [Details]

Nembaware, V., Said, M., Seoighe, C., Gehring, C.A. (2004) 'Molecular mimicry of a plant signaling molecule enables pathogen control of plant homeostasis'. BMC Evolution Biol, 4 (1). [Details]

Swart, E.C., Hide, W.H., Seoighe, C. (2004) 'FRAGS: estimation of coding sequence substitution rates from fragmentary data'. Bioinformatics, 5 (1). [Details]

Scheffler, K., Seoighe, C. (2005) 'Detecting molecular evidence of positive Darwinian selection'. In Information Processing and Living Systems, . [Details]

Seoighe, C., Scheffler, K. (2005) 'Low power to detect asymmetric divergence of duplicated genes'. Proceedings of the RECOMB 2005 International Workshop on Comparative Genomics, . [Details]

Seoighe, C., Gehring, C., Hurst, L.D. (2005) 'Gametophytic Selection in Arabidopsis thaliana Supports the Selective Model of Intron'. Length Reduction. PLoS Genet, 1 (2). [Details]

Nembaware, V., Wolfe, K.H., Bettoni, F., Kelso, J., Seoighe, C. (2005) 'Allele-specific transcript isoforms in human'. FEBS Lett, 577 (01-Feb):233-238. [Details]

Scheffler, K., Seoighe, C. (2005) 'A bayesian model comparison approach to inferring positive selection'. Molecular Biology & Evolution, 22 (12):2531-2540. [Details]

Seoighe, C., Nembaware, V., Scheffler, K. (2006) 'Maximum likelihood inference of imprinting and allele-specific expression from EST data'. Bioinformatics, 22 (24):3032-3039. [Details]

Scheffler, K., Martin, D.P., Seoighe, C. (2006) 'Robust inference of positive selection from recombining coding sequences'. Bioinformatics, 22 (20):2493-2499. [Details]

Schwegmann, A., Guler, R., Cutler, A.J., Arendse, B., Horsnell, W.G., Flemming, A., Kottmann, A.H., Ryan, G., Hide, W., Leitges, M., Seoighe, C., Brombacher, F. (2007) 'Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes'. Proc Natl Acad Sci U S A, 104 (41):16251-16256. [Details]

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, . [Details]

Keele, B.F., Giorgi, E.E., Salazar-Gonzalez, J.F., Decker, J.M., Pham, K.T., Salazar, M.G., Sun, C., Grayson, T., Wang, S., Li, H., Wei, X., Jiang, C., Kirchherr, J.L., Gao, F., Anderson, J.A., Ping, L., Swanstrom, R., Tomaras, G.D., Blattner, W.A., Goepfert, P.A., Kilby, M., Saag, M.S., Delwart, E.L., Busch, M.P., Cohen, M.S., Montefiori, D.C., Haynes, B.F., Gaschen, B., Athreya, G.S., Lee, H.Y., Wood, N., Seoighe, C., Perelson, A.S., Bhattacharya, T., Korber, B.T., Hahn, B.H., Shaw, G.M. (2008) 'Identification and Characterization of Transmitted and Early Founder Virus Envelopes in Primary HIV-1 Infection'. Proc Natl Acad Sci U S A, 105 (21):7552-7557. [Details]

D.R. Chopera, D.R., Woodman, Z., Mlisana, K., Mlotshwa, M., Martin, D.P., Seoighe, C., Treurnicht, F., Assis de Rosa, D., Hide, W., Abdool Karim, S., Gray, C.M., Williamson, C., The CAPRISA 002 study team (2008) 'Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage'. PLoS Pathogens p. e1000033, 4 (3). [Details]

Nembaware, V., Lupindo, B., Schouest, K., Spillane, K., Scheffler, K., Seoighe, C. (2008) 'Genome-wide survey of allele-specific splicing in humans'. MC Genomics BMC Genomics, 9 (1). [Details]

Delport, W., Scheffler, K., Seoighe, C. (2008) 'Models of coding sequence evolution'. Brief Bioinform, . [Details]

Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C. (2008) 'Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences'. Virol J, 2008 Dec 23;5:160 . [Details]

Poulter, G.L., Rubin, D.L., Altman, R.B., Seoighe, C. (2008) 'MScanner: a classifier for retrieving Medline citations'. BMC Bioinformatics, 9 (1). [Details]

Delport, W., Scheffler, K., Seoighe, C. (2008) 'Frequent toggling between alternative amino acids is driven by selection in HIV-1'. PLoS Pathog, 4 (12). [Details]

Gray, C.M., 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, S.A. (2009) '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, 83 (1):470-478. [Details]

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. (2009) 'HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC'. PLoS Pathogens, 5 . [DOI] [Details]

Ngandu, NK,Seoighe, C,Scheffler, K (2009) 'Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission'. Virology Journal, 6 . [DOI] [Details]

Illing N, Klak C, Johnson C, Brito D, Negrao N, Baine F, van Kets V, Ramchurn KR, Seoighe C, Roden L. (2009) 'Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae'. Dev Genes Evol, . [Details]

Berman P, Collins M, Baumgarten I, Seoighe C, Jennings CL, Joffe Y, Lambert EV, Levitt NS, Faulenbach MV, Kahn SE, Goedecke JH. (2009) 'Association between the 4 bp proinsulin gene insertion polymorphism (IVS-69) and body composition in black South African women'. Obesity, 17 :1298-1300. [DOI] [Details]

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. (2009) 'Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants'. J Virol, . [Details]

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. (2010) 'Adaptive changes in HIV-1 subtype C proteins during early infection are driven by changes in HLA-associated immune pressure'. Virology, . [Details]

Gaujoux, R,Seoighe, C (2010) 'A flexible R package for nonnegative matrix factorization'. Bmc Bioinformatics, 11 . [DOI] [Details]

Lacerda M, Scheffler K, Seoighe C. (2010) 'Epitope discovery with phylogenetic hidden Markov models'. Molecular Biology & Evolution, . [Details]

Seoighe C, Gehring C. (2010) 'Heritability in the efficiency of nonsense-mediated mRNA decay in humans'. Plos One, . [Details]

de Wit E, Delport W, Rugamika CE, Meintjes A, Möller M, van Helden PD, Seoighe C, Hoal EG. (2010) 'Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape'. Human Genetics, . [Details]

Faure, AJ,Seoighe, C,Mulder, NJ (2011) 'Investigating the effect of paralogs on microarray gene-set analysis'. Bmc Bioinformatics, 12 . [DOI] [Details]

Jankovic, B,Seoighe, C,Alqurashi, M,Gehring, C (2011) 'Is there evidence of optimisation for carbon efficiency in plant proteomes?'. Plant Biology, 13 :831-834. [DOI] [Details]

Gaujoux R, Seoighe C. (2011) 'Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study'. Infect Genet Evol, . [Details]

Millane RC, Kanska J, Duffy DJ, Seoighe C, Cunningham S, Plickert G,  Frank U  (2011) 'Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor'. Development, 138 (12):2429-2439. [Details]

Seoighe, C, Korir, P (2011) 'Evidence for intron length conservation in a set of mammalian genes associated with embryonic development'. BMC Bioinformatics, 12(Suppl 9):S16 . [Details]

Tikhanovich I, Liang B, Seoighe C, Folk WR, Nasheuer HP. (2011) 'Inhibition of human BK polyomavirus replication by small noncoding RNAs'. J Virol, 85 :6930-6940. [DOI] [Details]

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. (2011) 'Immune and Genetic Correlates of Vaccine Protection Against Mucosal Infection by SIV in Monkeys'. Science Translational Medicine, 3 . [DOI] [Details]