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CBIO Publications: 2004 - 2008

  1. Nembaware V, Lupindo B, Schouest K, Spillane C, Scheffler K, Seoighe C, "Genome-wide survey of allele-specific splicing in humans", BMC Genomics. 2008, 9:265
  2. 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 LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, 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, "Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection", Proc Natl Acad Sci U S A. 2008, 105(21):7552-7.
  3. Chopera DR, Woodman Z, Mlisana K, Mlotshwa M, Martin DP, Seoighe C, Treurnicht F, de Rosa DA, Hide W, Karim SA, Gray CM, Williamson C; CAPRISA 002 Study Team, "Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage", PLoS Pathog. 2008, 4(3):e1000033.
  4. Poulter GL, Rubin DL, Altman RB, Seoighe C, "MScanner: a classifier for retrieving Medline citations", BMC Bioinformatics 2008, 9:108.
  5. M. Kuttel, "Conformational free energy maps for globobiose (_-D-Gal-(1-4)-_-D-Gal) in implicit and explicit aqueous solution", Carbohyd. Res. 2008, 343(6):1091-8.
  6. Ngandu NK, Scheffler K, Moore P, Woodman Z, Martin D, Seoighe C, "Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences", Virol J. 2008, 5:160
  7. Delport W, Scheffler K, Seoighe C, "Frequent toggling between alternative amino acids is driven by selection in HIV-1", PLoS Pathog. 2008, 4(12):e1000242.
  1. Bredenkamp N, Seoighe C, Illing N, "Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation", Dev. Genes Evol. 2007, 217(3):227-33.
  2. 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, 24(4):1025-31
  3. 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, 23(8):1033-41.
  4. 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, 104(41):16251-6.
  5. Singh, L., Hallan, V., Jabeen, N., Singh, A.K., Ram, R., Martin, D.P. and Zaidi, A.A, "Coat protein gene diversity among Chrysanthemum virus B isolates from India", Archives of Virology 2007, 152(2):405-13.
  6. Inoue-Nagata, T., De Mello-Franco, C., Martin, D.P., Rezende, J.A.M., Ferreira, G.B., and Inoue-Nagata, A.K, "Genome analysis of a severe and a mild isolate of Papaya ringspot virus – type W found in Brazil", Virus Genes 2007, 35(1):119-27.
  7. Ribeiro, S.G., Martin, D.P., Lacorte, C., de Carmo, I., Orlandini, D. and Inoue-Nagata, A.K, "Molecular and biological characterization of Tomato chlorotic mottle virus suggest that recombination underlies the evolution and diversity of Brazilian tomato begomoviruses", Phytopathology 2007, 97(6):702-11.
  8. Bredell, H., Martin, D.P., van Harmelen, J, Varsani, A., Sheppard, H. W., Donovan, D., Gray, C.M., and Williamson, C, "HIV-1 Subtype C gag and nef Diversity in Southern Africa", AIDS and Human Retroviruses 2007, 23(3):477-81.
  9. Berger DK, Crampton B, Hein I, Vos W, "Screening cDNA libraries on glass slide microarrays", DNA Arrays (2nd Ed) (Editor J.Brampal), Series: Methods in Molecular Biology 2007, 382:177-203
  1. Seoighe C, Nembaware V, Scheffler K, "Maximum likelihood inference of imprinting and allele-specific expression from EST data", Bioinformatics 2006, 22(24):3032-9.
  2. Scheffler K, Martin DP, Seoighe C, "Robust inference of positive selection from recombining coding sequences", Bioinformatics 2006, 22(20):2493-9.
  3. Varsani A., Van der Walt, E., Heath L., Williamson, A.L., Rybicki, E.P., and Martin D.P, "Evidence of ancient papillomavirus recombination", J. General Virology 2006, 87:2527-2531
  4. Heath, L., van der Walt, E., Varsani, A., and Martin, D.P, "Recombination patterns in aphthoviruses mirror those found in other picornoviruses", J.Virology 2006, 80(23):11827-32
  5. Poke, F.S., Martin, D.P., Steane, D.A., Vaillancourt, R.E., and Reid, J.B, "The impact of intragenic recombination on phylogenetic reconstruction at the sectional level in Eucalyptus when using a single copy nuclear gene (cinnamoyl CoA reductase)", Phylogenetics and Evolution 2006, 39(1):160-70.
  6. Kuttel M, Gain J, Burger A, Eborn I, "Techniques for visualization of carbohydrate molecules", J Mol Graph Model 2006, 25(3):380-8.
  1. Scheffler, K., Seoighe, C, "A Bayesian Model Comparison Approach to Inferring Positive Selection", Molecular Biology and Evolution 2005, 22(12):2531-40.
  2. Seoighe, C., Gehring, C., Hurst, L.D, "Gametophytic Selection in Arabidopsis thaliana Supports the Selective Model of Intron Length Reduction", PLoS Genet. 2005, 1(2):e13.
  3. Scheffler, K., Seoighe, C, "Asymmetric divergence of duplicated genes", Proceedings of the RECOMB 2005 International Workshop, published in Lecture Notes in Bioinformatics Springer, 2005, McLysaght & Huson (Eds.). 
  4. Scheffler, K., Seoighe, C, "Detecting molecular evidence of positive Darwinian selection", Information Processing and Living Systems Imperial College Press, 2005, Tan & Bajic (Eds.).
  5. Martin, D. P., Van der Walt, E., Posada, D., and Rybicki, E. P, "The evolutionary value of recombination is constrained by genome modularity", PLoS Genetics 2005, 1(4):e51.
  6. Martin DP, Williamson C, Posada D, "Recombination detection and analysis from sequence alignments", Bioinformatics 2005, 21(2):260-2
  7. Kuttel MM, Naidoo KJ, "Free energy surfaces for the alpha (1 --> 4)-glycosidic linkage: implications for polysaccharide solution structure and dynamics", J Phys Chem B. 2005, 109(15):7468-74.
  8. Kuttel MM, Naidoo KJ, "Ramachandran free-energy surfaces for disaccharides: trehalose, a case study", Carbohydr Res. 2005, 340(5):875-9 
  1. Grobler J, Gray CM, Rademeyer C, Seoighe C, Ramjee G, Karim SA, Morris L, Williamson C, "Incidence of HIV-1 Dual Infection and Its Association with Increased Viral Load Set Point in a Cohort of HIV-1 Subtype C-Infected Female Sex Workers", J. Infect. Dis. 2004, 190(7):1355-1359.
  2. Nembaware V, Seoighe C, Sayed M, Gehring C, "A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry", BMC Evol. Biol. 2004, 4:10
  3. Swart EC, Hide WA, Seoighe C, "FRAGS: estimation of coding sequence substitution rates from fragmentary data", BMCBioinformatics 2004, 5:8.
  4. Seoighe C, Gehring C, "Genome duplication led to highly specific expansion of the Arabidopsis thaliana proteome", Trends Genet. 2004, 20(10):461-4.
  5. Chang CF, Wai KM, Patterton HG, "Calculating the statistical significance of physical clusters of co-regulated genes in the genome: the role of chromatin in domain-wide gene regulation", Nucleic Acids Res. 2004, 32:1798-1807.
  6. Nembaware V, Wolfe KH, Bettoni F, Kelso J, Seoighe C, "Alternative transcript isoforms in human", FEBS Lett. 2004, 577(1-2):233-8
  7. Sewell BT, Best RB, Chen S, Roseman AM, Farr GW, Horwich AL, Saibil HR: , "A mutant chaperonin with rearranged inter-ring electrostatic contacts,defective cooperativity, and temperature-sensitive dissociation of rings", Nature Structural and Molecular Biology 2004, 11(11):1128-33