Research Topics
| Cathal SeoigheSummaryAffiliation: University of Cape Town Country: South Africa Publications
| Collaborators
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Detail Information
Publications
Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantageDenis R Chopera
Institute of Infectious Diseases and Molecular Medicine, Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
PLoS Pathog 4:e1000033. 2008....
Maximum likelihood inference of imprinting and allele-specific expression from EST dataCathal Seoighe
Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
Bioinformatics 22:3032-9. 2006..Counts of SNP alleles derived from EST sequences have been used to identify both novel candidates for genomic imprinting as well as examples of genes with allelic differences in expression...- Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteomeCathal Seoighe
South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa
Trends Genet 20:461-4. 2004..Genes retained in duplicate form a functionally biased set and include a significant over-representation of genes involved in the regulation of transcription... - Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reductionCathal Seoighe
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
PLoS Genet 1:e13. 2005..These observations thus support the view that selection for efficiency contributes to the reduction in intron length and provide the first report of a molecular signature of strong gametophytic selection... - Frequent toggling between alternative amino acids is driven by selection in HIV-1Wayne Delport
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, South Africa
PLoS Pathog 4:e1000242. 2008.... - Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequencesNobubelo K Ngandu
National Bioinformatics Network Node, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
Virol J 5:160. 2008.... - Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmissionNobubelo K Ngandu
National Bioinformatics Node, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory 7925, South Africa
Virol J 6:164. 2009..However, to-date there has been little attempt to study permanent loss of CTL epitopes due to escape mutations without an effect on fitness... - Genome-wide survey of allele-specific splicing in humansVictoria Nembaware
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Private Bag, Rondebosch, 7700, Cape Town, South Africa
BMC Genomics 9:265. 2008..However, because the effect of a mutation on the efficiency of mRNA splicing is often difficult to predict, many mutations that cause disease through an effect on splicing are likely to remain undiscovered... - HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBECNatasha Wood
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
PLoS Pathog 5:e1000414. 2009..Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections... - Models of coding sequence evolutionWayne Delport
University of Cape Town, Observatory, 7925, Cape Town, South Africa
Brief Bioinform 10:97-109. 2009..We review some of the more recent developments that have improved their power and utility, laying a foundation for further advances in the modeling of coding sequence evolution... - Robust inference of positive selection from recombining coding sequencesKonrad Scheffler
Computational Biology Group, Institute of Infectious Disease and Molecular Medicine University of Cape Town, Private Bag, Rondebosch 7701, South Africa
Bioinformatics 22:2493-9. 2006..This is achieved by allowing tree topologies and branch lengths to change across detected recombination breakpoints. Further improvements are obtained by allowing synonymous substitution rates to vary across sites... 
Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case studyRenaud Gaujoux
Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
Infect Genet Evol 12:913-21. 2012..We conclude that the use of marker genes improves the accuracy of gene expression deconvolution using NMF and suggest modifications to how the marker gene information is used that may lead to further improvements...- Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulationNicholas Bredenkamp
Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
Dev Genes Evol 217:227-33. 2007.... - Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the RuschioideaeNicola Illing
Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
Dev Genes Evol 219:331-8. 2009..The recent duplication and subsequent selected gene loss of the ARP transcription factor correlates with the rapid diversification of plant forms in the Ruschioideae... - Turning the clock back on ancient genome duplicationCathal Seoighe
South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
Curr Opin Genet Dev 13:636-43. 2003..However, despite methodological advances and the availability of complete genome sequence data the debate over whether very ancient genome duplications have occurred early in the vertebrate lineage has not yet been fully resolved... - A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicryVictoria Nembaware
South African National Bioinformatics Institute, Private Bag X17, Bellville, 7535, South Africa
BMC Evol Biol 4:10. 2004..PNPs are up-regulated under conditions of osmotic stress and PNP-dependent processes include changes in ion transport and increases of H2O uptake into protoplasts and whole tissue... - A model of directional selection applied to the evolution of drug resistance in HIV-1Cathal Seoighe
Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
Mol Biol Evol 24:1025-31. 2007.... - FRAGS: estimation of coding sequence substitution rates from fragmentary dataEstienne C Swart
South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
BMC Bioinformatics 5:8. 2004.... - Investigating the effect of paralogs on microarray gene-set analysisAndre J Faure
Computational Biology Group, Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa
BMC Bioinformatics 12:29. 2011..We suspect that the presence of paralogs affects the ability of GSA methods to accurately identify the most important sets of genes for subsequent research... - 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 workersJandre Grobler
Institute for Infectious Diseases and Molecular Medicine, Division of Medical Virology, University of Cape Town, Observatory, South Africa
J Infect Dis 190:1355-9. 2004..There was a significant association between dual infection and elevated viral load set point... - A flexible R package for nonnegative matrix factorizationRenaud Gaujoux
Computational Biology Group, Department of Clinical Laboratory Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
BMC Bioinformatics 11:367. 2010..However, most NMF implementations have been on commercial platforms, while those that are freely available typically require programming skills. This limits their use by the wider research community... - Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologsVictoria Nembaware
South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, Cape Town, South Africa
Genome Res 12:1370-6. 2002..We have also found that shorter genes have a higher probability of being found duplicated in the human genome, possibly reflecting a mutational effect... - Allele-specific transcript isoforms in humanVictoria Nembaware
Computational Biology Group, University of Cape Town, Rondebosch 7701, Cape Town, South Africa
FEBS Lett 577:233-8. 2004..We provide a conservative lower bound of 6% on this estimate and point out that alternative splicing cannot be confirmed absolutely unless more than one transcript is observed from the same allele... - Association between the 4 bp proinsulin gene insertion polymorphism (IVS-69) and body composition in black South African womenPeter Berman
Division of Chemical Pathology, UCT MRC Research Unit for Exercise Science and Sports Medicine, Department of Human Biology, University of Cape Town, Cape Town, South Africa
Obesity (Silver Spring) 17:1298-300. 2009..In conclusion, the 4 bp proinsulin gene insertion allele is associated with extreme obesity, reflected by greater fat-free soft tissue mass and fat mass, particularly SAT, in obese black South African women... - MScanner: a classifier for retrieving Medline citationsGraham L Poulter
UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
BMC Bioinformatics 9:108. 2008.... - Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenesAnita Schwegmann
Division of Immunology, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
Proc Natl Acad Sci U S A 104:16251-6. 2007..Taken together these data identified PKCdelta as a critical factor for confinement of LM within macrophage phagosomes... - Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infectionBrandon F Keele
Departments of Medicine and Microbiology, University of Alabama at Birmingham, Birmingham, AL 35223, USA
Proc Natl Acad Sci U S A 105:7552-7. 2008.... - Significantly different patterns of amino acid replacement after gene duplication as compared to after speciationCathal Seoighe
Clinical Pharmacology Department, Royal College of Surgeons in Ireland, Dublin, Ireland
Mol Biol Evol 20:484-90. 2003..These findings have implications for our understanding of the nature of evolution after duplication and may help to shed light on the evolution of novel protein functions through gene duplication... - CTL response to HIV type 1 subtype C is poorly predicted by known epitope motifsNobubelo G Ngandu
Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Medical School, Observatory, South Africa 7925
AIDS Res Hum Retroviruses 23:1033-41. 2007..This can have important implications for understanding immune escape and predicting vaccine efficacy in the context of populations primarily infected with non-B subtype HIV-1...