Cathal Seoighe

Summary

Affiliation: University of Cape Town
Country: South Africa

Publications

  1. pmc Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage
    Denis 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
  2. ncbi request reprint Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
    Cathal Seoighe
    South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville, 7535, South Africa
    Trends Genet 20:461-4. 2004
  3. pmc Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
    Cathal Seoighe
    Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, South Africa
    PLoS Genet 1:e13. 2005
  4. ncbi request reprint Maximum likelihood inference of imprinting and allele-specific expression from EST data
    Cathal Seoighe
    Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
    Bioinformatics 22:3032-9. 2006
  5. pmc Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences
    Nobubelo 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
  6. pmc Frequent toggling between alternative amino acids is driven by selection in HIV-1
    Wayne Delport
    Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, South Africa
    PLoS Pathog 4:e1000242. 2008
  7. pmc Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission
    Nobubelo 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
  8. pmc Genome-wide survey of allele-specific splicing in humans
    Victoria 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
  9. pmc Models of coding sequence evolution
    Wayne Delport
    University of Cape Town, Observatory, 7925, Cape Town, South Africa
    Brief Bioinform 10:97-109. 2009
  10. pmc HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC
    Natasha Wood
    Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town, South Africa
    PLoS Pathog 5:e1000414. 2009

Collaborators

Detail Information

Publications31

  1. pmc Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage
    Denis 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
    ....
  2. ncbi request reprint Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome
    Cathal 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...
  3. pmc Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction
    Cathal 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...
  4. ncbi request reprint Maximum likelihood inference of imprinting and allele-specific expression from EST data
    Cathal 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...
  5. pmc Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences
    Nobubelo 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
    ....
  6. pmc Frequent toggling between alternative amino acids is driven by selection in HIV-1
    Wayne Delport
    Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Rondebosch, Cape Town, South Africa
    PLoS Pathog 4:e1000242. 2008
    ....
  7. pmc Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission
    Nobubelo 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...
  8. pmc Genome-wide survey of allele-specific splicing in humans
    Victoria 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...
  9. pmc Models of coding sequence evolution
    Wayne 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...
  10. pmc HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC
    Natasha 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...
  11. ncbi request reprint Robust inference of positive selection from recombining coding sequences
    Konrad 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...
  12. doi request reprint Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case study
    Renaud 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...
  13. ncbi request reprint Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation
    Nicholas 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
    ....
  14. doi request reprint Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae
    Nicola 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...
  15. ncbi request reprint A model of directional selection applied to the evolution of drug resistance in HIV-1
    Cathal 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
    ....
  16. ncbi request reprint Turning the clock back on ancient genome duplication
    Cathal 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...
  17. pmc 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
    Victoria 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...
  18. pmc Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression
    Melissa Rose Abrahams
    Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
    AIDS 27:507-18. 2013
    ..The purpose of this study was to characterize the earliest changes across the genome of subtype C viruses following transmission, to better understand early control of viremia...
  19. pmc FRAGS: estimation of coding sequence substitution rates from fragmentary data
    Estienne C Swart
    South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
    BMC Bioinformatics 5:8. 2004
    ....
  20. pmc Investigating the effect of paralogs on microarray gene-set analysis
    Andre 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...
  21. ncbi request reprint 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
    Jandre 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...
  22. ncbi request reprint Allele-specific transcript isoforms in human
    Victoria 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...
  23. pmc A flexible R package for nonnegative matrix factorization
    Renaud 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...
  24. pmc Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs
    Victoria 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...
  25. doi request reprint Association between the 4 bp proinsulin gene insertion polymorphism (IVS-69) and body composition in black South African women
    Peter 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...
  26. doi request reprint CellMix: a comprehensive toolbox for gene expression deconvolution
    Renaud Gaujoux
    Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, South Africa and School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Ireland
    Bioinformatics 29:2211-2. 2013
    ..cbio.uct.ac.za/∼renaud/CRAN/web/CellMix. It is currently being submitted to BioConductor. The package's vignettes notably contain additional information, examples and references...
  27. pmc MScanner: a classifier for retrieving Medline citations
    Graham L Poulter
    UCT NBN Node, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
    BMC Bioinformatics 9:108. 2008
    ....
  28. pmc Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes
    Anita 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...
  29. pmc Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
    Brandon 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
    ....
  30. ncbi request reprint Significantly different patterns of amino acid replacement after gene duplication as compared to after speciation
    Cathal 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...
  31. ncbi request reprint CTL response to HIV type 1 subtype C is poorly predicted by known epitope motifs
    Nobubelo 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...