Cathal Seoighe

Summary

Affiliation: National University of Ireland
Country: Ireland

Publications

  1. pmc A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing
    Paul K Korir
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, University Road, Galway, Republic of Ireland
    BMC Res Notes 7:401. 2014
  2. pmc Epitope discovery with phylogenetic hidden Markov models
    Miguel Lacerda
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    Mol Biol Evol 27:1212-20. 2010
  3. pmc Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts
    Thong T Nguyen
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    PLoS ONE 8:e79627. 2013
  4. ncbi request reprint Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models
    Miguel Lacerda
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
    Virol J 10:347. 2013
  5. pmc The regulatory effect of miRNAs is a heritable genetic trait in humans
    Paul Geeleher
    Department of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    BMC Genomics 13:383. 2012
  6. 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
  7. pmc Heritability in the efficiency of nonsense-mediated mRNA decay in humans
    Cathal Seoighe
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
    PLoS ONE 5:e11657. 2010
  8. pmc Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
    Cathal Seoighe
    National University of Ireland, Galway, University Road, Galway, Republic of Ireland
    BMC Bioinformatics 12:S16. 2011
  9. 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
  10. 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

Collaborators

Detail Information

Publications29

  1. pmc A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing
    Paul K Korir
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, University Road, Galway, Republic of Ireland
    BMC Res Notes 7:401. 2014
    ..We carried out a transcriptome-wide analysis of the effects of a mutation in a ubiquitous splicing factor that causes retinitis pigmentosa (RP) on mRNA splicing, using exon microarrays...
  2. pmc Epitope discovery with phylogenetic hidden Markov models
    Miguel Lacerda
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    Mol Biol Evol 27:1212-20. 2010
    ..As a demonstration, we apply the model to a data set of HIV-1 protein-coding sequences and host HLA genotypes...
  3. pmc Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts
    Thong T Nguyen
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    PLoS ONE 8:e79627. 2013
    ....
  4. ncbi request reprint Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models
    Miguel Lacerda
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
    Virol J 10:347. 2013
    ..Identification of the epitopes targeted by antibodies that can neutralize diverse HIV-1 strains can provide important clues for the design of a preventative vaccine...
  5. pmc The regulatory effect of miRNAs is a heritable genetic trait in humans
    Paul Geeleher
    Department of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
    BMC Genomics 13:383. 2012
    ..Given a gene expression dataset, Cheng et al. defined the regulatory effect score (RE-score) of a miRNA as the difference in the gene expression rank of targets of the miRNA compared to non-targeted genes...
  6. 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...
  7. pmc Heritability in the efficiency of nonsense-mediated mRNA decay in humans
    Cathal Seoighe
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
    PLoS ONE 5:e11657. 2010
    ..Yet recent reports have revealed that the efficiency of NMD varies across tissues and between individuals, with important clinical consequences...
  8. pmc Evidence for intron length conservation in a set of mammalian genes associated with embryonic development
    Cathal Seoighe
    National University of Ireland, Galway, University Road, Galway, Republic of Ireland
    BMC Bioinformatics 12:S16. 2011
    ....
  9. 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...
  10. 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
    ....
  11. 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
    ....
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. 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
    ....
  17. doi request reprint Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape
    Erika de Wit
    Molecular Biology and Human Genetics, MRC Centre for Molecular and Cellular Biology, DST NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, Stellenbosch University, PO Box 19063, Tygerberg, 7505, South Africa
    Hum Genet 128:145-53. 2010
    ..This is consistent with historical data. While of great historical and genealogical interest, this information is also essential for future admixture mapping of disease genes in this population...
  18. 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
    ....
  19. pmc Inhibition of human BK polyomavirus replication by small noncoding RNAs
    Irina Tikhanovich
    Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
    J Virol 85:6930-40. 2011
    ..These observations point to novel mechanisms for regulating DNA replication and suggest the design of synthetic agents for inhibiting replication of polyomaviruses and possibly other viruses...
  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 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...
  22. 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...
  23. 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...
  24. pmc The shared genomic architecture of human nucleolar organizer regions
    Ioanna Floutsakou
    Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, Galway, Ireland
    Genome Res 23:2003-12. 2013
    ..Our results provide a platform for investigating the role of NORs in nucleolar formation and function, and open the door for determining the role of these regions in the well-known empirical association of nucleoli with pathology. ..
  25. doi request reprint Inference of allele-specific expression from RNA-seq data
    Paul K Korir
    School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway NUI Galway, Ireland
    Methods Mol Biol 1112:49-69. 2014
    ....
  26. doi request reprint Gene-set analysis is severely biased when applied to genome-wide methylation data
    Paul Geeleher
    Section of Hematology Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637 USA
    Bioinformatics 29:1851-7. 2013
    ..We show that gene-set analysis, as it is typically applied to genome-wide methylation assays, is severely biased as a result of differences in the numbers of CpG sites associated with different classes of genes and gene promoters...
  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. 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
    ....
  29. 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...