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Browsing by Author "Seoighe, Cathal"

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CAGED: a tool to investigate the relationship between gene expression and genome organizations in Arabidopsis thaliana

Author: Somers, Sachin J Date: 2010 Read more
Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission

Author: Ngandu, Nobubelo ; Seoighe, Cathal ; Scheffler, Konrad Date: 2009 BACKGROUND:The cytotoxic T-lymphocyte immune response is important in controlling HIV-1 replication in infected humans. In this immune pathway, viral peptides within infected cells are presented to T-lymphocytes by the polymorphic human ... Read more c b
Evolutionary analyses of HIV-1 protein-coding sequences : adaptation to host cytotoxic immune responses and purifying selection at synonymous sites

Author: Ngandu, Nobubelo Kwanele Date: 2009 This thesis exposes previously ignored evolutionary characteristics of the synonymous sites of virus nucleotide sequences and contributes new findings to the understanding of the evolution of HIV-1 in relation to the human immune response. Read more
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences

Author: Ngandu, Nobubelo ; Scheffler, Konrad ; Moore, Penny ; Woodman, Zenda ; Martin, Darren ; Seoighe, Cathal Date: 2008 BACKGROUND: Positive selection pressure acting on protein-coding sequences is usually inferred when the rate of nonsynonymous substitution is greater than the synonymous rate. However, purifying selection acting directly on the nucleotide ... Read more c b
A flexible R package for nonnegative matrix factorization

Author: Gaujoux, Renaud ; Seoighe, Cathal Date: 2010 BACKGROUND: Nonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in ... Read more c b
Frequent toggling between alternative amino acids is driven by selection in HIV-1

Author: Delport, Wayne ; Scheffler, Konrad ; Seoighe, Cathal Date: 2008 Author Summary Viruses, such as HIV, are able to evade host immune responses through escape mutations, yet sometimes they do so at a cost. This cost is the reduction in the ability of the virus to replicate, and thus selective pressure exists ... Read more c b
Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction

Author: Seoighe, Cathal ; Gehring, Chris ; Hurst, Laurence D Date: 2005 Why do highly expressed genes have small introns? This is an important issue, not least because it provides a testing ground to compare selectionist and neutralist models of genome evolution. Some argue that small introns are selectively ... Read more c b
Genome-wide survey and analysis of allele-specific mRNA splicing in human and mouse

Author: Nembaware, Victoria Precious Date: 2008 This dissertation aims to examine allele-specific splicing in human and mouse using publicly available datasets. Such datasets, which have been generated from multiple tissue sources and from individuals of diverse backgrounds, are rich and ... Read more
Genome-wide survey of allele-specific splicing in humans

Author: Nembaware, Victoria ; Lupindo, Bukiwe ; Schouest, Katherine ; Spillane, Charles ; Scheffler, Konrad ; Seoighe, Cathal Date: 2008 BACKGROUND: Accurate mRNA splicing depends on multiple regulatory signals encoded in the transcribed RNA sequence. Many examples of mutations within human splice regulatory regions that alter splicing qualitatively or quantitatively have been ... Read more c b
A Genomic Portrait of Haplotype Diversity and Signatures of Selection in Indigenous Southern African Populations

Author: Chimusa, Emile R ; Meintjies, Ayton ; Tchanga, Milaine ; Mulder, Nicola ; Seoighe, Cathal ; Soodyall, Himla ; Ramesar, Rajkumar Date: 2015 We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between ... Read more c b
Heritability in the efficiency of nonsense-mediated mRNA decay in humans

Author: Seoighe, Cathal ; Gehring, Chris Date: 2010 BACKGROUND: In eukaryotes mRNA transcripts of protein-coding genes in which an intron has been retained in the coding region normally result in premature stop codons and are therefore degraded through the nonsense-mediated mRNA decay (NMD) ... Read more c b
Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts

Author: Nguyen, Thong T ; Seoighe, Cathal Date: 2013 Genetic variation in gene expression makes an important contribution to phenotypic variation and susceptibility to disease. Recently, a subset of cis -acting expression quantitative loci (eQTLs) has been found to result from polymorphisms ... Read more c b
Investigating the effect of paralogs on microarray gene-set analysis

Author: Faure, André Date: 2008 In order to interpret the results obtained from a microarray experiment, researchers often shift focus from analysis of individual differentially expressed genes to analyses of sets of genes. These gene-set analysis (GSA) methods use previously ... Read more
Investigating the effect of paralogs on microarray gene-set analysis

Author: Faure, Andre ; Seoighe, Cathal ; Mulder, Nicola Date: 2011 BACKGROUND: In order to interpret the results obtained from a microarray experiment, researchers often shift focus from analysis of individual differentially expressed genes to analyses of sets of genes. These gene-set analysis (GSA) methods ... Read more c b
Modelling the Evolution of HIV-1 Protein-Coding Sequences with Particular focus on the early stages of Infection

Author: Wood, Natasha Tandi Date: 2010 Modelling the Evolution of HIV-1 Protein-Coding Sequences with Particular Focus on the Early Stages of Infection Natasha Thandi Wood, February 2010 The evolution of the viral genome sequence over the course of HIV-1 infection is of interest ... Read more
MScanner: a classifier for retrieving Medline citations

Author: Poulter, Graham ; Rubin, Daniel ; Altman, Russ ; Seoighe, Cathal Date: 2008 BACKGROUND: Keyword searching through PubMed and other systems is the standard means of retrieving information from Medline. However, ad-hoc retrieval systems do not meet all of the needs of databases that curate information from literature, ... Read more c b
A mutation in a splicing factor that causes retinitis pigmentosa has a transcriptome-wide effect on mRNA splicing

Author: Korir, Paul K ; Roberts, Lisa ; Ramesar, Raj ; Seoighe, Cathal Date: 27 Jun 2014 Background: Substantial progress has been made in the identification of sequence elements that control mRNA splicing and the genetic variants in these elements that alter mRNA splicing (referred to as splicing quantitative trait loci – sQTLs). ... Read more c b
Prevalence and frequency spectra of single nucleotide polymorphisms at exon-intron junctions of human genes

Author: Lupindo, Bukiwe Date: 2008 In humans and other higher eukaryotes the observation of multiple splice isoforms for a given gene is common. However it is not clear whether all of these alternatively spliced isoforms are a product of true alternative splicing or some are ... Read more
Rapid statistical classification on the Medline database of biomedical literature

Author: Poulter, Graham L Date: 2008 Includes abstract. Includes bibliographical references (leaves 122-132). Read more
The regulatory effect of miRNAs is a heritable genetic trait in humans

Author: Geeleher, Paul ; Huang, Stephanie ; Gamazon, Eric ; Golden, Aaron ; Seoighe, Cathal Date: 2012 BACKGROUND:microRNAs (miRNAs) have been shown to regulate the expression of a large number of genes and play key roles in many biological processes. Several previous studies have quantified the inhibitory effect of a miRNA indirectly by ... Read more c b

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