244 research outputs found
KABOOM! A new suffix-array based algorithm for clustering expression data
No full textHazelhurst S, Lipták Z. KABOOM! A new suffix-array based algorithm for clustering expression data. Bioinformatics. 2011;27(24):3348-3355
A Method for Evaluating the Quality of String Dissimilarity Measures and Clustering Algorithms for EST Clustering.
No full textZimmermann J, Lipták Z, Hazelhurst S. A Method for Evaluating the Quality of String Dissimilarity Measures and Clustering Algorithms for EST Clustering. In: Proc. BIBE. 2004: 301-309
Building portable pipelines for reproducible scientific workflows: The H3ABionet Pipelines Project on E n
No full textPresentation given by Scott Hazelhurst at Galaxy Africa 2018 (Cape Town, South Africa)</div
An overview of the wcd EST clustering tool
No full textHazelhurst S, Hide W, Lipták Z, Nogueira R, Starfield R. An overview of the wcd EST clustering tool. BIOINFORMATICS. 2008;24(13):1542-1546.The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d(2) distance function or edit distance, improving existing implementations of d(2). It supports merging, refinement and reclustering of clusters. It is drop in compatible with the StackPack clustering package. wcd supports parallelization under both shared memory and cluster architectures. It is distributed with an EMBOSS wrapper allowing wcd to be installed as part of an EMBOSS installation (and so provided by a web server)
Medical population genetics and GWAS for complex diseases 19th April - 24th April 2015 Training Material Archive
No full textThis is an archive containing training materials for the H3ABioNet course: “Medical population genetics and GWAS for complex diseases 19th April - 24th April, 2015”.Brief description of the course: The workshop was split into two tracks:An introductory track that will cover fundamental assumptions, showcase recent successes and discuss limitations of current GWAS approaches in the field of complex diseases, particularly in the case of African populations with known low linkage disequilibrium (LD). It will also provide a ‘hands-on’ experience of data analysis and a stage for shaping the next generation of GWAS scientists/researchers.An advanced track which will draw upon the audience’s interdisciplinary expertise in mathematics, simulation studies, statistics and machine learning to overcome present challenges and identify the most promising avenues of future research for effective phenotype–genotype association.Course trainers/authors: Prof. Scott Hazelhurst, Dr. Noah Zaitlen, Dr. Bogdan Pasaniuc, Dr. Bjarni Vilhjalmsson and Shaun AronCourse sponsor/organisers:Prof. Nicola Mulder, Dr. Emile Chimusa, Dr. Judit Kumuthini and Dr. Gaston KuzamunuCourse level: IntermediateThe archive contains the following items:Trainer/creator file containing the names of the person/s responsible for organising and delivering the courseCourse information file - which contains the original information about the course and includes a course scheduleLecture materials which include lecture slides, tutorials and datasetsThis upload was performed by: Verena Ras | H3ABioNet Training and Outreach Coordinator</p
Compositional Model Checking Of Partially Ordered State Spaces
No full textSymbolic trajectory evaluation (STE) --- a model checking technique based on partial order representations of state spaces --- has been shown to be an effective model checking technique for large circuit models. However, the temporal logic that it supports is restricted, and as with all verification techniques has significant performance limitations. The demand for verifying larger circuits, and the need for greater expressiveness requires that both these problems be examined. The thesis develops a suitable logical framework for model checking partially ordered state spaces: the temporal logic TL and its associated satisfaction relations, based on the quaternary logic Q. TL is appropriate for expressing the truth of propositions about partially ordered state spaces, and has suitable technical properties that allow STE to support a richer temporal logic. Using this framework, verification conditions called assertions are defined, a generalised version of STE is developed, and three STE-..
Characterising the combined eects of cytochrome P450 missense variants within the star allele nomenclature
No full textA dissertation submitted in fulfillment of the requirements for the degree of Master of Science in Medicine to the Faculty of Health Sciences, School of Pathology University of the Witwatersrand, Johannesburg 2024Genetic variations in Cytochrome P450 (CYP) enzymes shape drug responses. However, many CYP haplotypes (star alleles) lack functional annotations, posing a barrier to under- standing drug metabolism comprehensively. To address this, our study investigates combined missense variant eects on CYP enzyme structures, analyzing 261 variants across 91 CYP haplotypes. We utilized Normal Mode Analysis (NMA; FoldX and ENCoM) to explore variant impact on protein stability. Subsequently, we conducted Molecular Dynamics (MD) simulations on key alleles, CYP2D6*2 and CYP2D6*17, to reveal star allele impact on protein dynamics. Integrating NMA and MD, we uncover the interactions that collectively shape the conformation and attributes of CYP enzymes. Notably, our investigation highlights significant deviations between wild-type and CYP2D6*17 -encoded proteins in the F/G loop region, pivotal for CYP functionality. Additionally, we compare
NMA results with CYP2C9 and CYP2C19 Deep Mutational Scanning (DMS) results, identifying 65% concordance. Furthermore, our NMA predictions show 80% concordance with commonly used Variant Eect Predictor tools. This alignment underscores our approach’s reliability in predicting variant eects. Our study illuminates missense variants’ nuanced impact on CYP protein structures, significant for personalized medicine and drug response prediction, as accurate drug response predictions hinge on a comprehensive understanding of CYP missense variants. Moreover, our study highlights multi-scalemodelling potential for interpreting CYP missense variants, especially in star alleles. The synergy of NMA, MD simulation, and assays like DMS is invaluable, each with distinct
strengths and limitations. This research deepens our understanding of the complexity of CYP metabolism profiles, providing insights into the functional assessment of CYP star alleles and missense variants with unknown functional classifications.MM202
The Gene Catalogue and Functional Analysis of the Gut Microbiome of Lions in Etosha National Park
No full textA dissertation submitted in fulfilment of the requirements for the degree Master of Science, to the Faculty of Science, School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, 2024.Characterising the microbiomes of free-living mammals may aid conservation efforts, yet the gut microbiome of carnivores is underrepresented. This study represents the first description of the gut microbiome of free-living African lions (Panthera leo melanochaita). Faecal samples from 20 lions were collected in Etosha National Park, Namibia and microbial DNA was extracted. Samples were then whole genome sequenced, and classified using MetaPhlAn and Genome Taxonomy Database toolkit. The two most abundant bacterial genera in the lions’ gut microbiomes were Bacteroides (16.9%) and Phocaeicola (16.6%). Microbiome diversity was similar between the sexes and across seasons as assessed through Bray-Curtis dissimilarity and Shannon diversity index. The genus Clostridium_AH was more abundant in male lions (P = 0.007; d.f. = 22), while Aphodousia (P = 0.003; d.f. = 22) was more abundant in females. Lions captured in winter had a high abundance of Plesiomonas relative to those captured in summer (P = 0.008), whereas lions captured in summer a high abundance of Dysosmobacter (P = 0.038; d.f. = 22), Pelethomonas (P = 0.021; d.f. = 22), Metalachnospira (P = 0.033; d.f. = 22) and Clostridium Q (P = 0.012; d.f. = 22) compared to those captured in winter. Following various taxonomic classification approaches, a third of the reads (33.6%) present in the lion gut microbiome remained unclassified. We constructed 272 metagenome assembled genomes, from seven bacterial phyla, representing mostly new species which will contribute to understanding of the carnivore gut microbiome.National Research Foundation (DST-NRF)MMM202
Women\u27s Council to Honor Lydia and Dan Jones With 2025 Legacy Award
No full textOXFORD, Miss. – The Ole Miss Women\u27s Council for Philanthropy is honoring Lydia and Dr. Dan Jones, former University of Mississippi chancellor, with it 2025 Legacy Award, recognizing the Hazelhurst couple\u27s decades of service to others
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