A5081386063- Genetic Associations and Epidemiology
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Rare Diseases
- Biomedical and Engineering Education
- Biomedical Text Mining and Ontologies
- Gene expression and cancer classification
- RNA modifications and cancer
- Air Quality Monitoring and Forecasting
- Scientific Computing and Data Management
- vaccines and immunoinformatics approaches
- Health, Environment, Cognitive Aging
- Global Health and Surgery
- Ethics in Clinical Research
- Pharmacogenetics and Drug Metabolism
- Bioinformatics and Genomic Networks
- Genomic variations and chromosomal abnormalities
- T-cell and B-cell Immunology
- Epigenetics and DNA Methylation
- Evolution and Genetic Dynamics
- Healthcare Systems and Public Health
- Labor Market and Education
- Cardiovascular Health and Risk Factors
- Genetics and Physical Performance
- Pulmonary Hypertension Research and Treatments
- Metabolomics and Mass Spectrometry Studies
University of Cape Town
2015-2023
University of Central Thailand
2023
African Organisation for Research and Training in Cancer
2015-2017
African Institute for Mathematical Sciences
2015
The H3ABioNet pan-African bioinformatics network, which is funded to support the Human Heredity and Health in Africa (H3Africa) program, has developed node-assessment exercises gauge ability of its participating research service groups analyze typical genome-wide datasets being generated by H3Africa groups. We describe a framework for assessment computational genomics analysis skills, includes standard operating procedures, training test datasets, process administering exercise. present...
Based on evaluations of imputation performed a genotype dataset consisting about 11,000 sub-Saharan African (SSA) participants, we show Trans-Omics for Precision Medicine (TOPMed) and the Genome Resource (AGR) to be currently best panels imputing SSA datasets. We report notable differences in number single-nucleotide polymorphisms (SNPs) that are imputed by different datasets from East, West, South Africa. Comparisons with subset 95 high-coverage whole-genome sequences (WGSs) despite being...
The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. H3ABioNet is part of the Human Health and Heredity Africa program (H3Africa), an African-led consortium funded by US National Institutes UK Wellcome Trust, aimed at using genomics to study improve health Africans. A key role support H3Africa projects building infrastructure such as portable reproducible workflows for use on heterogeneous computing environments. Processing analysis...
Abstract Pulmonary function is an indicator of well-being, and pulmonary pathologies are the third major cause death worldwide. We analysed UK Biobank genome-wide association summary statistics for Europeans individuals recent African descent to identify variants associated with trait in two ancestries. Here, we show 627 3 Africans three parameters. In addition 110 previously reported be phenotypes related function, 279 novel loci, including ISX intergenic variant rs369476290 on chromosome...
Introduction: Investigating variation in genes involved the absorption, distribution, metabolism, and excretion (ADME) of drugs are key to characterizing pharmacogenomic (PGx) relationships. ADME gene is relatively well characterized European Asian populations, but data from African populations under-studied—which has implications for drug safety effective use Africa. Results: We identified significant using 458 high-coverage whole genome sequences, 412 which novel, previously available...
Abstract Motivation: Despite numerous successful Genome-wide Association Studies (GWAS), detecting variants that have low disease risk still poses a challenge. GWAS may miss genes with weak genetic effects or strong epistatic due to the single-marker testing approach commonly used. thus generate false negative inconclusive results, suggesting need for novel methods combine of single nucleotide polymorphisms within gene increase likelihood fully characterizing susceptibility gene. Results: We...
Abstract Summary: Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating information contained in the structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable similarity-based Functional analysis). It is a portable software package all known content-based relevant applications associated with measures. has advantage not only of...
Sickle cell disease (SCD) is a debilitating single gene disorder caused by point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% SCD newborns world-wide occurs sub-Saharan Africa, where neonatal and childhood mortality from sickle related complications high. While research across the globe tackling on multiple fronts, advances have yet significantly impact health quality life patients, due lack coordination these disparate...
<ns4:p>The need for portable and reproducible genomics analysis pipelines is growing globally as well in Africa, especially with the growth of collaborative projects like Human Health Heredity Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized portable, adapted to heterogeneous computing environments, nurturing technical expertise workflow languages containerization technologies. Building on network’s Standard Operating Procedures (SOPs)...
Aim: To provide pharmacogenomics reporting guidelines, the information and tools required for to public omic databases. Material & methods: For effective DMET data interpretation, sharing, interoperability, reproducibility reporting, we propose Minimum Information a Experiment (MIDE) reporting. Results: MIDE provides guidelines describes storage sharing in form of XML. Conclusion: The will benefit scientific community with experiments, including from other technology platforms, that ease...
A shortage of practical skills and relevant expertise is possibly the primary obstacle to social upliftment sustainable development in Africa. The “omics” fields, especially genomics, are increasingly dependent on effective interpretation large complex sets data. Despite abundant natural resources population sizes comparable with many first-world countries from which talent could be drawn, Africa still lag far behind rest world terms specialized development. Moreover, there serious concerns...
Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic to researchers through an online ticketing platform. following article reports on the H3ABioNet HD (H3A-HD)'s development, outlining its design, management, usage evaluation framework, as well lessons learned implementation.The H3A-HD evaluated using automatically generated logs, user feedback qualitative...
<ns3:p>The need for portable and reproducible genomics analysis pipelines is growing globally as well in Africa, especially with the growth of collaborative projects like Human Health Heredity Africa Consortium (H3Africa). The Pan-African H3Africa Bioinformatics Network (H3ABioNet) recognized portable, adapted to heterogeneous compute environments, nurturing technical expertise workflow languages containerization technologies. To address this need, 2016 H3ABioNet arranged its first Cloud...
The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic thus difficult to impute. We therefore sought evaluate imputation accuracy, specifically West African population, since they are understudied known harbor high genetic diversity. study sets were selected from Gambian individuals within the Genome Variation Project (GGVP) Whole Sequence datasets. Two different arrays, Illumina Omni 2.5 Hereditary Health Africa...
The Human Leukocyte Antigen (HLA) region plays an important role in autoimmune and infectious diseases. HLA is a highly polymorphic thus difficult to impute. We, therefore, sought evaluate imputation accuracy, specifically West African population, since they are understudied known harbor high genetic diversity. study sets were selected from 315 Gambian individuals within the Genome Variation Project (GGVP) Whole Sequence datasets. Two different arrays, Illumina Omni 2.5 Hereditary Health...
The management and analyses of large datasets is one the grand challenges modern biomedical research. Establishing methods to harmonise standardise data collection, reporting, sharing employed dictionaries, can support resolution these whilst improving research quality, quality integrity, allowing sustainable knowledge transfer through re-usability, interoperability, reproducibility. current project aimed develop propose a standardised reporting guideline for stroke clinical reporting....
Abstract Investigating variation in genes involved the absorption, distribution, metabolism , and excretion (ADME) of drugs are key to characterising pharmacogenomic (PGx) relationships. ADME gene is relatively well characterised European Asian populations, but African populations under-studied – which has implications for safe effective drug use Africa. The genetic diversity across sub-Saharan large. Southern population cluster most distinct from that far West PGx strategies based on...
Objective This project aimed to develop and propose a standardised reporting guideline for kidney disease research clinical data reporting, in order improve quality integrity, combat challenges associated with the management of ‘Big Data’. Methods A list recommendations was proposed based on systematic review consolidation previously published collection standards, including PhenX measures Minimal Information about Proteomics Experiment (MIAPE). Thereafter, these were reviewed by...
Abstract We previously proposed a structure for recording consent-based data use ‘categories’ and ‘requirements’ – Consent Codes with view to supporting maximum integration of genomic research datasets, reducing uncertainty about permissible re-use shared data. Here we discuss clarifications subsequent updates the (v4) based on new areas application (e.g., neurosciences, biobanking, H3Africa), policy developments return results), further practical considerations, including in automated...