Ben Jeffery
A5057549841- Genomics and Phylogenetic Studies
- Malaria Research and Control
- Forensic and Genetic Research
- Mosquito-borne diseases and control
- CCD and CMOS Imaging Sensors
- Particle Detector Development and Performance
- RNA and protein synthesis mechanisms
- Electron and X-Ray Spectroscopy Techniques
- Radiation Detection and Scintillator Technologies
- Genetic diversity and population structure
- Evolution and Genetic Dynamics
- Mathematical Biology Tumor Growth
- X-ray Diffraction in Crystallography
- Particle physics theoretical and experimental studies
- Genetic and phenotypic traits in livestock
- Nuclear Physics and Applications
- Photocathodes and Microchannel Plates
- Crystallization and Solubility Studies
- Evolutionary Algorithms and Applications
- Blockchain Technology Applications and Security
- Life Cycle Costing Analysis
- Advanced Electron Microscopy Techniques and Applications
- Insect Resistance and Genetics
- Viral Infections and Outbreaks Research
- Hepatitis Viruses Studies and Epidemiology
Health Data Research UK
2024
University of Oxford
2007-2023
Genomics (United Kingdom)
2015-2021
Centre for Human Genetics
2015-2016
Health Protection Agency
2006
Central Electricity Generating Board
1964-1967
Abstract Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and usually only way of obtaining ground-truth data to evaluate inferences. Because this, large number specialized programs have been developed, each filling particular niche, but with largely overlapping functionality substantial duplication effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry mutation simulations based on...
MalariaGEN is a data-sharing network that enables groups around the world to work together on genomic epidemiology of malaria. Here we describe new release curated genome variation data 7,000 Plasmodium falciparum samples from partner studies in 28 malaria-endemic countries. High-quality genotype calls 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using standardised analysis pipeline. Copy number variants associated with drug resistance structural cause...
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding human history evolution. However, problem how best to characterize ancestral relationships totality genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us infer a unified genealogy humans. This compact representation multiple datasets explores challenges missing erroneous data uses samples constrain date relationships. We demonstrate...
Background: National Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for surveillance malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale projects by integrating simple sample collection procedures routine public health procedures. Methods: Samples from symptomatic patients are processed SpotMalaria, high-throughput system produces comprehensive set genotypes comprising...
Population genetic models only provide coarse representations of real-world ancestry. We used a pedigree compiled from 4 million parish records and genotype data 2276 French 20,451 Canadian individuals to finely model trace ancestry through space time. The loss ancestral population structure the appearance spatial regional highlights wide range expansion models. Geographic features shaped migrations, we find enrichments for migration, genetic, genealogical relatedness patterns within river...
<ns3:p>MalariaGEN is a data-sharing network that enables groups around the world to work together on genomic epidemiology of malaria. Here we describe new release curated genome variation data 7,000 <ns3:italic>Plasmodium falciparum</ns3:italic> samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using standardised analysis pipeline. Copy number variants associated...
Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex demographic histories are challenging, limiting our ability to benchmark statistical methods aimed at detecting and explore theoretical predictions. stdpopsim community-maintained simulation library already provides an extensive catalog species-specific population models. Here we present major...
Abstract Recombination is an ongoing and increasingly important feature of circulating lineages SARS-CoV-2, challenging how we represent the evolutionary history this virus giving rise to new variants potential public health concern by combining transmission immune evasion properties different lineages. Detection recombinant strains challenging, with most methods looking for breaks between sets mutations that characterise distinct In addition, many basic approaches fundamental study viral...
Abstract The sequencing of modern and ancient genomes from around the world has revolutionised our understanding human history evolution 1,2 . However, general problem how best to characterise full complexity ancestral relationships totality genomic variation remains unsolved. Patterns in each data set are typically analysed independently, often using parametric models or reduction techniques that cannot capture ancestry 3,4 Moreover, technology 5,6 , quality 7 silico processing 8,9 coupled...
Abstract Background Variant Call Format (VCF) is the standard file format for interchanging genetic variation data and associated quality control metrics. The usual row-wise encoding of VCF model (either as text or packed binary) emphasises efficient retrieval all a given variant, but accessing on field sample basis inefficient. Biobank scale datasets currently available consist hundreds thousands whole genomes terabytes compressed VCF. Row-wise storage fundamentally unsuitable more scalable...
The changes in sensitivity of the AEI electron probe microanalyser when used with samples various γ-activities have been estimated. Three methods for reducing background count were investigated: (i) use conventional electronic gates; (ii) reduction scintillator size to that x-ray beam; (iii) lead shielding from direct radiation. These reduce by factors 5, 102 and respectively. Nomograms are presented calculating any set conditions.
The size and complexity of modern large-scale genome variation studies demand novel approaches for exploring sharing the data. In order to unlock potential these data a broad audience scientists with various areas expertise, unified exploration framework is required that accessible, coherent user-friendly.Panoptes an open-source software collaborative visual associated metadata in web browser. It relies on technology choices allow it operate near real-time very large datasets. can be used...
ABSTRACT National Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for surveillance malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale projects by integrating simple sample collection procedures routine public health procedures. Samples are processed high-throughput technologies genotype several drug resistance markers, species markers and genomic barcode, delivering...
Abstract Population genetic models only provide coarse representations of real-world ancestry. We use a pedigree compiled from four million parish records and genotype data 2,276 French 20,451 Canadian (FC) individuals, to finely model trace FC ancestry through space time. The loss ancestral population structure the appearance spatial regional highlights wide range expansion models. Geographic features shaped migrations throughout, we find enrichments for migration, genealogical relatedness...
Abstract Artemisinin resistant Plasmodium falciparum is advancing across Southeast Asia in a soft selective sweep involving at least 20 independent kelch13 mutations. In large global survey, we find that mutations which cause resistance are present low frequency Africa. We show African have originated locally, and shows normal variation pattern relative to other genes Africa, whereas there great excess of non-synonymous mutations, many radical amino-acid changes. Thus, not currently...