David K. Jackson
A5036633643- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 Clinical Research Studies
- Animal Virus Infections Studies
- American Sports and Literature
- COVID-19 epidemiological studies
- Parallel Computing and Optimization Techniques
- Evolutionary Algorithms and Applications
- Genomics and Phylogenetic Studies
- Embedded Systems Design Techniques
- Teaching and Learning Programming
- COVID-19 diagnosis using AI
- Software Engineering Research
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- American Constitutional Law and Politics
- Evolution and Genetic Dynamics
- Software Testing and Debugging Techniques
- Geriatric Care and Nursing Homes
- Respiratory viral infections research
- Genetic Associations and Epidemiology
- RNA modifications and cancer
- American and British Literature Analysis
- Visual and Cognitive Learning Processes
- VLSI and FPGA Design Techniques
Wellcome Sanger Institute
2011-2022
Imperial College London
2022
Quadram Institute
2022
Genomics (United Kingdom)
2021-2022
UK Research and Innovation
2021
Public Health England
2019-2021
VIR Biotechnology (United States)
2021
National Institute for Health Research
2021
MRC Biostatistics Unit
2021
University of Cambridge
2021
The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK late summer to early autumn 20202. Whole-genome sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion B.1.1.7 during 2020, suggesting that it has a selective advantage. Here we changes VOC frequency inferred genetic correspond closely S gene target failures (SGTF) PCR testing. Analysis trends SGTF and...
The contribution of rare and low-frequency variants to human traits is largely unexplored. Here we describe insights from sequencing whole genomes (low read depth, 7×) or exomes (high 80×) nearly 10,000 individuals population-based disease collections. In extensively phenotyped cohorts characterize over 24 million novel sequence variants, generate a highly accurate imputation reference panel identify alleles associated with levels triglycerides (APOB), adiponectin (ADIPOQ) low-density...
The degree of protective immunity conferred by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently unknown. As such, the possibility reinfection SARS-CoV-2 not well understood. We describe an investigation two instances in same individual.
Abstract The SARS-CoV-2 lineage B.1.1.7, now designated Variant of Concern 202012/01 (VOC) by Public Health England, originated in the UK late Summer to early Autumn 2020. We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected community-based diagnostic testing provides an indication changing prevalence different genetic variants through time. Phylodynamic modelling additionally indicates that...
CpG islands (CGIs) are dense clusters of sequences that punctuate the CpG-deficient human genome and associate with many gene promoters. As CGIs also differ from bulk chromosomal DNA by their frequent lack cytosine methylation, we devised a CGI enrichment method based on nonmethylated affinity chromatography. The resulting library was sequenced to define novel blood set includes not detected current algorithms. Approximately half were associated annotated transcription start sites, remainder...
We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase affinity the ACE2 confer antibody escape. In vitro, we show that, although itself is not an evasion mechanism, it increases infectivity associated with enhanced incorporation cleaved into virions. able partially rescue proteins that have acquired Y453F escape...
We report a novel resource (methylation profiles of DNA, or mPod) for human genome-wide tissue-specific DNA methylation profiles. mPod consists three fully integrated parts, reference 13 normal somatic tissues, placenta, sperm, and an immortalized cell line, visualization tool that has been with the Ensembl genome browser new algorithm analysis immunoprecipitation-based demonstrate utility our by identifying first comprehensive set differentially methylated regions (tDMRs) may play role in...
Imputing genotypes from reference panels created by whole-genome sequencing (WGS) provides a cost-effective strategy for augmenting the single-nucleotide polymorphism (SNP) content of genome-wide arrays. The UK10K Cohorts project has generated data set 3,781 whole genomes sequenced at low depth (average 7x), aiming to exhaustively characterize genetic variation down 0.1% minor allele frequency in British population. Here we demonstrate value this resource improving imputation accuracy rare...
The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and recognised as most variable region in genome. primary aim MHC Haplotype Project was to provide a comprehensively annotated reference sequence single, leukocyte antigen-homozygous haplotype use it basis against which variations could be assessed from seven other similarly homozygous cell lines, representative common haplotypes European population. Comparison sequences,...
Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around world. The modest mutation rate rapid prevents reconstruction from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe patterns in 1181 samples sequenced to high depth duplicate. 95.1% show mutations at detectable allele frequencies. Analyses mutational spectra revealed strong...
The task of grading solutions to student programming exercises is laborious and error-prone. We have developed a software tool called ASSYST that designed relieve tutor much the burden assessing such programs. offers graphical interface can be used direct all aspects process, it considers wide range criteria in its automatic assessment. Experience with system has been encouraging.
One of the limitations on imaging fluorescent proteins within living cells is that they are usually present in small numbers and need to be detected over a large background. We have developed means isolate specific fluorescence signals from background by using lock-in detection modulated class optical probe termed "optical switches." This (OLID) approach involves modulating emission through deterministic, control its nonfluorescent states, subsequently applying method signal interest...
Long-read sequencing technologies such as Pacific Biosciences and Oxford Nanopore MinION are capable of producing long reads with average fragment lengths over 10,000 base-pairs maximum reaching 100,000 base- pairs. Compared short reads, the assemblies obtained from long-read platforms have much higher contig continuity genome completeness fragments able to extend paths into problematic or repetitive regions. Many successful assembly applications technology been reported ranging small...
Abstract The evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus leads to new variants that warrant timely epidemiological characterization. Here we use dense genomic surveillance data generated by COVID-19 Genomics UK Consortium reconstruct dynamics 71 different lineages in each 315 English local authorities between September 2020 and June 2021. This analysis reveals a series subepidemics peaked early autumn 2020, followed jump transmissibility B.1.1.7/Alpha...
The degree of protective immunity conferred by infection with SARS-CoV-2 is currently unknown. As such, the possibility reinfection this virus not well understood. Herein, we describe data from an investigation two instances in same individual. Through nucleic acid sequence analysis, viruses associated each instance were found to possess a genetic discordance that cannot be explained reasonably through short-term vivo evolution. We conclude it possible for humans become infected multiple...
The task of grading solutions to student programming exercises is laborious and error-prone. We have developed a software tool called ASSYST that designed relieve tutor much the burden assessing such programs. offers graphical interface can be used direct all aspects process, it considers wide range criteria in its automatic assessment. Experience with system has been encouraging.
A minor but significant fraction of samples subjected to next-generation sequencing methods are either mixed-up or cross-contaminated. These events can lead false inconclusive results. We have therefore developed SASI-Seq; a process whereby set uniquely barcoded DNA fragments added destined for sequencing. From the final data, one verify that all reads derive from original sample(s) and not contaminants other samples. By adding mixture three amplicons, different sizes spanning range insert...
Abstract Background Since the emergence of SARS-CoV-2, evolutionary pressure has driven large increases in transmissibility virus. However, with increasing levels immunity through vaccination and natural infection will switch towards immune escape. Genomic surveillance regions high is crucial detecting emerging variants that can more successfully navigate landscape. Methods We present phylogenetic relationships lineage dynamics within England (a country immunity), as inferred from a random...