Alan Tracey
A5047614339- Vanadium and Halogenation Chemistry
- Genomics and Phylogenetic Studies
- Parasite Biology and Host Interactions
- Parasites and Host Interactions
- Molecular spectroscopy and chirality
- Chromosomal and Genetic Variations
- Liquid Crystal Research Advancements
- Oxidative Organic Chemistry Reactions
- Genetic diversity and population structure
- Helminth infection and control
- Metal-Catalyzed Oxygenation Mechanisms
- Surfactants and Colloidal Systems
- Insect symbiosis and bacterial influences
- Polyoxometalates: Synthesis and Applications
- Catalysis and Oxidation Reactions
- Protein Tyrosine Phosphatases
- Carbohydrate Chemistry and Synthesis
- CRISPR and Genetic Engineering
- Nematode management and characterization studies
- Genetics, Bioinformatics, and Biomedical Research
- RNA and protein synthesis mechanisms
- Crystallization and Solubility Studies
- Electrochemical Analysis and Applications
- Genomics and Chromatin Dynamics
- Molecular Sensors and Ion Detection
Wellcome Sanger Institute
2016-2025
Rockefeller University
2024
Shepherd University
2023
University of Edinburgh
2020
Aarhus University
2020
The University of Texas Health Science Center at San Antonio
2020
Fundação Oswaldo Cruz
2020
University of Dundee
2020
Tufts University
2020
Bovey Tracey Hospital
2018
A high-quality sequence assembly of the zebrafish genome reveals largest gene set any vertebrate and provides information on key genomic features, comparison to human reference shows that approximately 70% protein-coding genes have at least one clear orthologue. The — a model organism for study development disease has now been sequenced published as well-annotated genome. Zebrafish turns out so far sequenced, few pseudogenes. Importantly studies, between sequences obvious second paper...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such available only a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling highly accurate nearly genomes. Here we present lessons learned from generating 16 that represent six major vertebrate...
Abstract Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free is therefore ultimate, but sadly still unachieved goal a multitude research projects. Despite ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near genome eukaryotes. Whilst working towards improved datasets fully evaluation curation actively used to bridge this shortcoming significantly reduce...
Tapeworms (Cestoda) cause neglected diseases that can be fatal and are difficult to treat, owing inefficient drugs. Here we present an analysis of tapeworm genome sequences using the human-infective species Echinococcus multilocularis, E. granulosus, Taenia solium laboratory model Hymenolepis microstoma as examples. The 115- 141-megabase genomes offer insights into evolution parasitism. Synteny is maintained with distantly related blood flukes but find extreme losses genes pathways...
Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans animals, decimate crop production are a major impediment to socioeconomic development. Here we report broad comparative study 81 genomes parasitic non-parasitic worms. We have identified gene family births hundreds expanded families at key nodes in the phylogeny that relevant parasitism. Examples include modulate host immune responses, enable parasite migration though tissues or...
Taisei Kikuchi, Mark Viney, Matthew Berriman and colleagues report the genome sequences of six species nematodes from Strongyloides clade nematodes, including human animal pathogens, facultative parasites a free-living species. They find that expansions astacin SCP/TAPS gene families are associated with parasitism in these Soil-transmitted genus, cause one most prevalent neglected tropical diseases. Here we compare genomes four species, pathogen stercoralis, their close relatives...
Abstract The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still many gaps and errors, does not represent biological genome as is blend multiple individuals 3,4 Recently, telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but derived from hydatidiform mole cell line nearly homozygous 5 To address these limitations, Human Pangenome...
Abstract Numerous novel adaptations characterise the radiation of notothenioids, dominant fish group in freezing seas Southern Ocean. To improve understanding evolution this iconic group, here we generate and analyse new genome assemblies for 24 species covering all major subgroups radiation, including five long-read assemblies. We present a estimate onset at 10.7 million years ago, based on time-calibrated phylogeny derived from genome-wide sequence data. identify two-fold variation size,...
Whipworms are common soil-transmitted helminths that cause debilitating chronic infections in man. These nematodes only distantly related to Caenorhabditis elegans and have evolved occupy an unusual niche, tunneling through epithelial cells of the large intestine. We report here whole-genome sequences human-infective Trichuris trichiura mouse laboratory model muris. On basis whole-transcriptome analyses, we identify many genes expressed a sex- or life stage-specific manner characterize...
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of counterion substitution on the type and nature nematic lyotropic phases from nuclear magnetic resonance studiesK. Radley, L. W. Reeves, A. S. TraceyCite this: J. Phys. Chem. 1976, 80, 2, 174–182Publication Date (Print):January 1, 1976Publication History Published online1 May 2002Published inissue 1 January 1976https://pubs.acs.org/doi/10.1021/j100543a018https://doi.org/10.1021/j100543a018research-articleACS PublicationsRequest reuse...
Abstract Haemonchus contortus is a globally distributed and economically important gastrointestinal pathogen of small ruminants has become key nematode model for studying anthelmintic resistance other parasite-specific traits among wider group parasites including major human pathogens. Here, we report using PacBio long-read OpGen 10X Genomics long-molecule methods to generate highly contiguous 283.4 Mbp chromosome-scale genome assembly resolved sex chromosome the MHco3(ISE).N1 isolate. We...
Abstract High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, biodiversity conservation. However, such only available a few non-microbial species 1–4 . To address this issue, international Genome 10K (G10K) consortium 5,6 has worked over five-year period evaluate develop cost-effective methods assembling most accurate genomes date. Here we summarize these developments, introduce set quality standards, present lessons...
Abstract Human onchocerciasis is a serious neglected tropical disease caused by the filarial nematode Onchocerca volvulus that can lead to blindness and chronic disability. Control of relies largely on mass administration single drug, development new drugs vaccines depends better knowledge parasite biology. Here, we describe chromosomes O. its Wolbachia endosymbiont. We provide highest-quality sequence assembly for any parasitic date, giving glimpse into evolution proteomes. This resource...
Abstract A ‘sibling’ species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations biological phenomena. Here, we describe first sibling C . , C. inopinata n. sp., isolated from fig syconia Okinawa, Japan. We investigate morphology, developmental processes and behaviour which differ significantly those The 123-Mb genome was sequenced assembled into six nuclear chromosomes, allowing delineation...
Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on infected red blood cell surface. We identified genomic processes driving diversity in genes encoding VESA (ves1) comparative analysis within and between three species, (B. bigemina, B. divergens bovis). Ves1 structure diverges rapidly after speciation, notably...
CRISPR/Cas9-based genome editing has yet to be reported in species of the Platyhelminthes. We tested this approach by targeting omega-1 (ω1) Schistosoma mansoni as proof principle. This secreted ribonuclease is crucial for Th2 polarization and granuloma formation. Schistosome eggs were exposed Cas9 complexed with guide RNA complementary ω1 electroporation or transduction lentiviral particles. Some also transfected a single stranded donor template. Sequences amplicons from gene-edited...
Abstract Background Modern sequencing technologies should make the assembly of relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address directly. Results As part Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification reads and de novo incorporates both long (> 10 kbp, PacBio or Nanopore) short (100–300 bp, Illumina) reads. Our leads to successful complete mitogenome assemblies 100...
Over 250 million people suffer from schistosomiasis, a tropical disease caused by parasitic flatworms known as schistosomes. Humans become infected free-swimming, water-borne larvae, which penetrate the skin. The earliest intra-mammalian stage, called schistosomulum, undergoes series of developmental transitions. These changes are critical for parasite to adapt its new environment it navigates through host tissues reach niche, where will grow reproductive maturity. Unravelling mechanisms...
Infections with helminths cause an enormous disease burden in billions of animals and plants worldwide. Large scale use anthelmintics has driven the evolution resistance a number species that infect livestock companion animals, there are growing concerns regarding reduced efficacy some human-infective helminths. Understanding mechanisms by which evolves is focus increasing interest; robust genetic analysis challenging, although many candidate genes have been proposed, basis remains poorly...
Schistosomes cause schistosomiasis, the world’s second most important parasitic disease after malaria in terms of public health and social-economic impacts. A peculiar feature these dioecious parasites is their ability to produce viable fertile hybrid offspring. Originally only present tropics, schistosomiasis now also endemic southern Europe. Based on analysis two genetic markers European schistosomes had previously been identified as hybrids between livestock- human-infective species...
Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis the unique physiological and ecological traits enabling these species to thrive in diverse habitats remains largely unknown. Additionally, many populations have drastically declined due anthropogenic activities past two centuries, their recovery is a high global conservation priority. We generated analyzed high-quality reference genomes for leatherback (...
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold increases contiguity 290-fold compared with its predecessor. Gene annotations are now more complete, improving mapping precision genomic, transcriptomic, proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains substrains using mRatBN7.2. defined...