A5058462619- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- SARS-CoV-2 and COVID-19 Research
- Mycobacterium research and diagnosis
- Animal Disease Management and Epidemiology
- Cancer Genomics and Diagnostics
- Microbial infections and disease research
- Tuberculosis Research and Epidemiology
- Listeria monocytogenes in Food Safety
- SARS-CoV-2 detection and testing
- Escherichia coli research studies
- Biosensors and Analytical Detection
- Genomics and Rare Diseases
- Environmental DNA in Biodiversity Studies
- Infectious Diseases and Mycology
- Evolution and Paleontology Studies
- Evolution and Genetic Dynamics
- Wildlife Ecology and Conservation
- Yersinia bacterium, plague, ectoparasites research
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- Plant-based Medicinal Research
- Scientific Computing and Data Management
- CRISPR and Genetic Engineering
European Bioinformatics Institute
2020-2025
University of Nottingham
2018-2024
Abstract The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to community contribute daily acceleration advance. Here, we outline major updates ENA’s services infrastructure that have been delivered over past year.
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), maintained by the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI), offers those producing data an open and supported platform for management, archiving, publication, dissemination of data; to scientific community as a whole, it globally comprehensive set through host discovery retrieval tools. Here, we describe recent updates ENA's submission services well focused efforts improve connectivity, reusability,...
Abstract The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena) is maintained by the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI). ENA one of three members International Sequence Database Collaboration (INSDC). It serves bioinformatics community worldwide via submission, processing, archiving and dissemination sequence data. supports data types ranging from raw reads, through alignments assemblies to functional annotation. enriched with contextual information...
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present world's public sequencing data benefit of entire scientific community acceleration global research effort. Here we highlight major developments ENA services content 2020, focussing particular on recently released updated browser, modernisation our release process...
Abstract Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis more than 2 million raw read datasets submitted to European COVID-19 Data Portal identify recombination. Co-infection was observed in 0.35% investigated cases. Two independent procedures were implemented detect We show that sensitivity is predominantly determined by...
The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level data sharing to open repositories, which actively supported identification SARS-CoV-2 structure, molecular interactions, mutations variants, facilitated vaccine development drug reuse studies design. European Data Platform was launched support this sharing, deposition several million raw reads. In paper we...
Antimicrobial resistance is undoubtedly one of the most significant threats to human health. Whilst finding alternative antimicrobials proves valuable, understanding how spread remains a necessity. The link between antimicrobial in agriculture and effect on medicine unclear, however contribution dissemination should not be overlooked. Escherichia coli (E. coli) are particular concern for health as common Gram-negative pathogen often used representative indicator resistance. Sheep hold unique...
The role of badgers in the geographic expansion bovine tuberculosis (bTB) epidemic England is unknown: indeed there have been few published studies bTB outside Southwest where infection now endemic cattle. Cheshire on edge expanding area which considered Previous studies, over a decade ago when was rare Cheshire, found no or only infected south eastern county. In this study, carried out 2014, road-killed were collected through network local stakeholders (farmers, veterinarians, wildlife...
Antimicrobial resistance is undoubtedly one of the most significant threats to human health. Whilst finding alternative antimicrobials proves valuable, understanding how spread remains a necessity. The link between antimicrobial in agriculture and effect on medicine unclear, however contribution dissemination should not be overlooked. Escherichia coli (E. coli) are particular concern for health as common Gram-negative pathogen often used representative indicator resistance. Sheep hold unique...
Abstract Bovine tuberculosis (bTB) is an important animal health and economic problem for the cattle industry a potential zoonotic threat. Wild badgers ( Meles meles ) play role on its epidemiology in some areas of high prevalence cattle, particularly UK Republic Ireland increasingly parts mainland Europe. However, little known about involvement spatial edge epidemic, where increasing seen. Here we report findings study found-dead (mainly road-killed) six counties English epidemic bTB...
Abstract Due to the constantly increasing number of mutations in SARS-CoV-2 genome, concerns have emerged over possibility decreased diagnostic accuracy reverse transcription-polymerase chain reaction (RT-PCR), gold standard test for SARS-CoV-2. We propose an analysis pipeline discover genomic variations overlapping target regions commonly used PCR primer sets. provide list these a publicly available format based on dataset more than 1.2 million samples. Our approach distinguishes among...
Abstract The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level data sharing to open repositories, which actively supported identification SARS-CoV-2 structure, molecular interactions, mutations variants, facilitated vaccine development drug reuse studies design. European Data Platform was launched support this sharing, deposition several million raw reads. In...
Abstract The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the Molecular Biology Laboratory's Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to community contribute daily acceleration advance. Outlined here changes updates on ENA service in 2024, aligning with broad goals enhancing interoperability, globalisation...
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for decisions. However, these international resources began primarily academic purposes, rather than surveillance or interventions. Now, queries need to access not only whole genomes multiple pathogens but also make...
Abstract European badgers ( Meles meles ) play an important role in the epidemiology of bovine tuberculosis (caused by Mycobacterium bovis England, but little is known about prevalence atypical mycobacteriosis. Badgers are also to be infected other infectious agents, and relationship between mycobacteriosis concomitant infections needs further investigation. Overall, 88 badger carcasses from Midlands England collected July 2016-August 2017 were selected for histopathological examination...
Fast, efficient public health actions require well-organized and coordinated systems that can supply timely accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for decisions. However, these international resources began primarily academic purposes, rather than surveillance or interventions. Now, queries need to access not only whole genomes multiple pathogens but also make...
Mycobacterium bovisis the causative agent of bovine tuberculosis (bTB), one most costly and persistent agricultural infectious diseases still widespread in England today. However, not all parts are created equally with respect to incidence bTB. In 2012 Department for Environment, Food Rural Affairs (DEFRA) divided country into three risk areas; high, low edge areas. The perpetuation bTB epidemic is often blamed on known wildlife host M. bovis , European badger (Meles meles). Despite this, no...