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Chronogram: an R package for data curation and analysis of infection and vaccination cohort studies.
Bioinform Adv
September 2024
The Francis Crick Institute, London, NW1 1AT, United Kingdom.
Motivation: Observational cohort studies that track vaccine and infection responses offer real-world data to inform pandemic policy. Translating biological hypotheses, such as whether different patterns of accumulated antigenic exposures confer differing antibody responses, into analysis code can be onerous, particularly when source data is dis-aggregated.
Results: The R package chronogram introduces the class chronogram, where metadata is seamlessly aggregated with sparse infection episode, clinical and laboratory data.
PhageDive: the comprehensive strain database of prokaryotic viral diversity.
Nucleic Acids Res
January 2025
Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, 38124 Braunschweig, Germany.
Prokaryotic viruses represent the most diverse and abundant biological entities on Earth. So far, data on bacteriophages are not standardized, not readily available for comparative analyses and cannot be linked to the rapidly growing (meta)genomic data. We developed PhageDive (https://phagedive.
View Article and Find Full Text PDFAnnotation of Functions of Sequences of Concern and Its Relevance to the New Biosecurity Regulatory Framework in the United States.
Appl Biosaf
September 2024
Signature Science, LLC, Austin, Texas, USA.
Introduction: Recent regulations from United States Government agencies reshape the screening of synthetic nucleic acids. These take a step away from categorizing hazard on the basis of "bad" taxa and invoke the function of the sequence in pathogenesis or intoxication. Ascertaining functions related to pathogenesis and distinguishing these from other molecular abilities that are unproblematic is not simple.
View Article and Find Full Text PDFWhat are the neurodevelopmental outcomes of children with asymptomatic congenital cytomegalovirus infection at birth? A systematic literature review.
Rev Med Virol
July 2024
Institute for Global Health, University College London, London, UK.
Article Synopsis
- Congenital cytomegalovirus (cCMV) is prevalent globally, with 85%-90% of infected infants showing no symptoms at birth, but 10%-15% may face issues like sensorineural hearing loss later on.
- A review of studies focused on the neurodevelopmental outcomes of asymptomatic cCMV (AcCMV) in children found that they generally performed better than symptomatic cCMV children, but the understanding of their long-term neurodevelopment is still unclear.
- Most studies showed AcCMV children had comparable outcomes to CMV-uninfected children, though limitations like a lack of control groups and inconsistent definitions hindered the findings; further research with standardized methods is needed.
A SARS-CoV-2 minimum data standard to support national serology reporting.
Ann Clin Biochem
November 2024
School of Medicine, University of Dundee, Dundee, UK.
Background: Healthcare laboratory systems produce and capture a vast array of information, yet do not always report all of this to the national infrastructure within the United Kingdom. The global COVID-19 pandemic brought about a much greater need for detailed healthcare data, one such instance being laboratory testing data. The reporting of qualitative laboratory test results (e.
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