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Related Concept Videos

Interpreting R Charts01:22

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R chart, or range chart, is a fundamental tool in statistical process control used to monitor the variability within a process. It complements the X-bar (x̄) chart by focusing on the range of the data, rather than individual values, providing a clear picture of the process dispersion over time.
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In the ever-evolving field of public health, statistical analysis serves as a cornerstone for understanding and managing disease outbreaks. By leveraging various statistical tools, health professionals can predict potential outbreaks, analyze ongoing situations, and devise effective responses to mitigate impact. For that to happen, there are a few possible stages of the analysis:
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Run charts, essentially line graphs plotted over time, serve as fundamental yet effective tools for process analysis. They chronicle data sequentially, facilitating the identification of trends, shifts, or cyclical movements. This graphical representation is instrumental in determining whether a process is stable or exhibits signs of potential instability indicative of special cause variation. In the healthcare domain, run charts depict infection rates over time, enabling hospitals to monitor...
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An unknown compound can be established by identifying the molecular ion peak in the mass spectrum. The molecular ion peak is often weak or absent due to the predominance of fragmentation in high-energy electron beams. In such cases, a soft-energy electron beam can be used to scan the spectrum to enhance the intensity of the molecular ion peak. Additionally, chemical ionization, field ionization, and desorption ionization spectra are used to obtain a relatively intense molecular ion peak.To...
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Interpreting x̄ charts, a type of control chart used in statistical process control helps monitor the variation in processes over time. The x̄ chart is based on the sample mean and allows for monitoring variations in the process mean over time. These charts are pivotal for quality assurance in manufacturing and other sectors.
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Related Experiment Video

Updated: Jan 24, 2026

Cell-Free Dot Blot as a Practical and Adaptable Immunoassay Platform for the Detection of Antibody Response in Human and Animal Sera
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Published on: May 23, 2025

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Human outbreak detection and best practice MPXV analysis and interpretation with squirrel.

Áine O'Toole1, Eddy Kinganda-Lusamaki2,3,4, Rachel Colquhoun1

  • 1Institute of Ecology & Evolution, University of Edinburgh, Edinburgh, EH93FL, United Kingdom.

Virus Evolution
|January 23, 2026
PubMed
Summary

A new bioinformatics tool, squirrel, aids in mpox virus (MPXV) genomic surveillance. It simplifies complex analyses, helping distinguish between animal-to-human and human-to-human mpox outbreaks for better public health responses.

Keywords:
APOBEC3MPXVbioinformaticsemerging diseasegenomic epidemiologympoxoutbreakphylogeneticssoftwaresurveillancezoonosis

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Area of Science:

  • Genomics
  • Bioinformatics
  • Virology

Background:

  • Rising mpox cases and sustained outbreaks necessitate advanced genomic surveillance tools.
  • The mpox virus (MPXV) genome presents unique analytical challenges, including large size, complex regions, distinct clades, and APOBEC3 mutations.
  • The SARS-CoV-2 pandemic increased global sequencing capacity, but MPXV requires specialized bioinformatics solutions.

Purpose of the Study:

  • To introduce squirrel, an open-source bioinformatics tool designed for robust MPXV genomic surveillance.
  • To provide researchers with a tool capable of clade-aware alignment, mutation assessment, phylogenetic inference, and APOBEC3 mutation classification.
  • To facilitate the distinction between zoonotic and sustained human mpox outbreaks through advanced genomic analysis.

Main Methods:

  • Development of the squirrel (Some Quick Reconstruction to Resolve Evolutionary Links) bioinformatics tool.
  • Implementation of clade-aware alignment, mutation quality assessment, and phylogenetic inference.
  • Automated classification of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like 3 (APOBEC3)-mediated mutations within phylogenetic branches.
  • Integration with EPI2ME graphical user interface via the squirrel-nf workflow for user accessibility.

Main Results:

  • Squirrel performs clade-aware alignment and phylogenetic inference for MPXV genomes.
  • The tool accurately assesses mutation quality and classifies APOBEC3-mediated mutations.
  • Interactive reports and publication-ready visualizations aid in interpreting genomic data.
  • Squirrel enables differentiation between zoonotic spillover and sustained human transmission events.

Conclusions:

  • Squirrel is an effective open-source tool for comprehensive MPXV genomic surveillance.
  • The tool addresses specific analytical challenges posed by MPXV, enhancing outbreak investigation.
  • Squirrel empowers researchers and public health officials with actionable insights for mpox response.