ArticlePLoS computational biology2019
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Discrimination betweenOne health (Amsterdam, Netherlands) · 2026Article
- Development of a Domestic Alternative Positive Control Strain toJournal of microbiology and biotechnology · 2025Article
- Genomic diversity and tracing ofMicrobial genomics · 2025Article
- Global epidemiology of Mycobacterium tuberculosis lineage 4 insights from Ecuadorian genomic data.Scientific reports · 2025Article
- Beyond H37Rv:Frontiers in microbiology · 2025Review
- A Genome-Focused Investigation Reveals the Emergence of aMicroorganisms · 2024Article
- Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas.Microbiology spectrum · 2023Article
- TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.Bioinformatics (Oxford, England) · 2023Article
- Accurate and rapid prediction of tuberculosis drug resistance from genome sequence data using traditional machine learning algorithms and CNN.Scientific reports · 2022Article
- Article
- One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.PLoS computational biology · 2021Article
- Improving tuberculosis surveillance by detecting international transmission using publicly available whole genome sequencing data.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2021Article
- Review
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4 authors.
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Abstract
Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across different Mycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis-a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance.
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