ArticleFrontiers in public health2023
TheiaEuk: a species-agnostic bioinformatics workflow for fungal genomic characterization.
Article in Frontiers in public health, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 8 citations in OpenAlex.
- Towards accurate genomic detection of fungal antimicrobial resistance: progress in fungal resistance databases and bioinformatic tools.Microbial genomics · 2026Review
- Wastewater intelligence predicts the emergence of clinically-relevant and drug-resistant Candidozyma auris at healthcare facilities.Nature communications · 2026Article
- [Diagnostic Performance of Metagenomic Next-Generation Sequencing for Mucormycosis: A Retrospective Cohort Study].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2026Article
- Molecular Identification and RNA-Based Management of Fungal Plant Pathogens: From PCR to CRISPR/Cas9.International journal of molecular sciences · 2026Review
- Acquired amphotericin B resistance attributed to a mutatedAntimicrobial agents and chemotherapy · 2025Article
- Genetic Confirmation of Clonal Spread ofJournal of fungi (Basel, Switzerland) · 2025Article
- Acquired Amphotericin B Resistance Attributed to a MutatedbioRxiv : the preprint server for biology · 2025Article
- Molecular Diagnostics for Invasive Fungal Diseases: Current and Future Approaches.Journal of fungi (Basel, Switzerland) · 2024Review
- Molecular Mechanism Analysis of Intensive Light-Induced Retinal Damages.Journal of lasers in medical sciences · 2024Article
- The use of whole-genome sequencing and development of bioinformatics to monitor overlapping outbreaks ofFrontiers in public health · 2023Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Introduction: The clinical incidence of antimicrobial-resistant fungal infections has dramatically increased in recent years. Certain fungal pathogens colonize various body cavities, leading to life-threatening bloodstream infections. However, the identification and characterization of fungal isolates in laboratories remain a significant diagnostic challenge in medicine and public health. Whole-genome sequencing provides an unbiased and uniform identification pipeline for fungal pathogens but most bioinformatic analysis pipelines focus on prokaryotic species. To this end, TheiaEuk_Illumina_PE_PHB (TheiaEuk) was designed to focus on genomic analysis specialized to fungal pathogens. Methods: TheiaEuk was designed using containerized components and written in the workflow description language (WDL) to facilitate deployment on the cloud-based open bioinformatics platform Terra. This species-agnostic workflow enables the analysis of fungal genomes without requiring coding, thereby reducing the entry barrier for laboratory scientists. To demonstrate the usefulness of this pipeline, an ongoing outbreak of Results: A primary result of this work is a curated fungal database containing 5,667 unique genomes representing 245 species. TheiaEuk also incorporates taxon-specific submodules for specific species, including clade-typing for Discussion: TheiaEuk demonstrated effectiveness in identifying fungal species from whole genome sequence. It further showed accuracy in both clade-typing of
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.