ArticleGenome biology2016
Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed.
- Validation of an integrated metagenomic pipeline combining optimized wet-lab processing and tiered reporting for CSF pathogen detection.Microbiology spectrum · 2026Article
- RNA in Plasma Extracellular Vesicles of Adolescent Rhesus Macaques Reveals Immune, Bioenergetic, and Microbial Imprints of Early-Life Adversity: An Exploratory Analysis.Biological psychiatry · 2026Article
- The application status of sequencing technology in global respiratory infectious disease diagnosis.Infection · 2024Review
- Laboratory validation of a clinical metagenomic next-generation sequencing assay for respiratory virus detection and discovery.Nature communications · 2024Article
- Accessible viral metagenomics for public health and clinical domains with Jovian.Scientific reports · 2024Article
- VirID: Beyond Virus Discovery-An Integrated Platform for Comprehensive RNA Virus Characterization.Molecular biology and evolution · 2024Article
- Challenges for pathologists in implementing clinical microbiome diagnostic testing.The journal of pathology. Clinical research · 2024Review
- Rethinking Aspergillosis in the Era of Microbiota and Mycobiota.Mycopathologia · 2024Review
- Clinical applications of metagenomics next-generation sequencing in infectious diseases.Journal of Zhejiang University. Science. B · 2024Review
- Determination of Ideal Factors for Early Adoption and Standardization of Metagenomic Next-generation Sequencing for Respiratory System Infections.Current pharmaceutical biotechnology · 2024Article
- Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples.Veterinary sciences · 2023Review
- UltraSEQ, a Universal Bioinformatic Platform for Information-Based Clinical Metagenomics and Beyond.Microbiology spectrum · 2023Article
- Metagenomic Sequencing of Positive Blood Culture Fluid for Accurate Bacterial and Fungal Species Identification: A Pilot Study.Microorganisms · 2023Article
- Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus.Sarcoidosis, vasculitis, and diffuse lung diseases : official journal of WASOG · 2022Article
- Article
- PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.Life (Basel, Switzerland) · 2022Article
- Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region.Transboundary and emerging diseases · 2022Article
- Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections.Journal of advanced research · 2022Review
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Article
27 more citing papers are in PubMed but not listed here.
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Authors and funding
23 authors.
Funding
Abstract
backgroundHigh-throughput sequencing enables unbiased profiling of microbial communities, universal pathogen detection, and host response to infectious diseases. However, computation times and algorithmic inaccuracies have hindered adoption.
resultsWe present Taxonomer, an ultrafast, web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. To facilitate data-sharing across geographic distances in outbreak settings, Taxonomer is publicly available through a web-based user interface.
conclusionsTaxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.
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