ArticleBioinformatics (Oxford, England)2015
Bayesian mixture analysis for metagenomic community profiling.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Masking recurrent contaminants in reference sequences improves specificity of clinical metagenomic sequencing.Journal of clinical microbiology · 2026Article
- Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.BMC infectious diseases · 2026Article
- Article
- Contaminating plasmid sequences and disrupted vector genomes in the liver following adeno-associated virus gene therapy.Nature medicine · 2026Article
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes.Diabetologia · 2025Article
- Detection of enterovirus RNA in pancreas and lymphoid tissues of organ donors with type 1 diabetes.medRxiv : the preprint server for health sciences · 2024Article
- Evaluating metagenomics and targeted approaches for diagnosis and surveillance of viruses.Genome medicine · 2024Article
- Untargeted metagenomics protocol for the diagnosis of infection from CSF and tissue from sterile sites.Heliyon · 2023Article
- Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data.Scientific reports · 2023Article
- Report of the third conference on next-generation sequencing for adventitious virus detection in biologics for humans and animals.Biologicals : journal of the International Association of Biological Standardization · 2023Article
- Article
- An Adagio for Viruses, Played Out on Ancient DNA.Genome biology and evolution · 2023Review
- Metagenomic evidence for a polymicrobial signature of sepsis.Microbial genomics · 2021Article
- Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples.Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2021Article
- Metagenomic analysis of a blood stain from the French revolutionary Jean-Paul Marat (1743-1793).Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2020Article
- Article
- DAMIAN: an open source bioinformatics tool for fast, systematic and cohort based analysis of microorganisms in diagnostic samples.Scientific reports · 2019Article
- CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads.Genes · 2018Article
- Encephalitis diagnosis using metagenomics: application of next generation sequencing for undiagnosed cases.The Journal of infection · 2018Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationDeep sequencing of clinical samples is now an established tool for the detection of infectious pathogens, with direct medical applications. The large amount of data generated produces an opportunity to detect species even at very low levels, provided that computational tools can effectively profile the relevant metagenomic communities. Data interpretation is complicated by the fact that short sequencing reads can match multiple organisms and by the lack of completeness of existing databases, in particular for viral pathogens. Here we present metaMix, a Bayesian mixture model framework for resolving complex metagenomic mixtures. We show that the use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species most likely to contribute to the mixture.
resultsWe demonstrate the greater accuracy of metaMix compared with relevant methods, particularly for profiling complex communities consisting of several related species. We designed metaMix specifically for the analysis of deep transcriptome sequencing datasets, with a focus on viral pathogen detection; however, the principles are generally applicable to all types of metagenomic mixtures. AVAILABILITY AND IMPLEMENTATION: metaMix is implemented as a user friendly R package, freely available on CRAN: http://cran.r-project.org/web/packages/metaMix CONTACT: sofia.morfopoulou.10@ucl.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bionformatics online.
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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.