ArticleBMC bioinformatics2024
SpeciateIT and vSpeciateDB: novel, fast, and accurate per sequence 16S rRNA gene taxonomic classification of vaginal microbiota.
Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Characterizing the bacterial surface profiles of menstrual cups and their association with user characteristics and vaginal microbiomes in an adolescent cohort from western Kenya.Gates open research · 2026Trial
- Comparing Asymptomatic Versus Symptomatic Bacterial Vaginosis: Clinical Characteristics, Vaginal Microbiota, and Lactic Acid Profiles.Sexually transmitted diseases · 2026Article
- Timing of menstrual cups to prevent transition from optimal to not optimal vaginal microbiome community state type: Results from a 6.5-year prospective observational cohort.Research square · 2026Article
- Resource landscape shapes the composition and stability of the human vaginal microbiota.PLoS biology · 2026Article
- The vaginal microbiota, symptoms, and local immune correlates in transmasculine individuals using sustained testosterone therapy.Cell reports · 2025Article
- The neovaginal microbiota, symptoms, and local immune correlates in transfeminine individuals with penile inversion vaginoplasty.Cell reports · 2025Article
- Association Between Vaginal Community States and Preeclampsia Status in Pregnant Individuals.bioRxiv : the preprint server for biology · 2025Article
- Cervicovaginal microbial features predictInfection and immunity · 2025Article
- Investigating Bacterial Vaginosis Pathogenesis Using Peptide Nucleic Acid-FluorescenceOpen forum infectious diseases · 2025Article
- Article
- Assessment of the vaginal microbiota before and after use of hyperosmolal lubricant during transvaginal ultrasound.American journal of obstetrics and gynecology · 2025Article
- Factors shaping vaginal microbiota long-term community dynamics in young adult women.Peer community journal · 2025Article
- Observational
- Genome wide association study of vaginal microbiota genetic diversity in French women.Open research Europe · 2025Article
- Affective symptoms in pregnancy are associated with the vaginal microbiome.Journal of affective disorders · 2025Article
- Menstrual cups to reduce bacterial vaginosis and STIs through reduced harmful sexual and menstrual practices among economically vulnerable women: protocol of a single arm trial in western Kenya.BMC public health · 2024Article
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3 authors.
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Abstract
backgroundClustering of sequences into operational taxonomic units (OTUs) and denoising methods are a mainstream stopgap to taxonomically classifying large numbers of 16S rRNA gene sequences. Environment-specific reference databases generally yield optimal taxonomic assignment.
resultsWe developed SpeciateIT, a novel taxonomic classification tool which rapidly and accurately classifies individual amplicon sequences ( https://github.com/Ravel-Laboratory/speciateIT ). We also present vSpeciateDB, a custom reference database for the taxonomic classification of 16S rRNA gene amplicon sequences from vaginal microbiota. We show that SpeciateIT requires minimal computational resources relative to other algorithms and, when combined with vSpeciateDB, affords accurate species level classification in an environment-specific manner.
conclusionsHerein, two resources with new and practical importance are described. The novel classification algorithm, SpeciateIT, is based on 7th order Markov chain models and allows for fast and accurate per-sequence taxonomic assignments (as little as 10 min for 10
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