ArticleGenome research2021
Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes.
Article in Genome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Gut dysbiosis in patients with chronic pain: a systematic review and meta-analysis.Frontiers in immunology · 2024Pooled it
- A split face study on the effect of an anti-acne product containing fermentation products of Enterococcus faecalis CBT SL-5 on skin microbiome modification and acne improvement.Journal of microbiology (Seoul, Korea) · 2022Trial
- Gestational dysbiosis is associated with altered early-life microbial seeding and favors pathobiont expansion in offspring.iScience · 2026Article
- Amoxicillin induces gut dysbiosis leading to long term suppression of type-17 immune tone in the lungs.bioRxiv : the preprint server for biology · 2026Article
- Effects ofFrontiers in microbiology · 2026Article
- Environmental and skin-nasal microbiome variation in South African children with atopic dermatitis.BMC microbiology · 2025Article
- Antidiabetic Effect of Bifidobacterium animalis TISTR 2591 in a Rat Model of Type 2 Diabetes.Probiotics and antimicrobial proteins · 2025Article
- Three eruptions at the Fagradalsfjall Volcano in Iceland show rapid and predictable microbial community establishment.Communications biology · 2025Article
- Precision Probiotics Regulate Blood Glucose, Cholesterol, Body Fat Percentage, and Weight Under Eight-Week High-Fat Diet.Metabolites · 2025Article
- The Gut Microbiota of Peruvian Children Under the Age of Two During the Complementary Feeding Period.International journal of environmental research and public health · 2025Article
- Article
- Systemic inflammation is associated with gut microbiota diversity in post-stroke patients.European geriatric medicine · 2025Article
- Article
- Personalized glucose prediction usingFrontiers in nutrition · 2025Article
- Clearing the plate: a strategic approach to mitigate well-to-well contamination in large-scale microbiome studies.mSystems · 2024Article
- Microbiome time series data reveal predictable patterns of change.Microbiology spectrum · 2024Article
- Prenatal Stress and Ethanol Exposure: Microbiota-Induced Immune Dysregulation and Psychiatric Risks.International journal of molecular sciences · 2024Review
- Seasonal dynamics and environmental drivers of tissue and mucus microbiomes in the staghorn coralPeerJ · 2024Article
- Responses of a soil fungal community to severe windstorm damages in an old silver fir stand.Frontiers in microbiology · 2023Article
- Evaluation of the representative of using rumen fluid samples from lambs fed pelleted TMR for analysis of prokaryotic communities.Frontiers in microbiology · 2023Article
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Authors and funding
23 authors.
Funding
Abstract
The number of publicly available microbiome samples is continually growing. As data set size increases, bottlenecks arise in standard analytical pipelines. Faith's phylogenetic diversity (Faith's PD) is a highly utilized phylogenetic alpha diversity metric that has thus far failed to effectively scale to trees with millions of vertices. Stacked Faith's phylogenetic diversity (SFPhD) enables calculation of this widely adopted diversity metric at a much larger scale by implementing a computationally efficient algorithm. The algorithm reduces the amount of computational resources required, resulting in more accessible software with a reduced carbon footprint, as compared to previous approaches. The new algorithm produces identical results to the previous method. We further demonstrate that the phylogenetic aspect of Faith's PD provides increased power in detecting diversity differences between younger and older populations in the FINRISK study's metagenomic data.
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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.