ArticleGenome biology2019
tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Subgingival microbiota composition is associated with brain health in the general population-the PAROMIND study.EBioMedicine · 2026Article
- Structural optimization of drug molecules with incrementally trained language models.Nature communications · 2026Article
- Gene-environment-brain topology reveals clinical subtypes of depression in UK Biobank.Scientific reports · 2025Article
- From variability to stability: Sensitivity of network properties in IBD human gut microbiome studies.Computational and structural biotechnology journal · 2025Article
- Analogous assembly mechanisms and functional guilds govern prokaryotic communities in mangrove ecosystems of China and South America.Microbiology spectrum · 2023Article
- Mycobacteriaceae Phenome Atlas (MPA): A Standardized Atlas for the Mycobacteriaceae Phenome Based on Heterogeneous Sources.Phenomics (Cham, Switzerland) · 2023Article
- Gut microbiota in dementia with Lewy bodies.NPJ Parkinson's disease · 2022Article
- Topological data analysis in biomedicine: A review.Journal of biomedical informatics · 2022Review
- The gut microbiome in human health and disease-Where are we and where are we going? A bibliometric analysis.Frontiers in microbiology · 2022Article
- COVID-19 severity is associated with population-level gut microbiome variations.Frontiers in cellular and infection microbiology · 2022Article
- The topology of data: opportunities for cancer research.Bioinformatics (Oxford, England) · 2021Article
- NFnetFu: A novel workflow for microbiome data fusion.Computers in biology and medicine · 2021Article
- Topological Data Analysis Highlights Novel Geographical Signatures of the Human Gut Microbiome.Frontiers in artificial intelligence · 2021Article
- Exploring the Microbiome Analysis and Visualization Landscape.Frontiers in bioinformatics · 2021Review
- Mathematical-based microbiome analytics for clinical translation.Computational and structural biotechnology journal · 2021Review
- Statistical and Machine Learning Techniques in Human Microbiome Studies: Contemporary Challenges and Solutions.Frontiers in microbiology · 2021Article
- Topological analysis reveals state transitions in human gut and marine bacterial communities.NPJ biofilms and microbiomes · 2020Article
- tmap: an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies.Genome biology · 2019Article
Corrections and comments
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Authors and funding
5 authors.
Funding
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Abstract
Untangling the complex variations of microbiome associated with large-scale host phenotypes or environment types challenges the currently available analytic methods. Here, we present tmap, an integrative framework based on topological data analysis for population-scale microbiome stratification and association studies. The performance of tmap in detecting nonlinear patterns is validated by different scenarios of simulation, which clearly demonstrate its superiority over the most commonly used methods. Application of tmap to several population-scale microbiomes extensively demonstrates its strength in revealing microbiome-associated host or environmental features and in understanding the systematic interrelations among their association patterns. tmap is available at https://github.com/GPZ-Bioinfo/tmap.
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