ArticleGenome biology2021
treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Maternal balanced energy-protein supplementation reshapes the maternal gut microbiome and enhances carbohydrate metabolism in infants: a randomized controlled trial.Nature communications · 2025Trial
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- Fiber mixtures containing chicory inulin, wheat dextrin, and cellulose, or tapioca dextrin alone, beneficially modulate microbial metabolic activity and composition in short-term colonic simulations.Frontiers in nutrition · 2026Article
- On feature selection to disentangle cell type and state transcriptional programs.BMC genomics · 2025Article
- Kontextual reframes analysis of spatial omics data and reveals consistent cell relationships across images.Cell reports methods · 2025Article
- Tree-based differential testing using inferential uncertainty for RNA-seq.Genome research · 2025Article
- Article
- Rumen fermentation shifts and microbial dynamics in mid-lactating Holstein dairy cows experiencing heat stress and subsequent recovery periods.Animal bioscience · 2025Article
- Tree-based differential testing using inferential uncertainty for RNA-Seq.bioRxiv : the preprint server for biology · 2025Article
- A specific blend of prebiotics and postbiotics improved the gut microbiome of dogs with soft stools in the in vitro Simulator of the Canine Intestinal Microbial Ecosystem.Journal of animal science · 2025Article
- UniCor and UniCorP: a novel metric and hierarchical feature selection algorithm for microbial community analysis.ISME communications · 2025Article
- Tributyrin (CoreBiomeFrontiers in nutrition · 2025Article
- Effects of NatureKnit™ organic, a blend of organic fruit and vegetable fibers rich in naturally occurring bound polyphenols, on the metabolic activity and community composition of the human gut microbiome using the M-SHIMEFrontiers in nutrition · 2025Article
- Modulation of Canine Gut Microbiota by Prebiotic and Probiotic Supplements: A Long-Term In Vitro Study Using a Novel Colonic Fermentation Model.Animals : an open access journal from MDPI · 2024Article
- In Vitro Human Gastrointestinal Digestibility and Colonic Fermentation of Wheat Sourdough and Yeast Breads.Foods (Basel, Switzerland) · 2024Article
- Article
- The role of Helicobacter suis, Fusobacterium gastrosuis, and the pars oesophageal microbiota in gastric ulceration in slaughter pigs receiving meal or pelleted feed.Veterinary research · 2024Article
- TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes.BMC bioinformatics · 2023Article
- Ex Vivo Colonic Fermentation of NUTRIOSENutrients · 2023Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
treeclimbR is for analyzing hierarchical trees of entities, such as phylogenies or cell types, at different resolutions. It proposes multiple candidates that capture the latent signal and pinpoints branches or leaves that contain features of interest, in a data-driven way. It outperforms currently available methods on synthetic data, and we highlight the approach on various applications, including microbiome and microRNA surveys as well as single-cell cytometry and RNA-seq datasets. With the emergence of various multi-resolution genomic datasets, treeclimbR provides a thorough inspection on entities across resolutions and gives additional flexibility to uncover biological associations.
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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.