ArticleBioinformatics (Oxford, England)2022
High-sensitivity pattern discovery in large, paired multiomic datasets.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed.
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- Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.Microbiome · 2026Article
- Navigating multi-omic integration methods for human microbiome research.Nature microbiology · 2026Review
- Integrative Analysis of Multiomic Pathways Predicts Cancer-Affected Lobes in Lung Cancer.Cancer prevention research (Philadelphia, Pa.) · 2026Article
- Enhanced multi-omic viral profiling from microbial community sequencing with BAQLaVa.bioRxiv : the preprint server for biology · 2026Article
- Fecal metabolic signals are associated with changes in microbiota and systemic metabolic pathways in Crohn's disease.Scientific reports · 2026Article
- Biofilm removal in hospital sink drains drives unintended surges in antibiotic resistance.npj antimicrobials and resistance · 2026Article
- Antibiotic-Mediated Modulation of the Gut Microbiome Identifies Taurine as a Modulator of Adipocyte Function Through TGR5 Signaling.International journal of molecular sciences · 2026Article
- Associations among diet, gut microbiota, and hypertension: a cross-sectional study in Thai subjects.PeerJ · 2026Article
- Baseline multi-omics signatures could predict therapeutic response to neoadjuvant anti-PD-1 immunochemotherapy in non-small-cell lung cancer.Clinical and translational medicine · 2026Article
- Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression.Cell host & microbe · 2025Article
- The immune response modulated by inoculation of commensal bacteria at birth impacts the gut microbiota and preventsGut microbes · 2025Article
- Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19.Gut microbes · 2025Article
- Disentangling the impact of obesity, diet, host factors, and microbiota on small intestinal antimicrobial peptide expression.Gut microbes · 2025Article
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
motivationModern biological screens yield enormous numbers of measurements, and identifying and interpreting statistically significant associations among features are essential. In experiments featuring multiple high-dimensional datasets collected from the same set of samples, it is useful to identify groups of associated features between the datasets in a way that provides high statistical power and false discovery rate (FDR) control.
resultsHere, we present a novel hierarchical framework, HAllA (Hierarchical All-against-All association testing), for structured association discovery between paired high-dimensional datasets. HAllA efficiently integrates hierarchical hypothesis testing with FDR correction to reveal significant linear and non-linear block-wise relationships among continuous and/or categorical data. We optimized and evaluated HAllA using heterogeneous synthetic datasets of known association structure, where HAllA outperformed all-against-all and other block-testing approaches across a range of common similarity measures. We then applied HAllA to a series of real-world multiomics datasets, revealing new associations between gene expression and host immune activity, the microbiome and host transcriptome, metabolomic profiling and human health phenotypes. AVAILABILITY AND IMPLEMENTATION: An open-source implementation of HAllA is freely available at http://huttenhower.sph.harvard.edu/halla along with documentation, demo datasets and a user group. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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