ArticleGenome biology2021
HiDeF: identifying persistent structures in multiscale 'omics data.
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 36 papers.
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Who cites it
36 citing papers in PubMed.
- Article
- Multiscale domain identification for spatial transcriptomics via persistent homology.Cell reports methods · 2026Article
- Arabidopsis acclimation to daily environmental fluctuations converts a defense response regulator into a susceptibility factor toward Sclerotinia.The New phytologist · 2026Article
- Common and rare genetic variants show network convergence for a majority of human traits.EMBO reports · 2026Article
- An optimization framework for hierarchical clustering.Bioinformatics advances · 2026Article
- Using Biological Networks to Guide Biomedical Prediction.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Multivariate genetic analyses of 2.2 million individuals reveal broad and substance-specific pathways of addiction risk.Nature. Mental health · 2026Article
- PHD-MS: Multiscale Domain Identification for Spatial Transcriptomics via Persistent Homology.ArXiv · 2025Article
- Probing omics data via harmonic persistent homology.Scientific reports · 2025Article
- A multi-dimensional computational framework of drug-induced hepatotoxicity: integrating molecular structure features with disease pathogenesis.Briefings in bioinformatics · 2025Article
- Multivariate genetic of 2.2 million individuals demonstrate genetic influences on substance use disorders operate via behavioral disinhibition and substance-specific risk.medRxiv : the preprint server for health sciences · 2025Article
- Cell Mapping Toolkit: an end-to-end pipeline for mapping subcellular organization.Bioinformatics (Oxford, England) · 2025Article
- Article
- Global siRNA screen identifies human host factors critical for SARS-CoV-2 replication and late stages of infection.PLoS biology · 2025Article
- Unifying proteomic technologies with ProteinProjector.Bioinformatics advances · 2025Article
- Multi-modal contrastive learning of subcellular organization using DICE.Bioinformatics (Oxford, England) · 2024Article
- Mapping the Multiscale Proteomic Organization of Cellular and Disease Phenotypes.Annual review of biomedical data science · 2024Review
- Building and analyzing metacells in single-cell genomics data.Molecular systems biology · 2024Review
- Illuminating function of the understudied druggable kinome.Drug discovery today · 2024Review
- The network structure of hematopoietic cancers.Scientific reports · 2023Article
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Authors and funding
6 authors.
Funding
Abstract
In any 'omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here, we use the concept of persistent homology, drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.
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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.