ArticleGenome biology2019
PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
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 1,058 papers, 1 of them a synthesis that pooled it.
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Who cites it
1,058 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- PRISM-GEP: Viewing single-cell expression through the lens of topic modeling.Bioinformatics (Oxford, England) · 2026Article
- Spatially resolved multiomics of human meningeal development reveal lineage and disease dynamics.Nature cell biology · 2026Article
- Multi-stromal organoid co-culture modelling reveals epithelial-fibroblast heterogeneity in pancreatic cancer and pancreatitis.Nature cell biology · 2026Article
- Pan-cancer epigenetic landscape of human tumor-associated macrophages reveals crucial enhancers governing their heterogenous formation by Pol II pausing modulation.Journal of advanced research · 2026Article
- FlowMap: Geometry-Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories.bioRxiv : the preprint server for biology · 2026Article
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- An lncRNA-aware single-cell framework with donor-level validation identifies reproducible MEG3 enrichment in human liver sinusoidal endothelial cells.Functional & integrative genomics · 2026Article
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- TopClust: Topological-based analysis of scRNA-seq data for data-driven identification of clusters and core cluster cells.Biophysical journal · 2026Article
- Learning stochastic dynamics and cell-fate landscapes from single-cell snapshots via optimal transport.Science advances · 2026Article
- Multi-stage single-cell atlas of a chordate non-embryonic development unveils dedifferentiating bud founder cells.Nature communications · 2026Article
- Hidden causal inference delineates dynamic lncRNA regulation in autism spectrum disorder.Briefings in bioinformatics · 2026Article
- Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.Nature immunology · 2026Article
- scGSI: Graph-guided self-supervised integration of paired single-cell multi-omics.PLoS computational biology · 2026Article
- Uncovering genes driving developmental stage progression in prostate cancer through spatial transcriptomics.Genes & diseases · 2026Article
998 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
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Abstract
Single-cell RNA-seq quantifies biological heterogeneity across both discrete cell types and continuous cell transitions. Partition-based graph abstraction (PAGA) provides an interpretable graph-like map of the arising data manifold, based on estimating connectivity of manifold partitions ( https://github.com/theislab/paga ). PAGA maps preserve the global topology of data, allow analyzing data at different resolutions, and result in much higher computational efficiency of the typical exploratory data analysis workflow. We demonstrate the method by inferring structure-rich cell maps with consistent topology across four hematopoietic datasets, adult planaria and the zebrafish embryo and benchmark computational performance on one million neurons.
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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.