ArticleCell2019
Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity.
Article in Cell, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 755 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
755 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Deep learning in single-cell and spatial transcriptomics data analysis: advances and challenges from a data science perspective.Briefings in bioinformatics · 2025Pooled it
- Single nucleus multiomics reveals an early inflammatory response to high-fat diet in mouse islets.Life science alliance · 2026Article
- Human microglia clear intraneuronal α-synuclein aggregates by GPNMB-mediated trogocytosis.Science translational medicine · 2026Article
- Unlocking the full potential of spatial omics in plants: practical challenges, solutions, and a path forward.The Plant cell · 2026Review
- Regulatory-prior-guided attention preserves biological structure during unpaired single-cell RNA-ATAC integration.Bioinformatics (Oxford, England) · 2026Article
- Unifying multimodal single-cell data with a mixture-of-experts β-variational autoencoder framework.Genome research · 2026Article
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Single-cell and spatial RNA sequencing in prostate cancer.Nature reviews. Urology · 2026Review
- SMORE: joint dimension reduction and cell population discovery on single-cell methylome data.bioRxiv : the preprint server for biology · 2026Article
- A Gene-Program Architecture of Mouse T cells.bioRxiv : the preprint server for biology · 2026Article
- LIGER2: Scalable Single-Cell Integration with On-Disk Datasets.bioRxiv : the preprint server for biology · 2026Article
- Corticotropin-releasing hormone neurons in the bed nucleus of the stria terminalis control wakefulness in physiological and stressful conditions in mice.Molecular psychiatry · 2026Article
- Scalable joint non-negative matrix factorization for paired single cell gene expression and chromatin accessibility data.NAR genomics and bioinformatics · 2026Article
- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- KSTITCH links cellular morphology and gene expression in spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- CoxFormer enables spatial omics inference with multimodal generative modeling.Nature communications · 2026Article
- DBP: Adaptive and Interpretable Factor Analysis for Single-cell RNA-seq Data with Deep Beta Processes.Genomics, proteomics & bioinformatics · 2026Article
- Enhancing pan-cancer spatial transcriptomics at single-cell resolution with stPainter.Nature communications · 2026Article
- Integrative Epigenomics: Bioinformatics Strategies for Multi-Omics Data Analysis in Health and Disease.Epigenomes · 2026Review
- α-Synuclein blocks endoplasmic reticulum co-translational protein translocation early in Parkinson's disease.Nature communications · 2026Article
695 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Defining cell types requires integrating diverse single-cell measurements from multiple experiments and biological contexts. To flexibly model single-cell datasets, we developed LIGER, an algorithm that delineates shared and dataset-specific features of cell identity. We applied it to four diverse and challenging analyses of human and mouse brain cells. First, we defined region-specific and sexually dimorphic gene expression in the mouse bed nucleus of the stria terminalis. Second, we analyzed expression in the human substantia nigra, comparing cell states in specific donors and relating cell types to those in the mouse. Third, we integrated in situ and single-cell expression data to spatially locate fine subtypes of cells present in the mouse frontal cortex. Finally, we jointly defined mouse cortical cell types using single-cell RNA-seq and DNA methylation profiles, revealing putative mechanisms of cell-type-specific epigenomic regulation. Integrative analyses using LIGER promise to accelerate investigations of cell-type definition, gene regulation, and disease states.
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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.