ArticleCell genomics2022
Functional inference of gene regulation using single-cell multi-omics.
Article in Cell genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 173 papers.
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.
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Who cites it
173 citing papers in PubMed, 219 citations in OpenAlex.
- DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- Spatial Proteomics and Epigenomics Reveal Cell Morphology and Epigenetic Gene Regulation in Human Hippocampus.Research square · 2026Article
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- Mapping enhancer-gene regulatory interactions from single-cell data.Nature genetics · 2026Article
- Integrated Single-Nucleus Multi-Omics Atlases Reveal Lineage Plasticity and Regulatory Networks of Luminal Epithelial Cells During Mammary Gland Lactation and Involution.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.Nature communications · 2026Article
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- A map of intra- and intercellular immune responses across diverse in vitro stimuli and inflammatory disease.Genome medicine · 2026Article
- Epigenetic landscape, key transcriptional regulators, and in vivo identification of human Tr1 cells.Science advances · 2026Article
- Graph-based contrastive learning enables unified integration and niche transfer across single-cell and spatial multi-omics.Briefings in bioinformatics · 2026Article
- Computational blueprints for cell fate programming.Stem cell reports · 2026Review
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- Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features.bioRxiv : the preprint server for biology · 2026Article
- Aberrant chromatin remodeling influences human neural cell fate change in Trisomy 21.bioRxiv : the preprint server for biology · 2026Article
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- Unveiling gene modules at Atlas scale through hierarchical clustering of single-cell data.Nature communications · 2026Article
- Chronic TGFβ1 Signaling Drives Aberrant Alveolar-Basaloid Metaplasia through a KRT17-Stratifin migratory complex.bioRxiv : the preprint server for biology · 2026Article
- Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.Nucleic acids research · 2026Article
- Functionally informed cis and trans proteome-wide association studies prioritize disease-critical genes.Research square · 2026Article
113 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 3 institutions in 1 country.
Funding
Abstract
Cells require coordinated control over gene expression when responding to environmental stimuli. Here we apply scATAC-seq and single-cell RNA sequencing (scRNA-seq) in resting and stimulated human blood cells. Collectively, we generate ~91,000 single-cell profiles, allowing us to probe the cis-regulatory landscape of the immunological response across cell types, stimuli, and time. Advancing tools to integrate multi-omics data, we develop functional inference of gene regulation (FigR), a framework to computationally pair scA-TAC-seq with scRNA-seq cells, connect distal cis-regulatory elements to genes, and infer gene-regulatory networks (GRNs) to identify candidate transcription factor (TF) regulators. Utilizing these paired multi-omics data, we define domains of regulatory chromatin (DORCs) of immune stimulation and find that cells alter chromatin accessibility and gene expression at timescales of minutes. Construction of the stimulation GRN elucidates TF activity at disease-associated DORCs. Overall, FigR enables elucidation of regulatory interactions across single-cell data, providing new opportunities to understand the function of cells within tissues.
Identifiers
What OpenQuestion holds
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.