ArticleiScience2022
IReNA: Integrated regulatory network analysis of single-cell transcriptomes and chromatin accessibility profiles.
Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Deciphering cell-type-and temporally specific matrisome expression signatures in human cortical development and neurodevelopmental disorders via scRNA-seq meta-analysis.Nature communications · 2025Pooled it
- Reference Regulatory Element-Guided Gene Expression Analysis for Mechanistic Inference of Gene Regulatory Networks.bioRxiv : the preprint server for biology · 2026Article
- A comprehensive survey on graph neural networks for gene regulatory network inference.Briefings in bioinformatics · 2026Review
- A Age Related Vascular Senescence: Mystery of Blood-brain Barrier Dysfunction in Neurodegeneration.Molecular neurobiology · 2026Review
- T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset.NAR genomics and bioinformatics · 2026Article
- MOSAIC: A Spectral Framework for Integrative Phenotypic Characterization Using Population-Level Single-Cell Multi-Omics.bioRxiv : the preprint server for biology · 2026Article
- MultiCausGRN: directed prior-guided graph attention model for multi-omics gene regulatory network inference.Frontiers in bioinformatics · 2026Article
- Analysis of the role of RNA regulatory networks in cancer treatment: Mechanisms, applications and future prospects (Review).Molecular and clinical oncology · 2025Review
- ScReNI: Single-cell Regulatory Network Inference Through Integrating scRNA-seq and scATAC-seq Data.Genomics, proteomics & bioinformatics · 2025Article
- A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize.Plant communications · 2025Article
- Leveraging transcription factor physical proximity for enhancing gene regulation inference.Bioinformatics (Oxford, England) · 2025Article
- scMINER: a mutual information-based framework for clustering and hidden driver inference from single-cell transcriptomics data.Nature communications · 2025Article
- A Compound Screen Based on Isogenic hESC-Derived β Cell Reveals an Inhibitor Targeting ZnT8-Mediated Zinc Transportation to Protect Pancreatic β Cell from Stress-Induced Cell Death.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Latent epigenetic programs in Müller glia contribute to stress and disease response in the retina.Developmental cell · 2025Article
- Inferring gene regulatory networks from single-cell multiome data using atlas-scale external data.Nature biotechnology · 2025Article
- A single-cell multimodal view on gene regulatory network inference from transcriptomics and chromatin accessibility data.Briefings in bioinformatics · 2024Review
- Advances in computational and experimental approaches for deciphering transcriptional regulatory networks: Understanding the roles of cis-regulatory elements is essential, and recent research utilizing MPRAs, STARR-seq, CRISPR-Cas9, and machine learning has yielded valuable insights.BioEssays : news and reviews in molecular, cellular and developmental biology · 2024Review
- CACIMAR: cross-species analysis of cell identities, markers, regulations, and interactions using single-cell RNA sequencing data.Briefings in bioinformatics · 2024Article
- Recent advances in exploring transcriptional regulatory landscape of crops.Frontiers in plant science · 2024Review
- Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods.Bioinformatics and biology insights · 2024Review
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Recently, single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) have been developed to separately measure transcriptomes and chromatin accessibility profiles at the single-cell resolution. However, few methods can reliably integrate these data to perform regulatory network analysis. Here, we developed integrated regulatory network analysis (IReNA) for network inference through the integrated analysis of scRNA-seq and scATAC-seq data, network modularization, transcription factor enrichment, and construction of simplified intermodular regulatory networks. Using public datasets, we showed that integrated network analysis of scRNA-seq data with scATAC-seq data is more precise to identify known regulators than scRNA-seq data analysis alone. Moreover, IReNA outperformed currently available methods in identifying known regulators. IReNA facilitates the systems-level understanding of biological regulatory mechanisms and is available at https://github.com/jiang-junyao/IReNA.
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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.