ArticleNAR genomics and bioinformatics2022
SMGR: a joint statistical method for integrative analysis of single-cell multi-omics data.
Article in NAR genomics and bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it, 39 citations in OpenAlex.
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- Integrative analysis of high-dimensional quantile regression with contrasted penalization.Journal of applied statistics · 2025Article
- Lorentz-regularized interpretable VAE for multi-scale single-cell transcriptomic and epigenomic embeddings.Frontiers in genetics · 2025Article
- A novel adenosine-to-inosine RNA editing-based nomogram for predicting prognosis of hepatocellular carcinoma.Frontiers in pharmacology · 2025Article
- T-reg transcriptomic signatures identify response to check-point inhibitors.Scientific reports · 2024Article
- Integration of single-cell transcriptome and chromatin accessibility and its application on tumor investigation.Life medicine · 2024Review
- Advancements and applications of single-cell multi-omics techniques in cancer research: Unveiling heterogeneity and paving the way for precision therapeutics.Biochemistry and biophysics reports · 2024Review
- Microfluidic design in single-cell sequencing and application to cancer precision medicine.Cell reports methods · 2023Review
- Integrating Single-Cell RNA-Seq and Bulk RNA-Seq Data to Explore the Key Role of Fatty Acid Metabolism in Breast Cancer.International journal of molecular sciences · 2023Article
- Toll-like Receptor 4 Inflammatory Perspective on Doxorubicin-Induced Cardiotoxicity.Molecules (Basel, Switzerland) · 2023Review
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- ADCY9 functions as a novel cancer suppressor gene in lung adenocarcinoma.Journal of thoracic disease · 2023Article
- spaCI: deciphering spatial cellular communications through adaptive graph model.Briefings in bioinformatics · 2023Article
- NLRP3 Gene Polymorphisms in Rheumatoid Arthritis and Primary Sjogren's Syndrome Patients.Diagnostics (Basel, Switzerland) · 2023Article
- A novel prognostic related lncRNA signature associated with amino acid metabolism in glioma.Frontiers in immunology · 2023Article
- Characterization of prognostic value and immunological roles of RAB22A in hepatocellular carcinoma.Frontiers in immunology · 2023Article
- Detection of sFas, sCD137, and IL-27 Cytokines as Potential Biomarkers for Hepatocellular Carcinoma Diagnosis.Journal of hepatocellular carcinoma · 2023Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
Abstract
Unravelling the regulatory programs from single-cell multi-omics data has long been one of the major challenges in genomics, especially in the current emerging single-cell field. Currently there is a huge gap between fast-growing single-cell multi-omics data and effective methods for the integrative analysis of these inherent sparse and heterogeneous data. In this study, we have developed a novel method, Single-cell Multi-omics Gene co-Regulatory algorithm (SMGR), to detect coherent functional regulatory signals and target genes from the joint single-cell RNA-sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data obtained from different samples. Given that scRNA-seq and scATAC-seq data can be captured by zero-inflated Negative Binomial distribution, we utilize a generalized linear regression model to identify the latent representation of consistently expressed genes and peaks, thus enables the identification of co-regulatory programs and the elucidation of regulating mechanisms. Results from both simulation and experimental data demonstrate that SMGR outperforms the existing methods with considerably improved accuracy. To illustrate the biological insights of SMGR, we apply SMGR to mixed-phenotype acute leukemia (MPAL) and identify the MPAL-specific regulatory program with significant peak-gene links, which greatly enhance our understanding of the regulatory mechanisms and potential targets of this complex tumor.
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.