ArticleGenome biology2022
A deep generative model for multi-view profiling of single-cell RNA-seq and ATAC-seq data.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 61 papers, 1 of them a synthesis that pooled it.
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Who cites it
61 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
- scGSI: Graph-guided self-supervised integration of paired single-cell multi-omics.PLoS computational biology · 2026Article
- Geneformer-guided multiomics integration identifies Pbx1 as a network hub of hematopoietic stem cell aging.Science advances · 2026Article
- Advancing bioinformatics with language models: components, applications, and perspectives.Briefings in bioinformatics · 2026Review
- Interpretable modality-aware mapping of gene regulation in single-cell multiomics with scMAGCA.Nature communications · 2026Article
- Cross-modality representation and multi-sample integration of spatially resolved omics data.Briefings in bioinformatics · 2026Article
- Game of clones: decipher lineage plasticity in hormone-driven cancers.Cellular and molecular life sciences : CMLS · 2026Review
- iAODE for benchmarking and continuum modeling of single-cell chromatin accessibility.Communications biology · 2026Article
- Chromatin Accessibility in Cancer: Biological Functions, Mechanisms, Therapeutic Potential, and Future Directions.MedComm · 2026Review
- A deep adversarial network model for multi-task analysis of single-cell omics data.Briefings in bioinformatics · 2026Article
- Spatial multi-omics integration by cross-modal graph contrastive learning.Briefings in bioinformatics · 2026Article
- AI-driven discovery in protein science for immunology and infectious disease research.Frontiers in bioinformatics · 2026Review
- Causal digital twin modeling of periodontal healing: personalized prediction of low-level laser therapy benefit using a tooth-graph ODE transformer.Frontiers in dental medicine · 2026Article
- Article
- Computational Analyses and Challenges of Single-cell ATAC-seq.Genomics, proteomics & bioinformatics · 2025Review
- Single-cell multiomics data integration and generation with scPairing.Cell reports methods · 2025Article
- Multitask benchmarking of single-cell multimodal omics integration methods.Nature methods · 2025Article
- Benchmarking single-cell multi-modal data integrations.Nature methods · 2025Article
- HALO: hierarchical causal modeling for single cell multi-omics data.Nature communications · 2025Article
- Integrating cross-sample and cross-modal data for spatial transcriptomics and metabolomics with SpatialMETA.Nature communications · 2025Article
1 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
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here, we present a multi-modal deep generative model, the single-cell Multi-View Profiler (scMVP), which is designed for handling sequencing data that simultaneously measure gene expression and chromatin accessibility in the same cell, including SNARE-seq, sci-CAR, Paired-seq, SHARE-seq, and Multiome from 10X Genomics. scMVP generates common latent representations for dimensionality reduction, cell clustering, and developmental trajectory inference and generates separate imputations for differential analysis and cis-regulatory element identification. scMVP can help mitigate data sparsity issues with imputation and accurately identify cell groups for different joint profiling techniques with common latent embedding, and we demonstrate its advantages on several realistic datasets.
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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.