ArticleBMC genomics2025
Integrating single-cell RNA-seq datasets with substantial batch effects.
Article in BMC genomics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Review
- RNA Sequencing Technologies in Acute Lymphoblastic Leukemia: A Comparative Technical Review.Current issues in molecular biology · 2026Review
- An Integrated Multi-omics Single Cell Atlas of the Human RPE and Choroid.bioRxiv : the preprint server for biology · 2026Article
- IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches.bioRxiv : the preprint server for biology · 2026Article
- An Integrated muti-omics cell atlas of the human trabecular meshwork and ciliary body.bioRxiv : the preprint server for biology · 2026Article
- A comparative transcriptomic analysis of mouse demyelination models and multiple sclerosis lesions.Nature communications · 2026Article
- New biological insights into osteosarcoma-lessons from single cell sequencing studies.Cancer metastasis reviews · 2026Review
- From the brain cell atlas to precision neurology: a review of the application of AI-driven multi-omics in brain science.GigaScience · 2026Review
- Revealing a coherent cell-state landscape across single-cell datasets with CONCORD.Nature biotechnology · 2026Article
- Integrated single-cell and transcriptomic profiling identifies machine-learning-based pyroptosis biomarkers in IBD.Frontiers in immunology · 2026Article
- Benchmarking porcine pancreatic ductal organoids for drug screening applications.EMBO molecular medicine · 2025Article
- Fast Optimization of Robust Transcriptomics Embeddings using Probabilistic Inference Autoencoder Networks for multi-Omics.bioRxiv : the preprint server for biology · 2025Article
- scSpecies: enhancement of network architecture alignment in comparative single-cell studies.Genome biology · 2025Article
- Single-cell multiomics data integration and generation with scPairing.Cell reports methods · 2025Article
- Transformative advances in single-cell omics: a comprehensive review of foundation models, multimodal integration and computational ecosystems.Journal of translational medicine · 2025Review
- A multimodal cross-species comparison of pancreas development.Nature communications · 2025Article
- Insights, opportunities, and challenges provided by large cell atlases.Genome biology · 2025Review
- Defining the vascular niche of human adipose tissue across metabolic states.bioRxiv : the preprint server for biology · 2025Article
- Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age.Nature immunology · 2025Article
- Review
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Integration of single-cell RNA-sequencing (scRNA-seq) datasets is standard in scRNA-seq analysis. Nevertheless, current computational methods struggle to harmonize datasets across systems such as species, organoids and primary tissue, or different scRNA-seq protocols, including single-cell and single-nuclei. Conditional variational autoencoders (cVAE) are a popular integration method, however, existing strategies for stronger batch correction have limitations. Increasing the Kullback-Leibler divergence regularization does not improve integration and adversarial learning removes biological signals. Here, we propose sysVI, a cVAE-based method employing VampPrior and cycle-consistency constraints. We show that sysVI integrates across systems and improves biological signals for downstream interpretation of cell states and conditions.
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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 Socratic graph.