ArticleGenome biology2019
CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data.
Article in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Single-cell Transcriptomics in Autoimmune Diseases: Mechanistic Insights, Cross-disease Convergence, and Translational Challenges in Rheumatoid Arthritis, Systemic Lupus Erythematosus, Type 1 Diabetes, and Multiple Sclerosis.Clinical reviews in allergy & immunology · 2026Review
- Specificity-driven graph learning for the identification of rare cell states.Advanced biotechnology · 2026Article
- Deep-learning-enabled multi-omics analyses for prediction of future metastasis in cancer.Nature communications · 2026Article
- RareCapsNet: An explainable capsule network enables robust discovery of rare cell populations from large-scale single-cell transcriptomics.PLoS computational biology · 2026Article
- Specificity-driven cell-gene graph learning identifies rare cell states in single-cell and spatial transcriptomic data.Advanced biotechnology · 2026Article
- RAG: a regularized adaptive graph-based method for rare-cell identification from single-cell expression data.Briefings in bioinformatics · 2026Article
- Cell neighborhood topology directs rare cell population identification.Nature communications · 2026Article
- BayesRare: Bayesian mixture model for population-level rare cell type detection in multi-subject single-cell RNA sequencing data.Briefings in bioinformatics · 2026Article
- Revealing the Best Strategies for Rare Cell Type Detection in Multi-Sample Single-Cell Datasets.Genes · 2025Article
- A systematic evaluation of highly variable gene selection methods for single-cell RNA-sequencing.Genome biology · 2025Article
- Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover.Genome research · 2025Article
- Advances in spatial transcriptomics and its application in the musculoskeletal system.Bone research · 2025Review
- Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics.Nature reviews. Molecular cell biology · 2025Review
- scSID: A lightweight algorithm for identifying rare cell types by capturing differential expression from single-cell sequencing data.Computational and structural biotechnology journal · 2024Article
- Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data.Genome research · 2024Article
- Leveraging gene correlations in single cell transcriptomic data.BMC bioinformatics · 2024Article
- scCAD: Cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data.Nature communications · 2024Article
- Mining alternative splicing patterns in scRNA-seq data using scASfind.Genome biology · 2024Article
- Unified cross-modality integration and analysis of T cell receptors and T cell transcriptomes by low-resource-aware representation learning.Cell genomics · 2024Article
- MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer.Nature communications · 2024Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We develop CellSIUS (Cell Subtype Identification from Upregulated gene Sets) to fill a methodology gap for rare cell population identification for scRNA-seq data. CellSIUS outperforms existing algorithms for specificity and selectivity for rare cell types and their transcriptomic signature identification in synthetic and complex biological data. Characterization of a human pluripotent cell differentiation protocol recapitulating deep-layer corticogenesis using CellSIUS reveals unrecognized complexity in human stem cell-derived cellular populations. CellSIUS enables identification of novel rare cell populations and their signature genes providing the means to study those populations in vitro in light of their role in health and disease.
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