ArticleGenome biology2021
scSorter: assigning cells to known cell types according to marker genes.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- Phosphoproteomic dysregulation promotes tumor proliferation in Cushing's disease.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
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- scUmaper: An automated framework for doublet removal and cell-type annotation in single-cell transcriptomics.iScience · 2026Article
- A mitochondrial ROS-dependent antiviral response promotes β cell resilience and is diminished in donors with type 1 diabetes.Science translational medicine · 2026Article
- Transformers for single-cell RNA sequencing: a survey.Briefings in bioinformatics · 2026Review
- Repeated TLR7 activation induces cell type- and brain region-specific transcriptome changes in male mice.Scientific reports · 2026Article
- A multi-omic atlas in the African turquoise killifish reveals increased glucocorticoid signaling as a hallmark of brain aging.bioRxiv : the preprint server for biology · 2026Article
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- From bats to humans: uncoveringbioRxiv : the preprint server for biology · 2026Article
- Epigenetic adaptation of beta cells across lifespan and disease.Nature metabolism · 2026Article
- Villification of the intestinal epithelium is driven by Foxl1 through activation of PDGFRα and BMPs.Nature communications · 2026Article
- Iron deficiency induces maturation-dependent loss of pancreatic β-cells.Nature communications · 2026Article
- Single-nuclei RNA-sequencing uncovers sexually divergent exercise signatures partially mimicked by TFEB overexpression in mouse skeletal muscle.bioRxiv : the preprint server for biology · 2026Article
- CeLLTra: aligning cell names with gene expression via a pathway-informed transformer.Bioinformatics (Oxford, England) · 2026Article
- CellPredX, a computational framework for cross-data type, cross-sample, and cross-protocol cell type annotation through domain adaptation and deep metric learning.PLoS computational biology · 2026Article
- scANMF: Prior Knowledge and Graph-Regularized NMF for Accurate Cell Type Annotation in scRNA-seq.International journal of molecular sciences · 2025Article
- Variable Schwann cell merlin inactivation is targetable with TEAD1 inhibition in schwannomas.bioRxiv : the preprint server for biology · 2025Article
- Islet-intrinsic sex differences in inflammatory signaling contribute to autoimmune diabetes susceptibility.bioRxiv : the preprint server for biology · 2025Article
- Global human myeloid replacement with peripheral progenitors induces interferonopathy and neurodegeneration.Research square · 2025Article
- Spatial pattern enhanced cellular and tissue recognition for spatial transcriptomics.NAR genomics and bioinformatics · 2025Article
22 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
On single-cell RNA-sequencing data, we consider the problem of assigning cells to known cell types, assuming that the identities of cell-type-specific marker genes are given but their exact expression levels are unavailable, that is, without using a reference dataset. Based on an observation that the expected over-expression of marker genes is often absent in a nonnegligible proportion of cells, we develop a method called scSorter. scSorter allows marker genes to express at a low level and borrows information from the expression of non-marker genes. On both simulated and real data, scSorter shows much higher power compared to existing methods.
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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.