ArticleGenome biology2021
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq.
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 33 papers.
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Who cites it
33 citing papers in PubMed.
- Interpretable scRNA-seq Analysis with Intelligent Gene Selection.Applied biochemistry and biotechnology · 2026Article
- Single-cell marker gene clustering: A unified deep learning framework for marker gene-based clustering of single-cell RNA-sequencing data.Quantitative biology (Beijing, China) · 2026Article
- Single-cell multi-omic atlas and morphogen screening informs midbrain and hindbrain organoid engineering.Nature neuroscience · 2026Article
- Optimal gene panel selection for targeted spatial transcriptomics experiments.Nucleic acids research · 2026Article
- Review
- scGPD: single-cell informed gene panel design for targeted spatial transcriptomics.Briefings in bioinformatics · 2026Article
- CiCLoDS: Joint cell clustering and gene selection for single-cell spatial transcriptomics.Scientific reports · 2026Article
- Article
- Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover.Genome research · 2025Article
- Optimal Gene Panel Selection for Targeted Spatial Transcriptomics Experiments.bioRxiv : the preprint server for biology · 2025Article
- scGPD: single-cell informed gene panel design for targeted spatial transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Spatial gene expression at single-cell resolution from histology using deep learning with GHIST.Nature methods · 2025Article
- Multi-view gene panel characterization for spatially resolved omics.Briefings in bioinformatics · 2025Article
- Gut microbiota and tuberculosis.iMeta · 2025Review
- Redefining the high variable genes by optimized LOESS regression with positive ratio.BMC bioinformatics · 2025Article
- Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics.Nature reviews. Molecular cell biology · 2025Review
- Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery.Nature neuroscience · 2024Review
- Probe set selection for targeted spatial transcriptomics.Nature methods · 2024Article
- Implementing distinct spatial proteogenomic technologies: opportunities, challenges, and key considerations.Clinical and experimental immunology · 2024Review
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
scRNA-seq datasets are increasingly used to identify gene panels that can be probed using alternative technologies, such as spatial transcriptomics, where choosing the best subset of genes is vital. Existing methods are limited by a reliance on pre-existing cell type labels or by difficulties in identifying markers of rare cells. We introduce an iterative approach, geneBasis, for selecting an optimal gene panel, where each newly added gene captures the maximum distance between the true manifold and the manifold constructed using the currently selected gene panel. Our approach outperforms existing strategies and can resolve cell types and subtle cell state differences.
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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.