ReviewComputational and structural biotechnology journal2024
Recent advances in spatially variable gene detection in spatial transcriptomics.
Review in Computational and structural biotechnology journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Artificial intelligence in spatial transcriptomics: a review of methods, datasets, and directions.Briefings in bioinformatics · 2026Review
- Diffusion-based representation integration for foundation models improves spatial transcriptomics analysis.Bioinformatics (Oxford, England) · 2026Article
- Spatial Gene Set Enrichment Analysis with Applications to Spatially Resolved Transcriptomic Data.bioRxiv : the preprint server for biology · 2026Article
- Systematic clustering alignment and feature characterization for single-cell omics using ACE-OF-Clust.bioRxiv : the preprint server for biology · 2026Article
- Logistic regression for estimating functional effects with spatial transcriptomics.Nucleic acids research · 2026Article
- MLN2SVG: domain-aware spatially variable gene detection using contrastive variational autoencoder and multi-level neighbor search.Briefings in bioinformatics · 2026Article
- Review
- Benchmarking cell-type-specific spatially variable gene detection methods.Briefings in bioinformatics · 2026Article
- Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis.bioRxiv : the preprint server for biology · 2026Article
- SpaceBF: spatial coexpression analysis using Bayesian fused approaches in spatial omics datasets.GigaScience · 2026Article
- Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?Briefings in bioinformatics · 2026Article
- SpaGene: A Deep Adversarial Framework for Spatial Gene Imputation.Computational and structural biotechnology journal · 2026Article
- Mapping safety in space: the emerging role of spatial transcriptomics in safe drug development.Frontiers in toxicology · 2026Review
- A unified framework for identification of cell-type-specific spatially variable genes in spatial transcriptomic studies.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- SPACE: Spatially variable gene clustering adjusting for cell type effect for improved spatial domain detection.Nucleic acids research · 2025Article
- Identifying spatially variable genes by projecting to morphologically relevant curves.bioRxiv : the preprint server for biology · 2025Article
- Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data.Nature communications · 2025Review
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4 authors.
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Abstract
With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered on identifying spatially variable genes (SVGs) or genes expressed with specific spatial patterns across the tissue. SVG detection is an important task since many downstream analyses depend on these selected SVGs. Over the past few years, a plethora of new methods have been proposed for the detection of SVGs, accompanied by numerous innovative concepts and discussions. This article provides a selective review of methods and their practical implementations, offering valuable insights into the current literature in this field.
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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.