ArticleGenome biology2024
Gene panel selection for targeted spatial transcriptomics.
Article in Genome biology, 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.
- RKMR: A Rapid Kernel Machine Regression Framework for Optimal Marker Detection in Spatial Omics Data.bioRxiv : the preprint server for biology · 2026Article
- Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.Nature methods · 2026Article
- SOFisher: reinforcement learning-guided experiment designs for spatial omics.Nature communications · 2026Article
- A transcriptomics-native foundation model for universal cell representation and virtual cell synthesis.bioRxiv : the preprint server for biology · 2026Article
- Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap.Nature protocols · 2026Review
- Single-cell multiomic human brain atlas reveals regulatory drivers of cortical regionality.Nature communications · 2026Article
- CELLama: Foundation Model for Single Cell and Spatial Transcriptomics by Cell Embedding Leveraging Language Model Abilities.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Why "Where" Matters as Much as "How Much": Single-Cell and Spatial Transcriptomics in Plants.International journal of molecular sciences · 2025Review
- Enhanced RNA Preservation in Mouse Brain Tissue: A Strategy Combining Cardiac Perfusion with Hypersaline Immersion.ACS omega · 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
- Comparison of spatial transcriptomics technologies using tumor cryosections.Genome biology · 2025Article
- Homebuilt Imaging-Based Spatial Transcriptomics: Tertiary Lymphoid Structures as a Case Example.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Combining Network Pharmacology and Transcriptomic Strategies to Explore the Pharmacological Mechanism of Total Ginsenoside Ginseng Root and Its Impact on Antidepressant Effects.International journal of molecular sciences · 2024Article
- Mapping human tissues with highly multiplexed RNA in situ hybridization.Nature communications · 2024Article
- Spatial multi-omics: novel tools to study the complexity of cardiovascular diseases.Genome medicine · 2024Review
- Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization.bioRxiv : the preprint server for biology · 2023Article
- Targeting the tumor microenvironment in pediatric gliomas: Advances and future directions in immunotherapy.Neuro-oncology advancesReview
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6 authors.
Funding
Abstract
Targeted spatial transcriptomics hold particular promise in analyzing complex tissues. Most such methods, however, measure only a limited panel of transcripts, which need to be selected in advance to inform on the cell types or processes being studied. A limitation of existing gene selection methods is their reliance on scRNA-seq data, ignoring platform effects between technologies. Here we describe gpsFISH, a computational method performing gene selection through optimizing detection of known cell types. By modeling and adjusting for platform effects, gpsFISH outperforms other methods. Furthermore, gpsFISH can incorporate cell type hierarchies and custom gene preferences to accommodate diverse design requirements.
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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.