ArticleGenome research2023
Partial alignment of multislice spatially resolved transcriptomics data.
Article in Genome research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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65 citing papers in PubMed.
- Semi-metric optimal transport enables robust spatial multi-omics integration.Research square · 2026Article
- STADiffuser: high-fidelity simulation and full-view 3D modeling of spatial transcriptomics.Nature communications · 2026Article
- Transposable elements and homotypic niches drive immune dynamics and resistance in melanoma epigenetic-based immunotherapy.Science advances · 2026Article
- Tissue and cellular spatiotemporal dynamics in colon aging.Nature biotechnology · 2026Article
- Multimodal spatial omics: From data acquisition to computational integration.Patterns (New York, N.Y.) · 2026Review
- Computational analysis in spatial transcriptomics: methods and perspectives.Briefings in bioinformatics · 2026Review
- Riemannian metric learning for alignment of spatial multiomics.Bioinformatics (Oxford, England) · 2026Article
- Diffusion-based representation integration for foundation models improves spatial transcriptomics analysis.Bioinformatics (Oxford, England) · 2026Article
- Accurate trajectory inference in time-series spatial transcriptomics with structurally-constrained optimal transport.Nature communications · 2026Article
- GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics.Genome biology · 2026Article
- Atlas-Level Single-Cell and Spatial Transcriptomics Data Integration via PRIME.bioRxiv : the preprint server for biology · 2026Article
- Exploring the structural lexicon of the Proteome via Metric Geometry.PLoS computational biology · 2026Article
- StPedf: Cell trajectory inference of spatial transcriptomics via spatial proximity embedding and spatial density-adaptive fusion.PLoS computational biology · 2026Article
- SPOmiAlign: a modality-agnostic computational framework for multimodal spatial omics alignment enabled by a feature matching foundation model.Briefings in bioinformatics · 2026Article
- Topography-aware optimal transport for alignment of spatial omics data.Cell reports methods · 2026Article
- Alignment of spatial transcriptomics slices across diseases, platforms and conditions.Genome medicine · 2026Article
- 3d-OT: a deep geometry-aware framework for heterogeneous slices alignment of spatial multi-omics.Nature methods · 2026Article
- Network model for alignment, stitching and slice-to-volume 3D reconstruction of large-scale spatially resolved slices.Nature communications · 2026Article
- Multimodal spatial alignment and morphology mapping with MOSAICField.bioRxiv : the preprint server for biology · 2026Article
- stVCR: spatiotemporal dynamics of single cells.Nature methods · 2026Article
5 more citing papers are in PubMed but not listed here.
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Abstract
Spatially resolved transcriptomics (SRT) technologies measure messenger RNA (mRNA) expression at thousands of locations in a tissue slice. However, nearly all SRT technologies measure expression in two-dimensional (2D) slices extracted from a 3D tissue, thus losing information that is shared across multiple slices from the same tissue. Integrating SRT data across multiple slices can help recover this information and improve downstream expression analyses, but multislice alignment and integration remains a challenging task. Existing methods for integrating SRT data either do not use spatial information or assume that the morphology of the tissue is largely preserved across slices, an assumption that is often violated because of biological or technical reasons. We introduce PASTE2, a method for
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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.