ArticleProceedings of the National Academy of Sciences of the United States of America2019
A computational framework for DNA sequencing microscopy.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Spatial transcriptomic imaging of an intact organism using volumetric DNA microscopy.Nature biotechnology · 2026Article
- Scalable spatial transcriptomics through computational array reconstruction.Nature biotechnology · 2026Article
- Spatial coherence in DNA barcode networks.Patterns (New York, N.Y.) · 2025Article
- Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction.Nature communications · 2025Article
- Scalable imaging-free spatial genomics through computational reconstruction.bioRxiv : the preprint server for biology · 2024Article
- Optics-free reconstruction of 2D images via DNA barcode proximity graphs.bioRxiv : the preprint server for biology · 2024Article
- Molecular pixelation: spatial proteomics of single cells by sequencing.Nature methods · 2024Article
- Molecular robotic agents that survey molecular landscapes for information retrieval.Nature communications · 2024Article
- An error correction strategy for image reconstruction by DNA sequencing microscopy.Nature computational science · 2024Article
- Enablers and challenges of spatial omics, a melting pot of technologies.Molecular systems biology · 2023Review
- The expanding vistas of spatial transcriptomics.Nature biotechnology · 2023Review
- Article
- Museum of spatial transcriptomics.Nature methods · 2022Review
- Article
- Cellular macromolecules-tethered DNA walking indexing to explore nanoenvironments of chromatin modifications.Nature communications · 2021Article
- A DNA-nanoassembly-based approach to map membrane protein nanoenvironments.Nature nanotechnology · 2021Article
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5 authors.
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Abstract
We describe a method whereby microscale spatial information such as the relative positions of biomolecules on a surface can be transferred to a sequence-based format and reconstructed into images without conventional optics. Barcoded DNA "polymerase colony" (polony) amplification techniques enable one to distinguish specific locations of a surface by their sequence. Image formation is based on pairwise fusion of uniquely tagged and spatially adjacent polonies. The network of polonies connected by shared borders forms a graph whose topology can be reconstructed from pairs of barcodes fused during a polony cross-linking phase, the sequences of which are determined by recovery from the surface and next-generation (next-gen) sequencing. We developed a mathematical and computational framework for this principle called polony adjacency reconstruction for spatial inference and topology and show that Euclidean spatial data may be stored and transmitted in the form of graph topology. Images are formed by transferring molecular information from a surface of interest, which we demonstrated in silico by reconstructing images formed from stochastic transfer of hypothetical molecular markers. The theory developed here could serve as a basis for an automated, multiplexable, and potentially superresolution imaging method based purely on molecular information.
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