{"id":"VC0024","type":"paper","title":"Nicheformer: a foundation model for single-cell and spatial omics.","authors_or_org":"Tejada-Lapuerta A, Schaar AC, Gutgesell R, Palla G, Halle L, Minaeva M, Vornholz L, Dony L, Drummer F, Richter T, Bahrami M, Theis FJ.","date":"2025-10-30","year":"2025","venue":"Nature methods","url":"https://doi.org/10.1038/s41592-025-02814-z","doi":"10.1038/s41592-025-02814-z","pmid":"41168487","brain_tumor_focus":"no","tags":["spatial","foundation-model"],"tag_slugs":["spatial","foundation-model"],"tag_labels":["Spatial omics","Foundation model"],"tag_labels_zh":["空间组学","基础模型"],"unmapped_tags":[],"one_line_summary_en":"Nicheformer (Theis lab): single-cell + spatial foundation model, Nat Methods 2025.","one_line_summary_zh":"Nicheformer：单细胞+空间组学基础模型（Theis团队）。","verified":"yes","verification_source":"Europe PMC","page_url":"https://gliostate.com/library/VC0024/","api_url":"https://gliostate.com/api/items/VC0024.json","sameAs":["https://doi.org/10.1038/s41592-025-02814-z","https://pubmed.ncbi.nlm.nih.gov/41168487/"],"is_preprint":false,"facets":{"type":"https://gliostate.com/library/type/paper/","year":"https://gliostate.com/library/year/2025/","tags":["https://gliostate.com/library/tag/spatial/","https://gliostate.com/library/tag/foundation-model/"]},"cited_by":[],"related":[{"id":"VC0025","title":"Novae: a graph-based foundation model for spatial transcriptomics data.","shared_tags":["spatial","foundation-model"],"page_url":"https://gliostate.com/library/VC0025/","api_url":"https://gliostate.com/api/items/VC0025.json"},{"id":"VC0026","title":"A visual-omics foundation model to bridge histopathology with spatial transcriptomics.","shared_tags":["spatial","foundation-model"],"page_url":"https://gliostate.com/library/VC0026/","api_url":"https://gliostate.com/api/items/VC0026.json"},{"id":"VC0023","title":"CellPLM: Pre-training of Cell Language Model Beyond Single Cells","shared_tags":["foundation-model","spatial"],"page_url":"https://gliostate.com/library/VC0023/","api_url":"https://gliostate.com/api/items/VC0023.json"},{"id":"VC0136","title":"AetherCell: A generative engine for virtual cell perturbation and in vivo drug discovery","shared_tags":["foundation-model"],"page_url":"https://gliostate.com/library/VC0136/","api_url":"https://gliostate.com/api/items/VC0136.json"},{"id":"VC0098","title":"Foundation Model Based on Routine Magnetic Resonance Imaging for Brain Tumor Molecular Profiling and Progression Prediction.","shared_tags":["foundation-model"],"page_url":"https://gliostate.com/library/VC0098/","api_url":"https://gliostate.com/api/items/VC0098.json"},{"id":"VC0034","title":"scPRINT-2: Towards the next-generation of cell foundation models and benchmarks","shared_tags":["foundation-model"],"page_url":"https://gliostate.com/library/VC0034/","api_url":"https://gliostate.com/api/items/VC0034.json"}]}