A State-Resolved Single-Cell and Spatial Atlas Reveals IDH-Associated Differences in Malignant and Immune Architecture in Diffuse Glioma.
Zaman A et al. · MedComm · 2026-10-04
State-resolved sc+spatial atlas of IDH-associated differences in glioma.
Tag: Spatial omics
20 items, newest first.
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Spatial and single-cell dissection of medulloblastoma identifies developmental hierarchies and a prognostic PPIA-BSG tumor-immune axis.
Chen M, Duan B, Zhang J, Daniels C, Hu C, Yuan J, Guo J, Taylor MD, Shi X, Zhang L, Li D, Sun T. · Journal of translational medicine · 2026-09-15
Spatial + single-cell dissection of medulloblastoma hierarchies (2026).
Single-cell and spatial transcriptomes reveal oligodendrocyte remodeling fatty acid metabolism microenvironment of lung cancer brain metastases.
Yang Y, Gao Y, Qi Z, Li S, Wang Z, Li D, Chen L, Zhou C, Feng M, Chen X, Hao B, Wu X, Li L, Cao Y. · Journal of translational medicine · 2026-06-16
Oligodendrocyte fatty-acid remodeling in brain metastasis (sc+spatial).
A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma.
Sussman JH et al. · Cell reports. Medicine · 2026-04-23
Longitudinal single-cell & spatial atlas of pediatric high-grade glioma.
Training transformers to solve cancer trial failure — Ron Alfa & Daniel Bear, Noetik
Latent Space · Latent Space podcast · 2026-04-20
Noetik's tumor spatial 'virtual cell' models (TARIO-2) and $50M GSK deal.
Novae: a graph-based foundation model for spatial transcriptomics data.
Blampey Q, Benkirane H, Bercovici N, Mulder K, Gessain G, Ginhoux F, André F, Cournède PH. · Nature methods · 2025-12-10
Novae: graph-based foundation model for spatial transcriptomics.
STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.
Huang T, Liu T, Babadi M, Ying R, Jin W. · NPJ digital medicine · 2025-11-14
STPath: generative model linking WSIs and spatial transcriptomics.
Nicheformer: a foundation model for single-cell and spatial omics.
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. · Nature methods · 2025-10-30
Nicheformer (Theis lab): single-cell + spatial foundation model, Nat Methods 2025.
Charting the single-cell and spatial landscape of IDH-wild-type glioblastoma with GBmap.
Ruiz-Moreno C et al. · Neuro-oncology · 2025-10-01
GBmap: single-cell & spatial reference atlas of IDH-wt GBM (>1M cells).
A visual-omics foundation model to bridge histopathology with spatial transcriptomics.
Chen W et al. · Nature methods · 2025-05-29
OmiCLIP/Loki: visual-omics foundation model bridging H&E and spatial transcriptomics.
Spatial epigenomic niches underlie glioblastoma cell state plasticity
Kint S et al. · bioRxiv · 2025-05-14
Spatial epigenomic niches underlie GBM cell-state plasticity.
Mapping the spatial architecture of glioblastoma from core to edge delineates niche-specific tumor cell states and intercellular interactions
Khan SM et al. · bioRxiv · 2025-04-04
Spatial architecture of GBM from core to edge; niche-specific states.
Single-cell and spatial genomic landscape of non-small cell lung cancer brain metastases.
Tagore S et al. · Nature medicine · 2025-02-27
Single-cell & spatial landscape of NSCLC brain metastases (Nat Med 2025).
scGPT-spatial: Continual Pretraining of Single-Cell Foundation Model for Spatial Transcriptomics
Wang C, Cui H, Zhang A, Xie R, Goodarzi H, Wang B. · bioRxiv · 2025-02-08
scGPT-spatial: continual pretraining for spatial transcriptomics.
Hypoxia coordinates the spatial landscape of myeloid cells within glioblastoma to affect survival.
Haley MJ et al. · Science advances · 2024-05-17
Hypoxia coordinates spatial landscape of myeloid cells in GBM.
Integrative spatial analysis reveals a multi-layered organization of glioblastoma.
Greenwald AC et al. · Cell · 2024-04-22
Greenwald et al.: multi-layered spatial organization of GBM.
CellPLM: Pre-training of Cell Language Model Beyond Single Cells
Wen H, Tang W, Dai X, Ding J, Jin W, Xie Y, Tang J. · bioRxiv · 2023-10-05
CellPLM: cell language model beyond single cells (spatial context).
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location.
Liu I et al. · Nature genetics · 2022-12-05
Liu et al.: tumor cell states and spatial organization of H3-K27M DMG across ages.
The spatial transcriptomic landscape of non-small cell lung cancer brain metastasis.
Zhang Q, Abdo R, Iosef C, Kaneko T, Cecchini M, Han VK, Li SS. · Nature communications · 2022-10-10
Spatial transcriptomic landscape of NSCLC brain metastasis.
Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma.
Ravi VM et al. · Cancer cell · 2022-06-01
Ravi et al.: spatial multi-omics of tumor-host interdependence in GBM.