Research graph
References from stFormer integrates spatial ligand signaling into a foundation model for spatial transcriptomics. Local targets link to admitted publications; unresolved targets remain external evidence.
Attention is all you need
2017 · External reference
Language models are few-shot learners
2020 · External reference
Transfer learning enables predictions in network biology
10.1038/s41586-023-06139-9 · 2023 · External reference
scGPT: toward building a foundation model for single-cell multi-omics using generative AI
10.1038/s41592-024-02201-0 · 2024 · External reference
Large-scale foundation model on single-cell transcriptomics
10.1038/s41592-024-02305-7 · 2024 · External reference
Advances in spatial transcriptomics and related data analysis strategies
10.1186/s12967-023-04150-2 · 2023 · External reference
Cell2location maps fine-grained cell types in spatial transcriptomics
10.1038/s41587-021-01139-4 · 2022 · External reference
CROST: a comprehensive repository of spatial transcriptomics
10.1093/nar/gkad782 · 2024 · External reference
Single-Cell Transcriptome Analysis Reveals Dynamic Cell Populations and Differential Gene Expression Patterns in Control and Aneurysmal Human Aortic Tissue
10.1161/circulationaha.120.046528 · 2020 · External reference
CellPLM: pre-training of cell language model beyond single cells
2024 · External reference
Benchmarking atlas-level data integration in single-cell genomics
10.1038/s41592-021-01336-8 · 2022 · External reference
Spatial multi-omic map of human myocardial infarction
10.1038/s41586-022-05060-x · 2022 · External reference
Umap: Uniform manifold approximation and projection for dimension reduction
2018 · External reference
Unresolved reference
External reference
Molecular signatures database (MSigDB) 3.0
10.1093/bioinformatics/btr260 · 2011 · External reference
WNT signaling in adult cardiac hypertrophy and remodeling: lessons learned from cardiac development
10.1161/circresaha.110.223768 · 2010 · External reference
Spatial transcriptomics reveals human cortical layer and area specification
10.1038/s41586-025-09010-1 · 2025 · External reference
Unresolved reference
External reference
PLK1/vimentin signaling facilitates immune escape by recruiting Smad2/3 to PD-L1 promoter in metastatic lung adenocarcinoma
10.1038/s41418-021-00781-4 · 2021 · External reference
Endogenous Glucocorticoid Signaling Regulates CD8+ T Cell Differentiation and Development of Dysfunction in the Tumor Microenvironment
10.1016/j.immuni.2020.08.005 · 2020 · External reference
Apolipoprotein E Promotes Immune Suppression in Pancreatic Cancer through NF-κB-Mediated Production of CXCL1
10.1158/0008-5472.can-20-3929 · 2021 · External reference
Tumor-derived macrophage migration inhibitory factor (MIF) inhibits T lymphocyte activation
10.1016/j.cyto.2006.01.006 · 2006 · External reference
SCANPY: large-scale single-cell gene expression data analysis
10.1186/s13059-017-1382-0 · 2018 · External reference
SciPy 1.0: fundamental algorithms for scientific computing in Python
10.1038/s41592-019-0686-2 · 2020 · External reference
Statsmodels: econometric and statistical modeling with python
10.25080/majora-92bf1922-011 · 2010 · External reference
Inference and analysis of cell-cell communication using CellChat
10.1038/s41467-021-21246-9 · 2021 · External reference
Predicting cell-to-cell communication networks using NATMI
10.1038/s41467-020-18873-z · 2020 · External reference
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis
2021 · External reference
CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice
10.1093/bib/bbaa269 · 2021 · External reference
ICELLNET v2: a versatile method for cell-cell communication analysis from human transcriptomic data
10.1093/bioinformatics/btae089 · 2024 · External reference
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk
10.1038/s41467-022-32111-8 · 2022 · External reference
CellPhoneDB v5: inferring cell-cell communication from single-cell multiomics data
10.1038/s41596-024-01137-1 · 2023 · External reference
From Louvain to Leiden: guaranteeing well-connected communities
10.1038/s41598-019-41695-z · 2019 · External reference
