Author

Jiachen Li

3 papers indexed here

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Open access Sep 2026

stFormer integrates spatial ligand signaling into a foundation model for spatial transcriptomics.

Recent foundation models for single-cell transcriptomic data generate informative, context-aware gene and cell representations. Spatial transcriptomic (ST) data offer extra positional insights but were not considered by these single-cell models. We introduce stFormer, a transformer model tailored for ST data, which emp...

Sheng-Hao Cao, Kai-Yuan Yang, Jia-Bei Cheng et al. · Cell Reports Methods · 0 citations

Open access Jul 2026

SPgen: Proteome-wide Spatial Proteomics generation using multi-modality foundation models

Spatial proteomics (SP) measures the spatial distribution of proteins within tissues, providing important insights into tissue function, disease, and therapeutic response. However, current SP technologies profile only a small fraction of the proteome and are limited by cost and measurement noise. Recent AI approaches e...

Jiachen Li, Kaiyuan Yang, Qiaoling Che et al. · bioRxiv · 0 citations

#artificial intelligence Preprint Sep 2026

Subcellularly Resolved Single-Cell Embedding Learning with Transcriptomic data, Protein Structure and Localization Information

This work proposes a multimodal framework for learning subcellularly resolved cell embeddings by jointly leveraging RNA expression profiles, protein sequence representations, and protein structural information, and is the first framework that produces subcellularly resolved cell embeddings by jointly incorporating tran...

Zhen Zhou, Jia-Chen Li, Yuan Liu et al. · 0 citations