Siyu He

Squidiff predicts transcriptomic changes across cell types in response to environmental stimuli using a diffusion model, enabling in silico screening for drug discovery and precision medicine.

The paper benchmarks large language models for cell-type and gene set annotation using AnnDictionary, finding high accuracy in cell-type annotation and strong functional gene set recovery.

This study uses spatial multi-omics and deep learning to identify immunotherapy response and resistance signatures in hepatocellular carcinoma.

The paper introduces CORAL, a deep generative model for spatial multiomics data that deconvolves low-resolution data into single-cell profiles and identifies spatial domains and cell-cell interactions.

This study examines the effects of chronic and acute fentanyl exposure on midbrain organoids, finding that chronic treatment arrests neuronal development and alters synaptic pathways.

This paper creates a vascular organoid model with an AKT1 mutation to study Proteus syndrome and finds AKT inhibitors reverse vascular malformations.

Starfysh integrates spatial transcriptomics and histology to analyze tumor microenvironments, identifying disease-specific spatial hubs and immune interactions in breast cancers.