Author

Yuanhua Huang

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Open access Aug 2026

CLEAR-ST: Physics-informed probabilistic decontamination of spatial transcriptomics by modeling mRNA lateral diffusion

Spatial transcriptomics is a rapidly evolving technology that allows for the measurement of gene expression in a spatially resolved manner. However, one technical problem that occurs for many sequencing-based spatial transcriptomics platforms is the presence of mRNA lateral diffusion, where mRNA from one spot can bind...

K. Ma, Yuan-Hua Huang, J. Ho · bioRxiv · 0 citations

Open access Aug 2026

stCNASim: Allele-aware spatial RNA-seq simulator enables systematic benchmarking of copy number inference

Spatial transcriptomics (ST) is revolutionizing the study of tumor evolution by enabling spatially resolved copy-number alteration (CNA) analysis. However, evaluating the accuracy and robustness of current single-cell (SC) and ST-specific CNA inference tools remains challenging due to the absence of ground-truth datase...

Xianjie Huang, Rongting Huang, Jiamu Qiao et al. · bioRxiv · 0 citations

Open access Jul 2026

xDecoder unlocks the potential of genomic foundation models for few-shot personal gene expression prediction.

Large-scale genomic language models (gLMs) hold promise for modeling gene regulation, yet their ability to capture personal gene expression variations remains unresolved. We developed xDecoder, a unified decoding framework that utilizes gLMs and sequence-to-function (S2F) embeddings to learn how personal genetic variat...

Shumin Li, Ruibang Luo, Yuanhua Huang · Molecular Systems Biology · 0 citations