Biostatistics · Spatial Omics

Musu
Yuan.

I develop statistical and computational methods that turn complex single-cell, spatial omics, and morphology data into clearer biological insight.

Explore my research ↓Download CV ↗GitHub ↗

Philadelphia, PA

01 — About

Statistics for a spatial view of biology.

I am a postdoctoral researcher in the Department of Biostatistics, Epidemiology and Informatics at the University of Pennsylvania, advised by Prof. Mingyao Li.

My work sits at the intersection of biostatistics, machine learning, single-cell genomics, spatial transcriptomics, and computational pathology.

CurrentPostdoctoral Researcher, UPenn

Ph.D.Integrated Life Sciences, Peking University

B.S.Statistics, Peking University

FocusSingle-cell & spatial multi-omics

Emailmusu.yuan@pennmedicine.upenn.edu

02 — Publications

Selected work, from tissue-scale maps to cell-level models.

Nature Cell Biology 2025

Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues

Musu Yuan, Kaitian Jin, Hanying Yan, Amelia Schroeder, et al., Mingyao Li*

Paper ↗Code ↗

Statistics and Computing 2024

Improving Tree Probability Estimation with Stochastic Optimization and Variance Reduction

Tianyu Xie†, Musu Yuan†, Minghua Deng*, Cheng Zhang*

Paper ↗arXiv ↗

Briefings in Bioinformatics 2024

scPLAN: A hierarchical computational framework for single transcriptomics data annotation, integration and cell-type label refinement

Qirui Guo†, Musu Yuan†, Lei Zhang*, Minghua Deng*

Paper ↗

Briefings in Bioinformatics 2024

SPANN: Annotating single-cell resolution spatial transcriptome data with scRNA-seq data

Musu Yuan†, Hui Wan†, Minghua Deng*

Paper ↗Code ↗

Briefings in Bioinformatics 2024

Continually adapting pretrained language model to universal annotation of single-cell RNA-seq data

Hui Wan, Musu Yuan, Yiwei Fu, Minghua Deng*

Paper ↗

Bioinformatics 2023

Clustering single-cell multi-omics data with MoClust

Musu Yuan, Liang Chen*, Minghua Deng*

Paper ↗Code ↗

Bioinformatics 2022

scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets

Musu Yuan†, Liang Chen†, Minghua Deng*

Paper ↗Code ↗

Frontiers in Genetics 2022

Clustering CITE-seq data with a canonical correlation-based deep learning method

Musu Yuan, Liang Chen, Minghua Deng*

Paper ↗Code ↗

bioRxiv Preprint

HistoSweep enables cellular-resolution tissue quality control for gigapixel images in digital pathology and spatial omics

Amelia Schroeder, Xiaokang Yu, Wei Li, Liran Mao, Musu Yuan, et al., Mingyao Li*

Preprint ↗

bioRxiv Preprint · 2026

Multiscale confidence quantification for virtual spatial transcriptomics with UTOPIA

Kaitian Jin, Zihao Chen, Xiaokang Yu, Musu Yuan, et al., Mingyao Li*

Preprint ↗

03 — Journey

Training across statistics, genomics, and medicine.

2026 — PRESENT

University of Pennsylvania

Postdoctoral Researcher · Department of Biostatistics, Epidemiology and Informatics · Advisor: Mingyao Li

2021 — 2026

Peking University

Ph.D. in Integrated Life Sciences (Biostatistics) · Academy for Advanced Interdisciplinary Studies · Advisor: Minghua Deng

2024 — 2025

University of Pennsylvania

Visiting Student · Department of Biostatistics, Epidemiology and Informatics

2017 — 2021

Peking University

B.S. in Statistics · School of Mathematical Sciences