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PhD

Columbia University, New York, NY, United States

• PhD in Systems Biology, Integrated Program in Cellular, Molecular, and Biomedical Studies

BS

Peking University, Beijing, China

• BS in Integrated Science, Yuanpei College

Postdoctoral Research Associate

Ren Lab, New York Genome Center, New York, NY, United States

• Develop deep learning methods (DNA language models) to predicting non-coding variant effect, prioritize causal variants for diagnosis and therapeutic target discovery.

Data Science & Machine Learning Intern

Insitro, Inc., South San Francisco, CA, United States

• Evaluate and improve the in-house drug target discovery pipeline by integration of GWAS, RNA-seq and PharmaProjects data.

Graduate Research Assistant

Shen Lab, Department of Systems Biology, Columbia University, New York, NY, United States

• Develop deep learning method to predict coding variant effect using representations of protein sequence, structure and functions.
• Develop statistical genetics methods to identify disease risk genes for developmental disorders.

Research Assistant

Zhang Lab, Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China

• Develop computational methods to reconstruct cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly.

PreMode

• PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context.

RESCVE

• A deep learning model to represent the modes of action of missense variants.

VBASS

• A Bayesian Mixture model with learnable prior to integrate single cell gene expression data in rare variants association analysis.

CSOmap

• Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly.

• Chinese Government Award for Outstanding Self-Financed Students Abroad

• Dean’s fellowship, Graduate School of Arts and Science, Columbia University

• 2014-2015 academic year Outstanding Freshman Scholarship, Peking University

• The 28th National Olympiad in Chemistry in Provinces, 1st prize, Zhejiang Province, China

Di Liu, summer rotation PhD student

Ren Lab, New York Genome Center, New York, NY, United States

• Assisted in the project of developing deep learning models to predict the pathogenicity of genetic variants.

• Chinese Government Award for Outstanding Self-Financed Students Abroad

Demi Zhuang, summer visiting undergraduate student

Shen Lab, Columbia University, New York, NY, United States

• Developed protein family specific benchmarking tasks and datasets for PreMode. Applied PreMode to those datasets and discovered several novel likely G/LoF variants.

Andrew Lee, summer visiting high school student

Shen Lab, Columbia University, New York, NY, United States

• Developed an R app to visualize the scRNA-seq data of autism risk genes in brain cell types from public datasets. Applied it to discovery of novel autism risk genes and identification of disease associated cell types.