About Me

I am a PhD student at The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, specializing in bioinformatics.

Contact & Links

• Email: liuwd15@gmail.com
• LinkedIn: wendao-liu
• GitHub: liuwd15
• Google Scholar: View Profile

Research Interests

My research focuses on developing computational methods for understanding biological systems at the single-cell level:

• Single-cell and spatial biology: Transcriptomics, multi-omics integration
• Computational methods: Machine learning applications in biology, foundation models for genomics
• Immune cell analysis: T-cell receptor sequencing, immune cell polarization, and functional states
• Cancer immunology: Tumor microenvironment analysis and therapeutic target identification
• Previous Experience: Collaborative research across computational biology, clinical medicine, and bioinformatics

Technical Skills

• Machine learning skills: Pytorch, Pytorch Lightling, Scikit-learn, Captum, Ray
• Programming language skills: Python, R, Bash, C, C++, Java, SQL
• Software development: Git & Github, Conda, Docker, R & Python package
• Statistic skills: Frequentist & Bayesian inference, Generative models, MCMC, Variational inference
• Single-cell and spatial transcriptomics tools: Scanpy, Scvi-tools, Pertpy, Scirpy, Squidpy, SpatialData, Seurat, Signac, single-cell foundation models (scGPT, scFoundation, UCE), etc
• Next generation sequencing analysis: DNA-seq, RNA-seq, ATAC-seq, TCR/BCR-seq, single-cell multiome, spatial transcriptomics
• Linux skills: Hardware & software configuration, Slurm system, AWS usage
• Flow cytometry analysis: FlowJo

💻 Software & Tools

I develop and maintain several open-source bioinformatics tools:

• irvi: Joint analysis of gene expression and T-cell receptor (TCR) sequence data
• Scupa: Single-cell unified polarization assessment of immune cells using foundation models
• GAN-DP: StyleGAN2-based method for semantic image-driven phenotypes
• tomoda: R/Bioconductor package for tomo-seq data analysis
• sc-miReg: Analysis of miRNA regulation in single cells
• scRIN: Measuring mRNA integrity in single-cell sequencing data

Interested in collaboration or have questions about my research tools? Feel free to reach out!