Automated Pipelines and Multi-Omics Integration
Peng He, Professor
UC San Francisco
Applications for Fall 2025 are closed for this project.
This project focuses on building robust and reusable computational pipelines to analyze bulk and single-cell transcriptomics data. Students will contribute to bioinformatics workflows for data processing, integration, and visualization across various tissues and disease contexts, including fibrosis and vascular diseases.
Role: Subprojects:
Develop Snakemake-based pipelines for bulk RNA-seq analysis
Automate clustering and visualization tools
Integrate published datasets across disease areas (e.g., IPF, fibrosis, vascular disorders)
Annotate large reference atlases and test multi-omics fusion strategies
Qualifications: Experience with Python, R, or workflow management systems (Snakemake, Nextflow); interest in scalable bioinformatics
Day-to-day supervisor for this project: Wenjiang Zhou
Hours: 9-11 hrs
Off-Campus Research Site: on site/hybrid/off-campus all acceptable
Related website: https://peng-he-lab.github.io/
Related website: https://profiles.ucsf.edu/peng.he