Work Experience
- Designed and implemented a custom Cellpose-based zebrafish cell segmentation model, increasing the F1 score from 53% to 85%.
- Developed novel methods to generate training/testing datasets from whole-embryo MERFISH images, including a new strategy to select training data using Shannon’s entropy.
- Contributed to the Tabula Spiens Rosetta Donor project by integrating isoform-level information with single-cell gene expression analyses.
- Performed high-throughput sequencing workflows (QC, MiSeq, NextSeq, NovaSeq) and post-run analysis, including demultiplexing and AWS-based data delivery.
- Developed a custom Cellpose2.0 model for spatial transcriptomic data analysis, achieving precision and recall metrics of 84% and 90%.
- Identified critical gene expression patterns in a human breast cancer model through spatial differential analysis, revealing insights into the tumor microenvironment.
- Visualized spatial distributions and performed clustering analyses (UMAP) using Python tools like Squidpy and Scanpy.
- Led a project on 3’-overhang dsDNA integration, significantly boosting CRISPR/Cas9 knock-in efficiency as validated by Next Generation Sequencing (NGS).
- Optimized T cell editing by integrating promoterless GFP transgenes and analyzing results with flow cytometry.
- Enhanced CAR-T cell performance by analyzing costimulatory domain variations and improving targeting efficiency.
- Evaluated cancer cell targeting outcomes using advanced flow cytometry and digital droplet PCR (ddPCR) techniques.
Skills
Programming & Tools
Python, Linux/Unix, R, C/C++, MATLAB, SQL, Jupyter, CellPose, AlphaFold, MatplotLib, Squidpy, Scanpy, Seaborn, Pandas, Git, AWS
Laboratory Techniques
Next Generation Sequencing, CRISPR/Cas9 Editing, PCR (qPCR, ddPCR), Flow Cytometry, Gel Electrophoresis, Tissue Culture
General
SnapGene, GraphPad Prism, FlowJo, Microsoft Office, Google Suite