work experience

Project: To advance analytics capabilities for cancer vaccine research using Nanopore sequencing technology by developing a real-time analysis pipeline for TCR repertoire analysis.

• Background Information: Long-read sequencing technologies, such as Nanopore, are prone to errors and require sophisticated data cleaning methods for accurate sequence recovery. Addressing this challenge is crucial for advancements in bioinformatics and cancer research.
• Final Pipeline
1. Analysed large-scale genomic datasets exceeding 7 million rows, producing critical insights that influenced shifts in research focus.
2. Integrated over 11 open-source bioinformatics tools into a custom automated pipeline, streamlining analysis for enhanced efficiency.
3. Developed Shell and Python automation scripts to extract and group cell barcodes, segment TCR α and β chains per cell, and reconstruct these chains using de novo assembly. This improved barcode recovery from 608,700 to 2,181,878, significantly advancing cell barcode extraction processes.
4. Implemented a Python-based method for categorizing sequences into TCR α and β chains without needing a whitelist. This method used Ward's Linkage clustering, achieving an average accuracy of 90% on sequences from 100 unique cell barcodes, demonstrating effectiveness in clonotype identification for long-read sequencing.
5. Proposed a novel approach for separating TCR chains that outperformed traditional methods, aiding in clonotype identification crucial for understanding immune responses in cancer vaccine research.
6. Customized Shasta for the assembly of TCR α and β sequences, addressing the lack of pre-existing configurations for TCR-specific assembly and pioneering new methodologies.
• Additional Achievements
1. Innovated and validated a method that separated TCR α and β chains without reference mapping, ensuring robustness in diverse data contexts.
2. Conducted multiple iterations of the pipeline, experimenting with over 20 bioinformatics tools and methodologies. This intensive work led to major research shifts based on in-depth data analysis.
3. Co-authored the paper titled Refining TCR Clonotype Identification With Long-Read Sequencing Technique, submitted to the Society for Immunotherapy of Cancer (SITC), contributing to advancements in cancer vaccine development.