Projects

sounDMR – ONT Methylation Analysis Tool

Co-developed an R-based tool for rapid analysis of Oxford Nanopore methylation data. Designed to streamline detection of differential methylation patterns across large genomic datasets.

GitHub Repository

Key impact: enabled scalable epigenetic analysis of plant genomes and improved speed of methylation inference pipelines.

AWS Genomics Pipeline (50TB+ Scale System)

Designed and implemented a cloud-based genomics processing pipeline using AWS Batch for large-scale sequencing analysis.

• Processes whole-genome sequencing datasets at 50+ TB scale
• Automated job orchestration and resource scaling
• Supports multi-sample parallel processing workflows

Key impact: enabled high-throughput genomic processing in production-scale environments.

Oligo Design Tool (Python)

Developed an internal Python-based tool for designing optimized oligonucleotides for experimental workflows.

• Automated primer/oligo generation
• Sequence constraint filtering and optimization
• Used by experimental biology teams for assay design

Key impact: reduced manual primer design time and improved experimental efficiency.

ARTEMIS-DELFI cfDNA Pipeline Integration

Built and maintained cfDNA fragmentomics pipelines used for brain tumor liquid biopsy analysis.

• Integration of fragment length and coverage features
• Multi-cohort cfDNA analysis (Illumina + ONT)
• Clinical feature integration (tumor burden, Ki67, imaging markers)

Key impact: supports early detection research in glioblastoma using non-invasive blood-based biomarkers.

Project Summary

• Built production-scale genomics pipelines (cloud + HPC)
• Developed bioinformatics tools in R and Python
• Worked across epigenomics, cfDNA, and plant genomics systems
• Bridged computational biology with experimental workflows