PROJECT_ARCHIVES
ACCESSING_DATABASE... [11 RECORDS FOUND]
EnrichRAG
A modular framework that augments gene set enrichment (GO/KEGG ORA) with knowledge graph retrieval (~39M relations from STRING, KEGG, Reactome, PubTator) and parallel literature search from PubMed and the web. An LLM pipeline extracts biomedical relations and synthesizes narrative reports, streamed in real time to a Vue 3 frontend with an interactive D3 network graph and result-grounded chat assistant.
WES CNV-HRD-CCF Pipeline
A Nextflow-orchestrated pipeline that chains Sequenza (CNV calling & purity/ploidy estimation), scarHRD (homologous recombination deficiency scoring), and PyClone-VI (clonal architecture inference) into a single reproducible workflow for WES tumor samples, with automated batch processing and structured output for downstream analysis.
Lab Website Redesign
Redesigned the lab website with a terminal-inspired UI. Enhanced member profiles with GitHub-style pixel avatars and contact links, added publication filtering and sorting by year, and integrated an interactive map with detailed location info. Deployed on Nginx with HTTPS via Certbot.
bioinformatics-tools
A reproducible toolkit of shell scripts and Python utilities covering the full NGS workflow: TCGA/SRA data download, BAM-to-FASTQ conversion with QC, WES variant calling (MuSE, MuTect2, VarScan, Pindel) with VCF merging and VEP/MAF annotation, RNA-seq quantification (kallisto, STAR + RSEM), methylation DMP/DMR analysis, and conda environment definitions for each pipeline.
Xenium Spatial RNA Cell Segmentation
Spatial transcriptomics analysis of 10x Xenium data, exploring both transcript-based and image-based cell segmentation approaches. Downstream analysis with Scanpy covers clustering, spatial visualization, and feature matrix construction from segmented cells.
dionic.xyz — A Bioinformatics Portfolio
A biomedical-themed portfolio built with Nuxt 3, where the visual narrative follows the story of cancer — from mutation to uncontrolled growth. Features a D3-powered skill graph inspired by Path of Exile, a git-graph experience timeline, terminal-aesthetic UI with DNA backgrounds, and an automated data layer that validates tag dependencies and generates a formatted CV PDF via Playwright in CI.
16S Microbiome Analysis & Taxonomy Refinement Pipeline
End-to-end 16S amplicon analysis pipeline built on QIIME2 and DADA2, covering QC, denoising, ASV construction, phylogenetic analysis, and alpha/beta diversity. Integrates BLAST-based NCBI taxonomy refinement for species-level resolution and PICRUSt2 functional prediction. Config-driven and deployed on Linux/GCP.
Alzheimer's Disease Multi-Modal Modeling
Developing a multi-modal AI system for Alzheimer's disease by integrating multi-plane MRI deep-learning models, radiomics features, and volumetric information. Built an automated MRI preprocessing pipeline, modular training framework, and fusion methods combining slice-level CNN probabilities with tabular signals for improved diagnostic performance.
Medical Imaging CAD UI Redesign & Dockerization
Frontend refactoring and UI architecture redesign for a medical imaging CAD system. Focused on modular panel layout, state isolation, and performance optimization, and packaged the application into a Docker container for reproducible deployment and environment consistency.
Genomic Landscape of Lung Adenosquamous Carcinoma
Comprehensive WES-based comparative genomics study of lung adenosquamous carcinoma (ASC) with lung adenocarcinoma and squamous cell carcinoma. Conducted SNV/INDEL, CNV, HRD, and mutational signature analyses, integrated multi-cohort datasets, and explored subtype- and component-level genomic patterns to investigate tumor evolution and cell-of-origin hypotheses.