I design and deploy end-to-end solutions in computational biology, structural bioinformatics, and biomedical AI. By bridging multi-omics pipelines, structural modeling, and clinical variant analysis, I transform raw genomic, transcriptomic, and metagenomic datasets into complete, publication-ready scientific insights.
My technical approach integrates high-performance cloud pipelines (Nextflow/WDL), interactive data visualization, and retrieval-augmented LLM architectures (RAG) to accelerate biomedical discovery and scientific translation.
| Specialization | Core Capabilities & Methodologies |
|---|---|
| Transcriptomics & Bulk RNA-Seq | Differential gene expression (DESeq2/limma), TMM normalization, high-res Volcano & Heatmap visualization. |
| Single-Cell Omics (scRNA-Seq) | scRNA-seq processing, quality control filtering, Harmony integration, Leiden clustering, UMAP/t-SNE projections, marker gene cell annotation. |
| Structural Biology & Docking | 3D protein structure visualization (AlphaFold DB), binding pocket evaluation, mutation hotspot modeling, py3Dmol WebGL rendering. |
| Metagenomics & Microbiome | 16S rRNA taxonomic profiling, QIIME2 pipelines, Alpha/Beta diversity indices, interactive 3D PCoA projections. |
| Antimicrobial Resistance (AMR) | Automated AMR gene identification via CARD & ResFinder databases, genome assembly validation, resistance heatmaps. |
| Clinical Genomics & Variants | Somatic & germline variant prioritization (Ensembl VEP, ClinVar, gnomAD), drug-target mapping, precision oncology reporting. |
| Interactive Scientific Web Apps | Custom Streamlit & Plotly scientific dashboard development, real-time dataset analysis & figure exports. |
| Data Mining & GSEA | Programmatic GEO/SRA database queries (GEOquery), Gene Set Enrichment Analysis (fgsea), KEGG pathway enrichment plotting. |
| Cloud HPC & Workflows | Workflow development (Nextflow, WDL/Cromwell), GATK somatic variant calling, Docker containerization, AWS Batch & GCP Life Sciences. |
| Biomedical AI & RAG Systems | Retrieval-Augmented Generation (RAG), vector database embeddings (FAISS), PubMed API integration, automated literature synthesis. |
Languages & Frameworks
Bioinformatics Packages
[!TIP] 🤖 Flagship Open-Source Project: Bioinformatics & Scientific AI Agent Skills — Open-source library of AI Agent Skills, tool specifications, and prompt protocols for Bioinformatics, Genomics, Drug Discovery, and Multi-Omics. Compatible with Cursor, Claude Code, Antigravity, and Agent Skills standard.
- 📍 Spatial Transcriptomics Microenvironment Atlas: Production framework for 10x Visium, Xenium, and MERFISH spatial transcriptomics. Includes Squidpy spatial neighborhood analysis and ligand-receptor communication networks.
- 🧬 AlphaFold3 Biomolecular Complex & Interaction Evaluator: Analysis toolkit for AlphaFold3 multi-chain complex predictions (Protein-DNA, Protein-RNA, Protein-Ligand). Parses PAE matrices and SASA binding energies.
- 🔄 Single-Cell RNA Velocity & Trajectory Inference Engine: Single-cell RNA velocity and cell fate trajectory inference pipeline powered by scVelo, CellRank, and AnnData. Calculates directional mRNA splicing dynamics.
- Clinical VCF Variant Annotator: Precision oncology platform integrating Ensembl VEP, ClinVar, 3D PDB mapping, pharmacogenomics (PGx), and clinical trials.
- Automated Systematic Reviews (PubMed RAG): Retrieval-augmented LLM system utilizing FAISS vectors and PubMed API to compile systematic reviews.
- Gene Expression Profiling (OmicsVis): Complete differential expression pipeline (DESeq2/limma) transforming transcriptomic counts into Volcano and Heatmap visualizations.
- Single-Cell Subpopulation Discovery: scRNA-seq workflow with Leiden clustering and UMAP modeling, backed by an AI-assisted annotation layer for cell classification.
- 3D Protein Binding Pocket Analysis: Structural dashboard pulling from AlphaFold DB to evaluate mutation hotspots and visualize active pockets using py3Dmol WebGL.
- Interactive Genomics Viewer (IGV): Custom IGV.js web track visualization for BAM/BAI read alignment validation in the browser.
- NCBI GEO Mining & GSEA: Automated public dataset mining from GEO query database followed by GSEA KEGG/MSigDB pathway enrichment ridge plotting.
- Cloud-Native Bioinformatics Pipelines: Cromwell WDL workflows built for scalable somatic variant calling (GATK) running on AWS Batch and GCP Life Sciences.
- Metagenomic Dysbiosis Profiling: 16S rRNA analysis tool calculating Shannon diversity, generating taxonomic abundance bar charts, and rendering interactive 3D PCoA projections.
- Antimicrobial Resistance Profiling: Nextflow workflow integrating SPAdes, Prokka, and CARD to identify resistance genes and map them to drug classes.
- Multi-Omics Tools & Reference Guide: Curated scientific reference directory and catalog of open-source tools, single-cell, spatial omics, and structural biology resources.
- Biomedical LLM RAG Resources: Production-grade architecture patterns, PubMedBERT embedding configurations, and FAISS vector search code for medical RAG.
- Nextflow DSL2 Production Template: Containerized Nextflow DSL2 workflow template with execution profiles for SLURM, Docker, and AWS Batch.
- Streamlit Bioinformatics UI Kit: Modular UI kit and component library for building biotech web applications in Streamlit with Plotly and py3Dmol.
- TCGA Pan-Cancer Immune Profiling: Reproducible R research pipeline evaluating immune cell infiltration (CIBERSORT) and PD-L1 expression across TCGA tumors.
- scRNA-seq COVID-19 Immune Atlas: Scanpy + Harmony single-cell RNA-seq integration pipeline mapping BALF immune subpopulation dynamics.
- AlphaFold Pocket SASA Evaluator: Command-line Python utility for calculating Solvent Accessible Surface Area (SASA) and pLDDT confidence scores.
- Small-Molecule QSAR ML Pipeline: Cheminformatics QSAR machine learning pipeline predicting small-molecule IC50 bioactivity via RDKit ECFP4 fingerprints and LightGBM.
- Bioinformatics One-Liners Cheatsheet: Battle-tested Linux, AWK, SAMtools, BCFtools, and Python CLI one-liners for daily genomic data processing.
- Biotech & Biomedical AI System Prompts: Domain-tuned system prompts for LLM paper review, VCF clinical report generation, and Nextflow code writing.
- Multi-Omics Production Docker Containers: Ready-to-use Dockerfiles for single-cell (Scanpy+Seurat), variant calling (GATK+VEP), and metagenomics.
- Bioinformatics Tools Performance Benchmarks: Benchmark suite comparing execution runtimes, RAM footprint, and AWS costs for RNA-seq aligners and scRNA tools.
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