Portfolio
NGS pipelines, genomics platforms, and the software behind them.
WES/WGS germline & somatic pipelines
Modular Nextflow DSL2 pipelines for clinical WES and WGS supporting FASTQ, BAM, and VCF entry points. Multi-caller variant detection (SNV/Indel via GATK4 and DeepVariant, CNV via CNVkit, SV via Manta) with integrated QC via FastQC, Fastp, and MultiQC.
ACMG/AMP classification engine
Python engine implementing ClinGen/SVI 2023 criteria with HPO/GADO phenotype prioritization, plus automated PDF/HTML clinical reporting per sample.
RNA-seq workflows
STAR/HISAT2 alignment, Salmon/Kallisto quantification, and DESeq2/edgeR differential expression for bulk and targeted transcriptomics.
De novo bacterial/yeast assembly & annotation
End-to-end Nextflow DSL2 pipeline: Kraken2 decontamination, SPAdes assembly, structural/functional annotation (Prokka, BRAKER3, RepeatMasker, tRNAscan-SE, Barrnap, InterProScan, eggNOG-mapper), AMR profiling via RGI/CARD, and SSR marker discovery with MISA.
Species identification correction
Resolved a client-reported species misidentification using fastANI and ortholog-based taxid cross-validation, correcting the final report before delivery.
Sequencing QC dashboard
Nextflow-driven QC pipeline with a live web dashboard tracking sequencing yield against client requirements across multiple runs.
16S rRNA amplicon profiling
ASV-based taxonomic profiling with QIIME2/DADA2, alpha/beta diversity analysis, and differential abundance testing via PERMANOVA and LEfSe.
Shotgun metagenomics
Kraken2/Bracken taxonomic profiling and HUMAnN3 functional pathway analysis, with MetaWRAP for MAG reconstruction and QC.
Predictive Genomics & Polygenic Risk Scoring
A multi-domain predictive genomics framework for calculating trait-specific polygenic risk scores from GWAS-derived genetic effects and sample genotype data. Integrates variant and allele harmonization, effect-size processing, statistical scoring, SNP-level contribution analysis, and structured genomic reporting. Supports domain-organized PDF reports and interactive HTML dashboards for exploring genetic predisposition across diverse traits.
vcfilt — VCF streaming filter
Zero-heap-allocation streaming VCF filter in Go, benchmarked at 147,000 variants/second — 12.2x faster than bcftools 1.18 on an 18GB VCF, with byte-for-byte identical output. MIT-licensed, distributed as a static binary, Docker image, and Singularity container. Published as a bioRxiv preprint, April 2026.
Protein folding molecular dynamics
Long-timescale MD simulations of protein folding dynamics; PCA, clustering, and autoencoders to identify dominant conformational states, validated against DSSP. Contributed to a published study on protein energy landscapes.
Protein-ligand docking
Modeled protein-ligand interactions with AutoDock Vina and RDKit to characterize antibiotic resistance binding pose shifts; GROMACS MD extracting RMSD, RMSF, and binding free energy trajectories.