Portfolio

Bench↗ (external site)

Python · FastAPI · React · Nextflow · Docker · GCP · Cloud Run · Vertex AI

Production omics platform ingesting varied sequencing data into a centralized API and running containerized Nextflow workflows on Cloud Run under strict IAM.

Preleukemia and AML transcriptomics: single-cell + bulk RNA-seq

R · Python · Quarto · R Shiny · Seurat · Harmony · Scanpy · Nextflow

Two projects on the road into AML: a revised single-cell analysis of preleukemic mouse HSPCs (38 samples, eight mutation models) with a TCGA-LAML survival arm and an R Shiny dashboard, and a Nextflow bulk RNA-seq differential-expression pipeline with an interactive volcano.

Spatial transcriptomics: Visium breast-cancer cell-type deconvolution (Nextflow)

Nextflow · Python · scanpy · anndata · squidpy · SciPy · scikit-learn

A reproducible Nextflow DSL2 pipeline that takes a 10x Visium breast-cancer section plus an annotated scRNA-seq atlas and maps cell types back into tissue space: per-spot NNLS deconvolution and spatially variable genes, rendered as interactive figures.

TCR Clonality Analysis

Python · Jupyter · tcrdist3 · pandas · SciPy

Bulk TCR-β repertoire analysis testing whether clonality and TB-specific clonotype frequency differ between TB progressors and controllers, revised to respect the cohort's matched case-control design.

Fiber Photometry Web App

R · R Shiny

R Shiny web app for fiber photometry data processing and figure generation, built for the Sweeney Lab.

R Meta-Analysis Walkthrough

R

Seven-part video walkthrough of an end-to-end meta-analysis in R, produced as a Thom Lab onboarding resource.

PID Controller for Anaesthetic Dosing

MATLAB · Simulink

MATLAB/Simulink PID controller for patient-specific anaesthetic dosing, achieving top cohort performance on steady-state error and settling time.

EMG-Controlled Saxophone

Arduino · C/C++ · surface EMG circuitry

Assistive prosthetic concept actuating saxophone keys via a surface-EMG analog front end and an Arduino servo system, exhibited at the 2023 Engineering Open House.