Portfolio

AML transcriptomics: single-cell + bulk RNA-seq

Two complementary acute myeloid leukemia projects: a single-cell pipeline characterizing pre-leukemic populations (R Shiny dashboard) and a Nextflow bulk RNA-seq differential-expression pipeline (interactive volcano).

PID Controller for Anaesthetic Dosing

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

EMG-Controlled Saxophone

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.

Fiber Photometry Web App

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

R Meta-Analysis Walkthrough

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

Plant bulk RNA-seq: drought tolerance differential expression (Nextflow)

A reproducible Nextflow DSL2 pipeline taking raw Illumina bulk RNA-seq reads from drought-tolerant and drought-susceptible rice cultivars through alignment, quantification, and differential expression to a GO-enrichment view of the genes and processes that separate the two phenotypes.

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

A reproducible Nextflow DSL2 pipeline that takes a 10x Visium breast-cancer section plus a matched 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

Bulk TCR-β repertoire analysis comparing clonality and antigen-specific frequencies in TB progressors vs. controllers.