ProteoNexus v0.1-alpha is the inaugural release of the official backend analysis pipeline supporting our manuscript submission. This version encapsulates all computational workflows used to characterize the genetic architecture of the plasma proteome, estimate mediation effects, and build predictive models for disease incidence in the UK Biobank PPP cohort. Key highlights: • Genetic Architecture Analysis • Mediation Effect Estimation • Prediction Model Development • Prediction Execution & Validation • Sex-Specific Analyses IMPORTANT: This repository includes only the backend analysis code and command-line scripts. The web server frontend (interactive visualizations, exploration, and prediction interface) is available at https://www.proteonexus.com/. Full Changelog: https://github.com/KaishinShaw/ProteoNexus/commits/v0.1-alpha