Nicholas Sizemore

I turn scientific models into reproducible systems and public tools.

Computational scientist and research software engineer working across modeling code, containers, cloud pipelines, and interactive software.

01Selected Work

JHEEM modeling platformlive

Architecture & implementation lead

A public HIV-modeling platform spanning the interactive product, model-execution workflows, versioned simulation data, and cloud delivery. I designed the system and implemented its frontend, orchestration, and integration layers.

  • 31-metro and multi-state policy analyses
  • One model configuration drives workflows and frontend behavior
  • On-demand model runs with cached, shareable results
  • Reusable orchestration cut workflow code by 54%
Next.js · TypeScript · R · Docker · GitHub Actions · AWS S3

Reproducible model execution & deliverymigration active

Architecture & implementation lead

The execution layer behind JHEEM: reproducible R model images, versioned simulation artifacts, numerical regression checks, and production-safe release workflows. I am currently consolidating five container repositories into a history-preserving monorepo with path-aware matrix CI.

  • 180GB+ of versioned simulation artifacts
  • Four model images reproduce production outputs bit-for-bit
  • Digest-pinned base image and renv-locked dependencies
  • Monorepo migration preserves image names and production pins
Docker · R · renv · GitHub Actions · Self-hosted runners

Digital twin of the infant microbiomepublished

First author · modeling & analysis

First-author research developing a generative, patient-specific model of infant microbiome dynamics to forecast ecosystem trajectories and identify early signals associated with neurodevelopmental risk.

  • Published in Science Advances in 2024
  • 88 preterm infants and 398 longitudinal samples
  • Forecasted microbial abundance dynamics with R² = 0.69
  • Open-source qbiome research implementation
Python · Generative modeling · Longitudinal data · Biomedical ML

Tech2Check intervention modelingresearch in progress

Model design & analysis

An active HIV intervention-modeling study in JHEEM. I designed the intervention lifecycle, built the calibrated analysis and verification pipeline, and used decomposition and sensitivity analysis to distinguish structural limits from implementation assumptions.

  • Mechanistic compartment and transition design
  • Calibrated multi-simulation analysis with provenance
  • Structural, directional, and base-preservation verification
  • First-author manuscript work in progress
R · Compartmental modeling · Sensitivity analysis · Quarto · LaTeX

Computational Epidemiology Lab site + Global HIV Aging applive

Designed & built

The public web presence for a Johns Hopkins modeling group, including an interactive application for exploring country-level HIV aging projections and the evidence behind them.

  • Data-driven country projection explorer
  • Research findings and publications presented for mixed audiences
Next.js · TypeScript · React · Tailwind

02Trajectory

mathematics+modeling+machine learning+production systems

  1. Design and operate the platforms behind HIV-policy modeling, while contributing directly to model implementation, analysis, and reproducibility.

    jheem.org

03Capabilities

Modeling
Compartmental / ODE models · Stochastic simulation · Sensitivity analysis · Applied & generative ML
Scientific computing
Reproducible environments · Versioned data · Provenance · Numerical verification
Systems
Data pipelines · APIs · Interactive applications · Config-driven architecture
Infrastructure
AWS · Docker · GitHub Actions · Linux / RHEL · Self-hosted runners
Languages
R · Python · TypeScript / JavaScript · Shell

04Publications

A digital twin of the infant microbiome to predict neurodevelopmental deficits

Sizemore, Nicholas, Oliphant, Kaitlyn, Zheng, Ruolin, Martin, Camilia R, Claud, Erika C, Chattopadhyay, Ishanu
Science Advances, 10(15), eadj0400, 202440+ citations
[DOI]

Partition numbers of finite solvable groups

Foguel, Tuval, Sizemore, Nick
Advances in group theory and applications, 6, 55-67, 2018
[DOI]

05Contact

I'm interested in conversations about scientific software, computational modeling, and reproducible research infrastructure.