About

Across scientific problems and machine-learning systems.

I am an AI engineer and computational scientist based in Houston. I have spent my career close to both the data-generating problem and the model: first in biology and genomics, then across model development, evaluation, scientific software, and production AI systems.

I am most interested in work that requires understanding the problem, the data, the model, the evaluation, and the system around it. Biomedical science is an area of genuine depth for me, not a boundary on the kinds of engineering and research problems I take on.

Portrait of Johnathan Jia

Professional arc

  1. 01Biology & chemistry
  2. 02Quantitative sciences
  3. 03Computational biology
  4. 04Machine learning
  5. 05AI engineering
  6. 06ML research

Experience

Recent work

  1. 2024–Present

    AI Engineer

    Baylor College of Medicine

    Model development, clinical sequence modeling, retrieval and ranking systems, computer vision, scientific software, and production engineering.

  2. 2023–2024

    Data Analyst Associate

    Baylor College of Medicine

    RAG-based mentor discovery and analysis across more than 30 single-cell and bulk omics datasets in 10+ collaborations.

  3. 2020–2022

    Graduate Research Assistant

    UTHealth / UTHSC Graduate School of Biomedical Sciences

    Machine learning for viral genomics and single-cell studies of disease, including sequence models and trajectory analysis.

Capabilities

Selected methods and tools

Machine Learning

Developing models, designing evaluations, and understanding failure modes.

  • PyTorch
  • TensorFlow / Keras
  • Hugging Face
  • Transformer pretraining
  • SFT
  • RLVR
  • RAG
  • Retrieval / reranking
  • Evaluation
  • Representation analysis
  • Computer vision

Scientific ML

Working with biological data whose structure and provenance shape the model.

  • Single-cell RNA-seq
  • scATAC-seq
  • Trajectory inference
  • Differential expression
  • Computational genomics

Engineering

Building the data, service, and compute systems around models.

  • Python
  • R
  • SQL
  • Bash
  • FastAPI
  • PostgreSQL
  • Docker
  • AWS
  • Slurm
  • Git

Education

Background

2020–2022

M.Sc. Quantitative Sciences

UTHealth / UTHSC Graduate School of Biomedical Sciences

2011–2015

B.S. Biology & B.A.

Emory University

Connect

Based in Houston, working across engineering and research.

Email meGitHubResume