CV
Professional Summary
Physician-scientist applying agentic AI to accelerate biomedical research. Currently using Claude Code to orchestrate multi-domain EHR phenotyping and genomics projects across respiratory viruses, sarcoidosis, HPV-associated cancers, long COVID prediction, and more. Track record developing validated computational methods at scale (400,000+ patient records, 500M+ observations) while maintaining clinical grounding that prevents AI outputs from diverging from biomedical reality.
Technical Skills
AI & Automation: Claude Code (agentic orchestration), Claude API, LLM-augmented research workflows
Programming & Analytics: Python, SQL, Polars, R, Google BigQuery, Google Cloud Platform, dsub, Google Batch
Statistical Methods: GWAS, PheWAS, phenotype risk scores, regression, propensity score matching, survival analysis
Healthcare Data: OMOP CDM, ICD, CPT, SNOMED, LOINC, RxNorm, EHR phenotyping, cohort development
Experience
Research Data Scientist
National Human Genome Research Institute, NIH | Aug 2023 – Present
- Use Claude Code to orchestrate concurrent research projects across multiple disease domains (respiratory viruses, sarcoidosis, HPV-associated anal disease, long COVID, adverse drug events)
- Architected distributed computing pipelines processing 155 survey-item PheWAS jobs and 26 ancestry-stratified GWAS using Google Batch/dsub
- Developed phenotype risk score for long COVID prediction (AUC 0.94) that outperforms semi-supervised approaches, integrating wearable device data with EHR records
- Built and validated computable phenotyping algorithms for 8 respiratory pathogens achieving 79-97% PPV; first-author publication in Scientific Reports (2025)
- Lead multi-investigator projects spanning EHR-survey phenotype comparison for genetic discovery, clinical risk factor identification, and genetic variant validation
Infectious Diseases Clinical Fellow
National Institute of Allergy and Infectious Diseases, NIH | Jul 2021 – Jun 2026
- Manage complex infectious disease cases providing clinical grounding that informs computational research design
- Board certified in Internal Medicine, Pediatrics, and Adult Infectious Diseases
Medicine-Pediatrics Resident
University of Chicago Medicine | Jun 2017 – Jun 2021
- Conducted retrospective EHR analysis identifying differential treatment responses in septic shock using machine learning-derived patient subgroups (American Thoracic Society Conference 2020)
- Completed Summer Program in Outcomes Research Training (SPORT) fellowship
Graduate Student
NIH-Cambridge Scholars Programme, University of Cambridge | Aug 2010 – Nov 2016
- Developed quantitative analysis pipelines for microscopy image data
- First-author publication in Journal of Cell Science; co-authored Nature Cell Biology
Education
| Degree | Institution | Year |
|---|---|---|
| Infectious Diseases Fellowship | NIAID, NIH | 2021–2026 |
| Medicine-Pediatrics Residency | University of Chicago | 2017–2021 |
| MD | UT Southwestern Medical School | 2008–2017 |
| PhD, Clinical Biochemistry | NIH, University of Cambridge | 2010–2016 |
| BA, Biology & Chemistry | Texas Christian University | 2004–2008 |
Selected Publications
Waxse BJ, Bustos Carrillo FA, Tran TC, Mo H, Ricotta EE, Denny JC. Computable phenotypes to identify respiratory viral infections in the All of Us research program. Scientific Reports. 2025;15(1):18680. DOI
Waxse BJ, Rao S. Data Science for Pediatric Infectious Disease: Utilizing COVID-19 as a Model. Current Opinion in Infectious Diseases. 2025;38(5):493-498. DOI
Goleva SB, Williams A, Schlueter DJ, Keaton JM, Tran TC, Waxse BJ, et al. Racial and Ethnic Disparities in Antihypertensive Medication Prescribing Patterns. Clin Pharmacol Ther. 2024;116(6):1544-1553.
Selected Presentations
- Waxse BJ, et al. Higher Step Count is Associated with Reduced Risk of Long COVID. IDWeek 2025, Accepted Podium.
- Waxse BJ, Tran TC, Mo H, Denny JC. Identification and Validation of Common Respiratory Infections in All of Us. AMIA Annual Symposium, Podium. November 2024.
Contact
| 📧 bennettwaxse@gmail.com | 📍 Washington, DC → Denver, CO (June 2026) |