Before residency, I was a medical student at Stanford University School of Medicine (grad. 2024), and work in the lab of Nigam Shah on deploying and monitoring clinical machine learning models, funded by the MedScholars reserach fund for medical students.

Before that, I was a bachelor’s (grad. 2018) and master’s student (grad. 2019) in computer science at Princeton University, where I was lucky and grateful to work in the group of Barbara Engelhardt, on inferring causal networks from gene expression time series. I’ve also worked on analyzing protein complex mass spectra in the group of Alma Burlingame at UCSF.

Journal Papers

A model for comprehensive climate and medical education
Ashley Jowell, Anna Lachenauer, Jonathan Lu, Benjamin Maines, Lisa Patel, Kari Nadeau, Barbara C Erny
The Lancet Planetary Health, 2023
PDF

Considerations in the reliability and fairness audits of predictive models for advance care planning
Jonathan Lu, Amelia Sattler*, Samantha Wang*, Ali Raza Khaki*, Alison Callahan, Scott Fleming, Rebecca Fong, Benjamin Ehlert, Ron C. Li, Lisa Shieh, Kavitha Ramchandran, Michael F. Gensheimer, Sarah Chobot, Stephen Pfohl, Siyun Li, Kenny Shum, Nitin Parikh, Priya Desai, Briththa Seevaratnam, Melanie Hanson, Margaret Smith, Yizhe Xu, Arjun Gokhale, Steven Lin, Michael A. Pfeffer, Winifred Teuteberg**, Nigam H. Shah**
Frontiers in Digital Health, 2022
Paper (PDF, Supplement)
* indicates equal contribution
** indicates equal contribution and shared senior authorship

Assessment of Adherence to Reporting Guidelines by Commonly Used Clinical Prediction Models From a Single Vendor - A Systematic Review
Jonathan H. Lu, Alison Callahan, Birju S. Patel, Keith E. Morse, Dev Dash, Michael A. Pfeffer, Nigam H. Shah
JAMA Network Open, 2022
Paper (PDF, Supplement) | Story by Stanford HAI

Using AI to Empower Collaborative Team Workflows: Two Implementations for Advance Care Planning and Care Escalation
Ron C. Li, Margaret Smith, Jonathan Lu, Anand Avati, Samantha Wang, Winifried G. Teuteberg, Kenny Shum, Grace Hong, Briththa Seevaratnam, Jerri Westphal, Margaret Dougherty, Pooja Rao, Steven Asch, Steven Lin, Christopher Sharp, Lisa Shieh, Nigam H. Shah
NEJM Catalyst Innovations in Care Delivery, 2022
Paper (PDF)

Monitoring Approaches for a Pediatric Chronic Kidney Disease Machine Learning Model
Keith E. Morse, Conner Brown, Scott Fleming, Irene Todd, Austin Powell, Alton Russell , David Scheinker , Scott M. Sutherland , Jonathan Lu, Brendan Watkins , Nigam H. Shah , Natalie M. Pageler , Jonathan P. Palma
Applied Clinical Informatics, 2022
Abstract

Nursing Workflow Change in a COVID-19 Inpatient Unit Following the Deployment of Inpatient Telehealth: Observational Study Using a Real-Time Locating System
Stacie Vilendrer, Mary E Lough, Donn W Garvert, Monique H Lambert, Jonathan Hsijing Lu, Birju Patel, Nigam H Shah, Michelle Y Williams, Samantha M R Kling
Journal of Medical Internet Research, 2022
Paper (PDF)

Causal network inference from gene transcriptional time-series response to glucocorticoids
Jonathan Lu*, Bianca Dumitrascu*, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
PLOS Computational Biology, 2021
Paper (PDF) | Code | Analysis
* indicates equal contribution

COVID-19 Solutions Are Climate Solutions: Lessons From Reusable Gowns
Natalie Baker*, Rebecca Bromley-Dulfano*, Joshua Chan*, Anshal Gupta*, Luciana Herman,3 Navami Jain*, Anita Lowe Taylor*, Jonathan Lu*, Jaspreet Pannu*, Lisa Patel, and Mary Prunicki
Frontiers of Public Health, 2020
Paper (PDF)
* indicates equal contribution

Improved Peak Detection and Deconvolution of Native Electrospray Mass Spectra from Large Protein Complexes
Jonathan Lu*, Michael J. Trnka*, Soung-Hun Roh, Philip J. J. Robinson, Carrie Shiau, Danica Galonic Fujimori, Wah Chiu, Alma L. Burlingame, Shenheng Guan
Journal of the American Society of Mass Spectrometry, 2015
Paper (PDF) | Code
* indicates equal contribution

Conference/Poster Presentations

Evaluation of Community-Partnered Curricular Intervention on Climate Change and Mental Health in Preclinical Psychiatry Curriculum
** Jonathan Lu,** Charbel Bou-Khalil, Shammah Ike, Violet Saena, Shana Uhihamoelangi, Cecilia Taylor, Heleine Grewe, Barbara Erny, Yasmin Owusu
2023, April 30th
Society of Teachers of Family Medicine Annual Spring Conference. Tampa, FL, United States.
Poster | References

Can Advance Care Planning AI models support better End-of-life Care planning?
Jonathan Lu, Amelia Sattler*, Samantha Wang*, Ali Raza Khaki*, Alison Callahan, Scott Fleming, Rebecca Fong, Benjamin Ehlert, Ron C. Li, Lisa Shieh, Kavitha Ramchandran, Michael F. Gensheimer, Sarah Chobot, Stephen Pfohl, Siyun Li, Kenny Shum, Nitin Parikh, Priya Desai, Briththa Seevaratnam, Melanie Hanson, Margaret Smith, Yizhe Xu, Arjun Gokhale, Winifred Teuteberg**, Nigam H. Shah**
American College of Physicians, NorCal Meeting, 2022 Poster | References Thank you to Malathi Srinivasan and Kathleen Kenny for their feedback and support for this poster!

Reliability and Fairness Audits of Clinical AI Models using STARR-OMOP
Jonathan Lu, Amelia Sattler*, Samantha Wang*, Ali Raza Khaki*, Alison Callahan, Scott Fleming, Rebecca Fong, Benjamin Ehlert, Ron C. Li, Lisa Shieh, Kavitha Ramchandran, Michael F. Gensheimer, Sarah Chobot, Stephen Pfohl, Siyun Li, Kenny Shum, Nitin Parikh, Priya Desai, Briththa Seevaratnam, Melanie Hanson, Margaret Smith, Yizhe Xu, Arjun Gokhale, Winifred Teuteberg**, Nigam H. Shah**
2nd STARR Informatics Summit. Stanford, CA, United States.
Presentation
* indicates equal contribution
** indicates joint senior authorship

Low adherence to model reporting guidelines for commonly used clinical prediction models
Jonathan Lu, Alison Callahan*, Birju Patel*, Keith Morse*, Dev Dash, Nigam Shah
37th Stanford Medical Student Research Symposium. Stanford, CA, United States.
Abstract | Presentation
* indicates equal contribution

Roots Telehealth Support Program
Sidney Owen, Jonathan Lu, Mayra Reyes, Kalijah Terilli, Alex Gomez-Lara, Jadyn Lee, Louis McKinnon, Akshara Shankar, Temesgen Woldeyesus
Community Partner: Roots Community Health Center.
Stanford Community Health Symposium, 2022
Abstract Poster Poster Presentation

Bridging the Gap of Access to Affordable Medication
Sarah Ludington, Jonathan Lu, Elizabeth Zudock, Solomiia Savchuk, Harrison Besser, Xichong Liu, Wendy Caceres MD, Baldeep Singh MD
Partner: Stanford Pacific Free Clinic
Society of Student-Run Free Clinics Conference, 2021
Poster

Advocacy and Assessment of Climate Change Integration into Stanford Medical Preclinical Curriculum Jonathan Lu, Ashley Jowell, Josh Carter, Barbara Erny, Anna Lachenauer
Society of Teachers of Family Medicine Conference on Medical Student Education, 2021
Poster Abstract Video Presentation
(Not my work, but check out these other resources for climate & health curriculum interventions in medical schools, from Medical Students for a Sustainable Future) (also contact Medical Students for a Sustainable Future)

Review On Evaluating Associations Between Air Pollution Burden And Rates Of ED Visits And Hospitalization In Stockton’s Disadvantaged Communities
India Rogers-Shepp, Jonathan Lu, Maïté Van Hentenryck, Sohayla Eldeeb, Navami Jain, Avanthi Puvvala, Lisa Patel
Community Partner: Catholic Charities Of The Diocese Of Stockton, Environmental Justice Program
Stanford Community Health Symposium, 2021
Poster Abstract Poster presentation

Characterizing Respiratory Symptoms and COVID-19 Trends from OMOP-CDM database for Public Health Reporting
Marcello Chang*, Jonathan Lu*, Birju Patel, Nigam H. Shah, Jonathan H. Chen American Medical Informatics Summit, 2021
Abstract | Poster
* indicates equal contribution

Student Community OutReach and Physician Support (S-CORPS): Educating Medical Students and Enhancing Patient Support During the COVID-19 Crisis
Lydia Tam*, Jonathan Lu*, Mike Dacre*, Olivia Jee, Jordan Chavez, Erika Schillinger, Tamara Montecute, Matthew Mesias
The 4th Annual Medical and Bioscience Education Day / SIMEC V, 2020
Poster | Poster presentation
* indicates equal contribution

Causal profile subgraph embeddings of metabolic and immune response mediated gene regulation from time series gene expression
Jonathan Lu*, Bianca Dumitrascu*, Ian C. McDowell, Soledad Villar, Timothy E. Reddy, Barbara Engelhardt
2nd Annual Probabilistic Modeling in Genomics Conference, 2016
* indicates equal contribution

Reports

Opportunities and Barriers for the Clean Energy Transition for Rural Communities in the United States: A Qualitative Interview Approach
Joshua Chan *, Aboli Ghatpande *, Jonathan Lu, *, Josie Pearce *, Kate Hoppe, Lisa Patel
This was a final report for the Spring 2024 course at Stanford University: PEDS 199/299 - Independent Study on Rural Health in the Clean Energy Transition.
Report
* indicates equal contribution

Theses

Effective and Scalable Causal Inference from Gene Expression Time Series
Senior Thesis
Jonathan Lu, Barbara Engelhardt
2018
Report | Slides

Improved Methods for Causal Inference and Experimental Prioritization in Gene Regulatory Networks
Junior Thesis
Jonathan Lu, Barbara Engelhardt
2017
Report | Poster | Slides