Chenyu Li, MD, PhD

2026 Ben J. Lipps Research Fellowship

Institution: University of Pennsylvania, Perelman School of Medicine

Project Title: Nephrobase: A Multimodal Kidney Foundation Model for Precision Nephrology

How would you sum up your overall research focus in one sentence?

My research focuses on developing kidney-specific foundation models that integrate single-cell, spatial, and genetic data to translate molecular heterogeneity into precision diagnostics and individualized treatment decisions for patients with kidney disease.

Provide a brief overview of the research you will conduct with help from the grant.

With this fellowship, I will develop Nephrobase, the largest kidney-specific foundation model to date, into a clinically actionable platform by scaling it from 1 billion to 10 billion parameters and integrating gene expression, genetic variants, spatial transcriptomics, and chromatin accessibility into a unified virtual kidney. I will then validate the top predicted drivers of kidney fibrosis using cell-based assays, mouse models of acute and chronic kidney injury, and conditional knockouts, and build a HIPAA-compliant web portal so clinicians can simulate gene and drug perturbations on patient data without coding expertise.

What inspired you to focus your research in this area?

During my clinical training in China, I repeatedly saw how patients with very similar eGFR values had completely different disease trajectories and responses to therapy, and the current one-size-fits-all paradigm in nephrology felt deeply inadequate to me. My PhD at LMU Munich with Prof. Hans-Joachim Anders taught me to dissect kidney injury at the molecular level, and joining Prof. Katalin Susztak's lab at Penn allowed me to combine that clinical and wet-lab background with modern AI to finally match the biological complexity of kidney disease.

What impact do you hope your research will have on patients?

I hope Nephrobase will help shift nephrology from reactive care driven by a single number like eGFR toward truly personalized medicine grounded in each patient's unique cellular and molecular profile. My longer-term goal is to make these AI-driven insights freely available to community nephrologists and underserved populations, so that the benefits of precision medicine reach the patients most often left behind.

What are your career goals at the end of the grant period? Five years out? Ten years out?

By the end of the grant period, I aim to have established a clear scientific identity in computational nephrology, with the preliminary data and first-author publications needed for a competitive K award. Five years out, I see myself as an Assistant Professor leading an independent translational program that builds and deploys kidney AI tools alongside a continuity clinic, and ten years out, my goal is to direct a Center for AI in Kidney Disease that serves as a national resource for the nephrology community.

What are the major challenges to beginning a career in nephrology research today?

The most pressing challenge is bridging deep clinical training with the rapidly advancing computational and genomic technologies now reshaping the field, as few training pathways formally combine nephrology, multi-omics, and modern AI. At the same time, funding lines are increasingly competitive and protected research time is fragile, which is exactly why fellowships like the Ben J. Lipps award are so critical for early-career investigators.

What advice would you give to others to encourage them to apply for this grant funding?

Do not wait until your project feels perfect, because the application itself will sharpen your scientific identity and force you to articulate why your work matters. Lean on your mentors and prior awardees, and remember that KidneyCure is genuinely invested in helping young nephrology investigators succeed.

Something you may not know about me is…

I am actually a pretty proficient coder. My main languages are Python and C++, which lets me move quickly between biological questions and the engineering needed to answer them at scale.

In my free time I like to…

Play video games, mostly strategy titles.