Jonathan Ouyang

citables

2027
Ouyang, J., Green, R., Buskirk, A. “Structure Prediction and Screening of Ribosomal Complexes With RiBoltz2.” Biophysical Society Annual Meeting. Submitted.
Ouyang, J., Buskirk, A. “Evidence for convergent evolution of ribosome pausing mechanisms in cotranslational folding.” Biophysical Society Annual Meeting. In progress.
2026
Ouyang, J. “Hidden non-conservativity in structure prediction models.” Paper accepted at the NeurIPS 2026 Workshop on Interpretability for Discovery (Interp4Discovery). paper (2026, Paper accepted at the NeurIPS 2026 Workshop on Interpretability for Discovery (Interp4Discovery))
Ouyang, J. “Annealed atomistic diffusion with Boltz-2 and MD relaxation for rapid pseudo-timescale dynamics.” CASP17.
Ouyang, J. “Hidden non-conservativity in structure prediction models.” Poster, NeurIPS 2026 Workshop ICBINB-Bio. paper (2026, Poster, NeurIPS 2026 Workshop ICBINB-Bio)
Ouyang, J., Green, R., Buskirk, A. “Predicting ribosome-protein complexes with RiBoltz2.” Under review.
Ouyang, J., Green, R., Buskirk, A. “Structure Prediction and Screening of Ribosomal Complexes With RiBoltz2.” Poster, 35th Annual Institute for Biophysical Research Retreat.
Ouyang, J., Buskirk, A. “SAM-RFM: Stalling-Aware Modified Ribosome Flow Model for de novo Translation Efficiency Prediction.” Poster presented at the Biophysical Society Annual Meeting (BPS2026). program (2026, Poster presented at the Biophysical Society Annual Meeting (BPS2026))
2025
Ouyang, J., Jin, H. “Characterization of Rbg2: DRGs as Model Proteins for Reanalysis of the Cation-Dependent GTPase Motif.” Poster presented at the Annual Frontiers in Bioengineering Symposium.First high-school presenter accepted in the 20-year history of the symposium.
Ouyang, J. “Purification Method for Weakly Binding Proteins Reveals Proteome-Scale Structural Determinants of Ribosome-Associated Interactions.” Oral presentation at JHU REAL (formerly DREAMS).
Ouyang, J., Jin, H. “Characterization of Rbg2: DRGs as Model Proteins for Reanalysis of the Cation-Dependent GTPase Motif.” Oral presentation at the UIUC Undergraduate Research Symposium. program (2025, Oral presentation at the UIUC Undergraduate Research Symposium)Only high-school oral presenter accepted in the 17-year history of the symposium.
2024
Ouyang, J., Jin, H. “Biochemical Characterization of Developmentally-Regulated GTPase Rbg2/Gir2 under Influence of K+.” Oral presentation at the UIUC Undergraduate Research Symposium. program (2024, Oral presentation at the UIUC Undergraduate Research Symposium)First high-school oral presenter accepted in the 16-year history of the symposium.

awards

$60,000 in credits from Anthropic and Modal, as one of ~30 teams worldwide in Track 1 of the Anthropic × Adaptyv Protein Design Competition (UPET, 2026)
~$20,000 in wet-lab validation from Adaptyv, in the same competition (UPET, 2026)
$3,000 from BlueDot Impact to host an event on AI safety and biosecurity, co-organized with Dr. William Walden (ASBS, 2026)
$1,000 research grant, Frankel Fund for Learning Innovation, University Laboratory High School
Verified under Anthropic’s Life Sciences Verification Program (UPET, 2026)
National Champion and Illinois all-star representative, National All-Star Academic Tournament (2025)
AIME qualifier with distinction (10th grade)

experience

research 5,500+ hours

2025–now
full-time paid researcher, Green Lab, Johns Hopkins Medicine
- Structure prediction models at megadalton scale for ribosomal complex structure determination (1st author).
2025–now
full-time paid researcher, Buskirk Group, Johns Hopkins Medicine
- Ribosome profiling (Ribo-seq): pausing, stalling, translation efficiency, and the evolution of cotranslational folding (1st author).
2025–now
researcher, Trcek Lab, Johns Hopkins University
- Single-molecule RNA microscopy, modeling the formation of condensates.
- Agentic frameworks and harnesses for complex multimodal data analysis (1st author).
now
research fellow, AfterQuery
- Developing AI4Science agent evaluations, paid.
2023–2025
researcher, Jin Lab, UIUC
- 2,700+ hours as a Group D university employee while still in high school. Sole (1st author) responsibility for conceptualization, hypotheses, experimental design, execution, analysis, and manuscript.
- $1,000 Frankel Fund research grant.

building

2026–now
founder, Collide Therapeutics
- AI-native drug design; ribosome-associated targets in neurodegeneration. Spinout from research done in the Green Lab.
- All IP cleared by Johns Hopkins Technology Ventures (JHTV). Provisional patent filing in progress.
2026–now
founder & president, AI Safety & Biosecurity at Hopkins
- In collaboration with the HLTCOE and HopAI.
2025–now
founder & president, Undergraduate Protein Engineering Team, JHU
- Recruited and lead a ~30-member team spanning BME, Biophysics, ChemBE, CS, and Applied Math, sponsored by Dr. Jeffrey Gray.
- Accepted to Track 1 of the Anthropic × Adaptyv Protein Design Competition: $60,000 in credits and ~$20,000 in wet lab.
2026–now
host, JHU Popup, Forge, and biocomphack (paused)
- Guests have included the CEO of Cortical Labs. Financial support from major student orgs.

teaching

2026–now
tutor, The Learning Den, Johns Hopkins University
- Organic Chemistry I and lab, Molecular Biology, Calculus I–⁠II, Intro Chemistry I–⁠II, Intro Computing, Linear Algebra.
2021–2025
earlier teaching, recruiting, and community-building
- Trained incoming researchers and wrote the standing protein-purification and kinetics protocols still in use in the Jin Lab, UIUC.
- Grew a student-run club to 110+ members out of a ~320-student body (34% of the school). Built joint programming with DREAAM House supporting underserved youth.
- Schoolhouse.world tutor: college-level biology and math, 100% positive reviews (n = 34). Math Circle instructor, K–12 curriculum development, four years.
- Captain, Scholastic Bowl: recruited and trained a team from a ~320-student school to 8th in the nation, the best result since 2019.

education

2025–2028
Johns Hopkins University, B.S. Biophysics
2023–2025
University of Illinois Urbana-Champaign, concurrent enrollment while in high school
- MCB 250 Molecular Genetics (A+), CS 124 (A), CS 128 (A), CHEM 232 Organic Chemistry I (A).
- Computational Genomics @ Mayo Clinic.
2020–2025
University Laboratory High School