Dianzhuo(John) Wang's Website

About Me

I am a Ph.D. candidate in Applied Physics at Harvard, advised by Prof. Eugene Shakhnovich. I hold an M.S. in Applied Mathematics from Harvard SEAS. I am the CSO and cofounder of a stealth startup addressing biosecurity risk in the age of AI.

I work at the intersection of AI and biology. My research focuses on building and interpreting powerful AI-enabled biological tools while ensuring they are deployed safely. During my PhD, I apply tools from physics and machine learning to forecast viral evolution and perform functional mapping of biological sequences, informed by wet-lab data.

Feel free to email me about any questions or collaborations. If you are interested in working in the Shakhnovich lab on either protein evolution or AI-Bio security, please apply here for the 2026 internship.

Research

See the full research profile on Google Scholar. ^* indicates equal first contribution, ^† indicates co-corresponding author.

Biophysical Priors Enhance Protein-Protein Binding ΔΔG Prediction

Antoine Maechler^*, Jonathan Feldman^*, Dianzhuo Wang^*,†, Eugene I. Shakhnovich^†

NeurIPS MLSB 2025 / Paper / bibtex

@article{maechler2025biophysical,
  title={Biophysical Priors Enhance Protein-Protein Binding $\Delta\Delta G$ Prediction},
  author={Maechler, Antoine and Feldman, Jonathan and Wang, Dianzhuo and Shakhnovich, Eugene I},
  journal={NeurIPS MLSB Workshop},
  year={2025},
  url={https://www.mlsb.io/papers_2025/115.pdf}
}

Constrained evolutionary funnels shape viral immune escape

Marian Huot, Dianzhuo Wang, Eugene Shakhnovich^†, Rémi Monasson, Simona Cocco^†

PNAS / Paper / Code / bibtex

@article{huot2025constrained,
  title={Constrained evolutionary funnels shape viral immune escape},
  author={Huot, Marian and Wang, Dianzhuo and Shakhnovich, Eugene I and Monasson, R{\'e}mi and Cocco, Simona},
  journal={Proceedings of the National Academy of Sciences},
  pages={e2536956123},
  year={2025},
  doi={10.1073/pnas.2536956123},
  publisher={National Academy of Sciences}
}

Complete Enzyme Clustering Enhances Substrate Channeling in Coenzyme Q Biosynthesis

Dianzhuo Wang^*, Andrea Gottinger^*, Jio Jeong^*, Callum R. Nicoll^*, Junlang Liu, Tereza Kadavá, Domiziana Cecchini, Marco Malatesta, Albert J.R. Heck, Andrea Mattevi, and Eugene I. Shakhnovich

Paper / Code / bibtex

@article {Wang2025.05.24.655883,
  author = {Wang, Dianzhuo and Gottinger, Andrea and Jeong, Jio and Nicoll, Callum R. and Liu, Junlang and Kadav, Tereza and Cecchini, Domiziana and Malatesta, Marco and Heck, Albert J.R. and Mattevi, Andrea and Shakhnovich, Eugene},
  title = {Complete Enzyme Clustering Enhances Coenzyme Q Biosynthesis via Substrate Channeling},
  elocation-id = {2025.05.24.655883},
  year = {2025},
  doi = {10.1101/2025.05.24.655883},
  publisher = {Cold Spring Harbor Laboratory},
  URL = {https://www.biorxiv.org/content/early/2025/05/28/2025.05.24.655883},
  eprint = {https://www.biorxiv.org/content/early/2025/05/28/2025.05.24.655883.full.pdf},
  journal = {bioRxiv}
}

Without Safeguards, AI-Biology Integration Risks Accelerating Future Pandemics

Dianzhuo Wang^*†, Marian Huot^*, Zechen Zhang, Kaiyi Jiang, Eugene Shakhnovich^†, Kevin Esvelt^†

Frontiers in Microbiology / NeurIPS AI BioSafety 2025 (Best Paper) / bibtex

@article{wang16without,
  title={Without Safeguards, AI-Bio Integration Risks Accelerating Future Pandemics},
  author={Wang, Dianzhuo and Huot, Marian and Zhang, Zechen and Jiang, Kaiyi and Shakhnovich, Eugene I and Esvelt, Kevin M},
  journal={Frontiers in Microbiology},
  volume={16},
  pages={1734561},
  publisher={Frontiers}
}

Predicting high-fitness viral protein variants with Bayesian active learning and biophysics

Marian Huot^*, Dianzhuo Wang^*,†, Jiacheng Liu, Eugene Shakhnovich^†

PNAS / Paper / Code / bibtex

@article{huot2025predicting,
  title={Predicting high-fitness viral protein variants with Bayesian active learning and biophysics},
  author={Huot, Marian and Wang, Dianzhuo and Liu, Jiacheng and Shakhnovich, Eugene I},
  journal={Proceedings of the National Academy of Sciences},
  volume={122},
  number={24},
  pages={e2503742122},
  year={2025},
  publisher={National Academy of Sciences}
}

Biophysical principles predict fitness of SARS-CoV-2 variants

Dianzhuo Wang, Marian Huot, Vaibhav Mohanty, Eugene Shakhnovich

PNAS / Paper / Code / bibtex

@article{doi:10.1073/pnas.2314518121,
  author = {Dianzhuo Wang and Marian Huot and Vaibhav Mohanty and Eugene I. Shakhnovich},
  title = {Biophysical principles predict fitness of SARS-CoV-2 variants},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {121},
  number = {23},
  pages = {e2314518121},
  year = {2024},
  doi = {10.1073/pnas.2314518121},
  URL = {https://www.pnas.org/doi/abs/10.1073/pnas.2314518121},
  eprint = {https://www.pnas.org/doi/pdf/10.1073/pnas.2314518121}
}

A spatial signal of niche differentiation in tropical forests

Mihir S Umarani^*, Dianzhuo Wang^*, James P O'dwyer, Rafael D'andrea

The American Naturalist / Paper / Code / bibtex

@article{umarani2024spatial,
  title={A spatial signal of niche differentiation in tropical forests},
  author={Umarani, Mihir S and Wang, Dianzhuo and O'dwyer, James P and D'andrea, Rafael},
  journal={The American Naturalist},
  volume={203},
  number={4},
  pages={445--457},
  year={2024},
  publisher={The University of Chicago Press Chicago, IL}
}

Effects of Vimentin Intermediate Filaments on the Structure and Dynamics of In Vitro Multicomponent Interpenetrating Cytoskeletal Networks

Yinan Shen, Huayin Wu, Peter J Lu, Dianzhuo Wang, Marjan Shayegan, Hui Li, Weichao Shi, Zizhao Wang, Li-Heng Cai, Jing Xia, Meng Zhang, Ruihua Ding, Harald Herrmann, Robert Goldman, Fred C MacKintosh, Arturo Moncho-Jordá, David A Weitz

Physical Review Letters / Paper / Particle Tracking Code / bibtex

@article{shen2021effects,
  title={Effects of vimentin intermediate filaments on the structure and dynamics of in vitro multicomponent interpenetrating cytoskeletal networks},
  author={Shen, Yinan and Wu, Huayin and Lu, Peter J and Wang, Dianzhuo and Shayegan, Marjan and Li, Hui and Shi, Weichao and Wang, Zizhao and Cai, Li-Heng and Xia, Jing and others},
  journal={Physical review letters},
  volume={127},
  number={10},
  pages={108101},
  year={2021},
  publisher={APS}
}

More Structures, Less Accuracy: ESM3's Binding Prediction Paradox

Thomas Loux, Dianzhuo Wang, Eugene Shakhnovich

NeurIPS MLSB / Paper / bibtex

@article{loux2024more,
  title={More Structure, Less Accuracy: ESM3's Binding Prediction Paradox},
  author={Loux, Thomas and Wang, Dianzhuo and Shakhnovich, Eugene I},
  journal={bioRxiv},
  pages={2024--12},
  year={2024},
  publisher={Cold Spring Harbor Laboratory}
}

Education

	Harvard University Ph.D. in Applied Physics Cambridge, MA	Sep. 2020 – present
	Harvard University M.S. in Applied Mathematics Cambridge, MA	Sep. 2020 – Jun. 2023
	University of Illinois Urbana-Champaign B.S. in Physics Urbana, IL	Sep. 2018 – May 2020

News

Dec 2025

Our research is selected as Best Paper at NeurIPS 2025 Workshop on Biosecurity Safeguards for Generative AI

Jul 2025

Our research is highlighted in PNAS commentary: "Mechanistic modeling or machine learning for detecting variants of concern: Why not both?"

Jul 2025

Our research is highlighted on Harvard Gazette: "Forecasting the next variant - Harvard team fuses biophysics and AI to predict viral threats"

Jun 2024

Our research is highlighted in PNAS commentary: "The biophysical landscape of viral evolution"

Mentoring

I had the privilege of mentoring these exceptional students for their master's thesis:
Arthur Bigot (2026), ETH Zurich
Antoine Maechler (2025), École Polytechnique, now Stanford
Maxime Basse (2024), École Polytechnique, now Palantir
Thomas Loux (2024), École Polytechnique, now ENS Paris-Saclay
Marian Huot (2023), École Polytechnique, now PhD at ENS

And in undergraduate research:
Jonathan Feldman (2025), Georgia Tech

Service

Reviewer for Journal of Biomolecular Structure and Dynamics, ICLR and NeurIPS workshops.