publications

2026

1. arXiv

   MIMIC: A Generative Multimodal Foundation Model for Biomolecules

   Siavash Golkar, Jake Kovalic^*, Irina Espejo Morales^*, Samuel Sledzieski^*, Minhuan Li^*, and 26 more authors

   arXiv preprint arXiv:2604.24506, 2026

   Bib HTML Blog

   @article{golkar2026mimic,
     title = {MIMIC: A Generative Multimodal Foundation Model for Biomolecules},
     author = {Golkar, Siavash and Kovalic, Jake and Morales, Irina Espejo and Sledzieski, Samuel and Li, Minhuan and Sokolova, Ksenia and Krawezik, Geraud and Bietti, Alberto and Gibbs, Claudia Skok and Klypa, Roman and Xiong, Shengwei and Lanusse, Francois and Parker, Liam and Cho, Kyunghyun and Cranmer, Miles and Hehir, Tom and McCabe, Michael and Meyer, Lucas and Morel, Rudy and Mukhopadhyay, Payel and Pettee, Mariel and Qu, Helen and Shen, Jeff and Fouhey, David and Sotoudeh, Hadi and Mulligan, Vikram and Cossio, Pilar and Hanson, Sonya M. and Jones, Alisha N. and Troyanskaya, Olga G. and Ho, Shirley},
     journal = {arXiv preprint arXiv:2604.24506},
     year = {2026},
     show_authors = {5},
   }

2. Nat. Methods

   AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network

   Alisia Fadini^*, Minhuan Li^*, and 11 more authors

   Nature Methods, 2026

   Bib HTML Code

   @article{fadini2026alphafold,
     title = {AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network},
     author = {Fadini, Alisia and Li, Minhuan and McCoy, Airlie J and Banjara, Suresh and Okumura, Hiroki and Napier, Eve and Fontana, Pietro and Khan, Amir R and Jovine, Luca and Terwilliger, Thomas C and Read, Randy J and Hekstra, Doeke R and AlQuraishi, Mohammed},
     journal = {Nature Methods},
     pages = {1--11},
     year = {2026},
     publisher = {Nature Publishing Group US New York},
     show_authors = {2},
   }

3. arXiv

   Robust Inference-Time Steering of Protein Diffusion Models via Embedding Optimization

   Minhuan Li^*†, Jiequn Han, Pilar Cossio, and Luhuan Wu^*†

   arXiv preprint arXiv:2602.05285, 2026

   Bib HTML Code

   @article{li2026robust,
     title = {Robust Inference-Time Steering of Protein Diffusion Models via Embedding Optimization},
     author = {Li, Minhuan and Han, Jiequn and Cossio, Pilar and Wu, Luhuan},
     journal = {arXiv preprint arXiv:2602.05285},
     year = {2026},
     show_authors = {4},
   }

2025

1. bioRxiv

   Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images

   Geoffrey Woollard, David Herreros, Minhuan Li^†, Pilar Cossio^†, and 1 more author

   bioRxiv, 2025

   Bib HTML Code

   @article{woollard2025improving,
     title = {Improving Cryo-EM Optimization Robustness with an Optimal Transport Loss Function for Noisy Images},
     author = {Woollard, Geoffrey and Herreros, David and Li, Minhuan and Cossio, Pilar and Duc, Khanh Dao},
     journal = {bioRxiv},
     year = {2025},
     publisher = {Cold Spring Harbor Laboratory},
     show_authors = {4},
   }

2. bioRxiv

   SFCalculator: connecting deep generative models and crystallography

   Minhuan Li, Kevin Dalton, and Doeke Hekstra^†

   BioRxiv, 2025

   Bib HTML Code

   @article{li2025sfcalculator,
     title = {SFCalculator: connecting deep generative models and crystallography},
     author = {Li, Minhuan and Dalton, Kevin and Hekstra, Doeke},
     journal = {BioRxiv},
     year = {2025},
     show_authors = {3},
   }

2024

1. Phys. Rev. Lett.

   Phase reentrances and solid deformations in confined colloidal crystals

   Xiaoxia Li, Huang Fang, Krongtum Sankaewtong, Minhuan Li, Yanshuang Chen, Jiping Huang, and 3 more authors

   Physical Review Letters, 2024

   Bib HTML

   @article{li2024phase,
     title = {Phase reentrances and solid deformations in confined colloidal crystals},
     author = {Li, Xiaoxia and Fang, Huang and Sankaewtong, Krongtum and Li, Minhuan and Chen, Yanshuang and Huang, Jiping and Ni, Ran and Tanaka, Hajime and Tan, Peng},
     journal = {Physical Review Letters},
     volume = {132},
     number = {1},
     pages = {018202},
     year = {2024},
     publisher = {APS},
     show_authors = {6},
   }

2021

1. Nat. Commun.

   Revealing thermally-activated nucleation pathways of diffusionless solid-to-solid transition

   Minhuan Li, Zhengyuan Yue, Yanshuang Chen, and 3 more authors

   Nature Communications, 2021

   Bib HTML

   @article{li2021revealing,
     title = {Revealing thermally-activated nucleation pathways of diffusionless solid-to-solid transition},
     author = {Li, Minhuan and Yue, Zhengyuan and Chen, Yanshuang and Tong, Hua and Tanaka, Hajime and Tan, Peng},
     journal = {Nature Communications},
     volume = {12},
     number = {1},
     pages = {4042},
     year = {2021},
     publisher = {Nature Publishing Group UK London},
   }

2. Nat. Mater.

   Fast crystal growth at ultra-low temperatures

   Qiong Gao, Jingdong Ai, Shixiang Tang, Minhuan Li, and 7 more authors

   Nature Materials, 2021

   Bib HTML

   @article{gao2021fast,
     title = {Fast crystal growth at ultra-low temperatures},
     author = {Gao, Qiong and Ai, Jingdong and Tang, Shixiang and Li, Minhuan and Chen, Yanshuang and Huang, Jiping and Tong, Hua and Xu, Lei and Xu, Limei and Tanaka, Hajime and others},
     journal = {Nature Materials},
     year = {2021},
     publisher = {Nature Publishing Group UK London},
     show_authors = {4},
   }

2020

1. Sci. Adv.

   Revealing roles of competing local structural orderings in crystallization of polymorphic systems

   Minhuan Li, Yanshuang Chen, Hajime Tanaka^†, and 1 more author

   Science advances, 2020

   Bib HTML

   @article{li2020revealing,
     title = {Revealing roles of competing local structural orderings in crystallization of polymorphic systems},
     author = {Li, Minhuan and Chen, Yanshuang and Tanaka, Hajime and Tan, Peng},
     journal = {Science advances},
     year = {2020},
     publisher = {American Association for the Advancement of Science},
   }