đź—¨ About Me
Hi! my name is Shiyu Jiang. I am currently a PhD student in computer science at the University of Florida working
with Prof. Yanjun Li and Prof. Matthew Disney.
My research lies at the intersection of AI and biology, where I design computational approaches to accelerate discoveries
in synthetic biology, drug discovery, and molecular interaction. Specifically, I primarily focus on those areas:
- : generative modeling and representation learning for molecular prediction, sequence design, and optimization; drug-induced cellular phenotype prediction; and structural data resources for ligand recognition.
- : single-cell foundation models and language models for protein and nucleic acid sequences, spanning model development, evaluation, and applications.
- : building the computational core of wet-lab campaigns, from sequence–activity landscape modeling to variant prioritization for enzyme and Cas nuclease evolution.
- Agentic systems, memory, and continual learning: parametric and non-parametric memory, long-horizon adaptation, self-evolving agents, reinforcement learning, and agentic systems for scientific discovery.
Before starting my PhD, I was very fortunate to work with and learn from really brilliant, inspiring mentors and collaborators across these fields, you can find them in the experience panel.
AI-driven drug discovery
Related work, most recent first.
- Jiang, S., Yang, Z., Taghavi, A., Wei, J., Childs-Disney, J. L., Li, C., Disney, M. D., & Li, Y. (2026). SMARTFlexDB: A database of paired apo–holo RNA structures for analyzing conformational remodeling and small-molecule recognition. In preparation. https://aidd.rc.ufl.edu/app/smartflexdb/
- Jiang, S.†, Taghavi, A.†, Wang, T., Sung, K., Meyer, S. M., Springer, N. A., Wei, J., Childs-Disney, J. L., Li, C., Disney, M. D., & Li, Y. (2026). Small molecule approach to RNA targeting binder discovery (SMARTBind) using deep learning without structural input [Preprint]. bioRxiv. Under review at Nature Portfolio. https://pmc.ncbi.nlm.nih.gov/articles/PMC12485756/
- Zheng, X., Jiang, S., Seabra, G., Li, C., & Li, Y. (2026). Apo2Mol: 3D molecule generation via dynamic pocket-aware diffusion models. Proceedings of the AAAI Conference on Artificial Intelligence. https://ojs.aaai.org/index.php/AAAI/article/view/37138
† Equal contribution.
Foundation models for life sciences
Related work, most recent first.
- Jiang, S.†, Fang, Z.†, Zhang, Y., Zhang, X., Kalfon, J., Wang, W., . . . Ding, J. (2026). The landscape of single-cell foundation models: Design principles, applications, and open challenges [Manuscript submitted for publication, under review]. https://github.com/OmicsML/awesome-foundation-model-single-cell-papers
- Ding, J.†, Lin, J.†, Miao, Z.†, Mechtel, N.†, Jiang, S., Wang, Y., Fang, Z., Martin-Rufino, J. D., Weng, C., Saunders, R., Xu, W., Weissman, J. S., Ouyang, W., Li, M., Tang, J., Lu, Y. R., & Qiu, X. (2026). Predictive single cell foundation model for gene regulation and aging with privacy-preserving tabular learning [Preprint]. arXiv. https://arxiv.org/abs/2607.19400
- Zhou, X.†, Han, C.†, Zhang, Y.†, Du, H.†, Tian, J.†, Su, J.‡, Liu, R.‡, Zhuang, K.‡, Jiang, S.‡, Gitter, A., . . . Yuan, F. (2026). Decoding the molecular language of proteins with Evolla [Preprint]. bioRxiv. https://doi.org/10.1101/2025.01.05.630192
- Jiang, S., Liu, X., & Wang, J. Z. (2026). Evaluating DNA function understanding in genomic language models using evolutionarily implausible sequences. ACS Synthetic Biology. https://doi.org/10.1021/acssynbio.6c00024
- Su, J.†, He, Y.†, You, S.†, Jiang, S., Zhou, X., Zhang, X., Wang, Y., Su, X., Tolstoy, I., Chang, X., Lu, H., & Yuan, F. (2025). A tri-modal protein language model enables advanced protein searches. Nature Biotechnology. https://doi.org/10.1038/s41587-025-02836-0
- Su, J., Li, Z., Tao, T., Han, C., He, Y., Dai, F., Yuan, Q., Gao, Y., Si, T., Zhang, X., Zhou, Y., Shan, J., Zhou, X., Chang, X., Jiang, S., Ma, D., The OPMC, Steinegger, M., Ovchinnikov, S., & Yuan, F. (2025). SaprotHub: Democratizing protein language model training, sharing and collaboration for the biology community. Nature Biotechnology. https://doi.org/10.1038/s41587-025-02859-7
- Ding, J.†, Lin, J.†, Jiang, S.†, Wang, Y., Mao, Z., Fang, Z., Tang, J., Li, M., & Qiu, X. (2025). Tabula: A tabular self-supervised foundation model for single-cell transcriptomics. Advances in Neural Information Processing Systems. https://openreview.net/forum?id=Vk2sfKAdeu
- Jiang, S., Liu, X., & Wang, J. Z. (2025). Predicting function of evolutionarily implausible DNA sequences. ICML 2025 Generative AI and Biology Workshop. https://icml.cc/virtual/2025/51254
† Equal contribution. ‡ Equal secondary contribution.
Experiment-driven protein and cellular engineering
Related work, most recent first.
- Cheng, L.†, Zheng, X.†, Ding, H.†, Jiang, S., Hu, Y., Wang, C., Li, C.-L., Tian, Z., Leeuwon, R. J., Rui, J., Ye, H., Yuan, T., Liu, Y., Yang, K., Zhou, B., Huang, X., & Xiao, H. (2026). Sequence Display generates large-scale sequence–activity datasets for reprogramming SlugCas9 toward difficult-to-access PAMs. Nature Communications. Accepted in principle.
- Cheng, L.†, Zheng, X.†, Jiang, S.†, Hu, Y., Liu, Y., Yang, K., Rui, J., Ding, H., Zhang, M., Yuan, T., Ye, H., Li, C., Yang, K. K., Huang, X., & Xiao, H. (2026). Sequence Display: Generating large-scale sequence–activity datasets to advance universal protein evolution. Nature Biotechnology. https://doi.org/10.1038/s41587-026-03087-3
- Yuan, T., Zhang, M., Cheng, L., Zheng, X., Jiang, S., Huang, X., & Xiao, H. (2025). Biocatalytic synthesis of N-protected α-amino acids through 1,3-nitrogen migration by nonheme iron enzymes. Journal of the American Chemical Society, 147(48), 44041–44047. https://doi.org/10.1021/jacs.5c11008
- Hu, Y., Wang, Yixian, Cheng, L., Wang, C., Liu, Y., Wang, Yufei, Chen, Y., Yang, S., Guo, Y., Jiang, S., Yang, K., & Xiao, H. (2025). Engineering unnatural cells with a 21st amino acid as a living epigenetic sensor. Nature Communications, 16, 9388. https://doi.org/10.1038/s41467-025-64448-1
- Hu, Y.†, Cheng, L.†, Liu, Y., Liu, R., Jiang, S., Yuan, T., Wang, Y., Ye, H., & Xiao, H. (2025). Biosynthesis of unnatural cyclodipeptides through genetic code expansion and cyclodipeptide synthase evolution. Journal of the American Chemical Society. https://doi.org/10.1021/jacs.5c08627
- Guo, Y.†, Cheng, L.†, Hu, Y., Zhang, M., Liu, R., Wang, Y., Jiang, S., & Xiao, H. (2024). Biosynthesis of halogenated tryptophans for protein engineering using genetic code expansion. ChemBioChem, 25(20), e202400366. https://doi.org/10.1002/cbic.202400366
- Ye, H., Jiang, S., Yan, Y., Zhao, B., Grant, E. R., Kitts, D. D., Yada, R. Y., Pratap-Singh, A., Baldelli, A., & Yang, T. (2024). Integrating metal–phenolic networks-mediated separation and machine learning-aided surface-enhanced Raman spectroscopy for accurate nanoplastics quantification and classification. ACS Nano. https://doi.org/10.1021/acsnano.4c08316
† Equal contribution.
đź“– Educations
- 2026 - Present, PhD student, Computer Science. University of Florida. Gainesville, FL
- 2025 - 2026, PhD student, Computational Biology and Bioinformatics. University of Southern California. Los Angeles, CA
- 2022 - 2024, Master of Science in Engineering, Computer Science. Johns Hopkins University. Baltimore, MD
- 2018 - 2022, Bachelor of Science, Computer Science. Wenzhou-Kean University. Wenzhou, China
đź“° News
- 2026.08: One co-authored paper “Sequence Display generates large-scale sequence-activity datasets for reprogramming SlugCas9 toward difficult-to-access PAMs” is accepted by Nature Communications!
- 2026.07: One co-authored paper “Predictive single cell foundation model for gene regulation and aging with privacy-preserving tabular learning” is released on arXiv. Check out our post.
- 2026.05: One first authored paper “Evaluating DNA function understanding in genomic language models using evolutionarily implausible sequences” is accepted by ACS Synthetic Biology!
- 2026.05: Our sequence display paper is featured as a research highlight in Nature Methods and Rice News!
- 2026.02: One co-first authored paper “Sequence Display: Generating Large-Scale Sequence–Activity Datasets to Advance Universal Protein Evolution” is accepted by Nature Biotechnology!
Earlier News (Click to Expand)
- 2026.01: “Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input” is presented at UF Health Cancer Institute Annual Research Showcase 2026, see our poster.
- 2025.11: One co-authored paper “Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models” is accepted by AAAI 2026!
- 2025.10: One co-authored paper “Engineering Unnatural Cells with a 21st Amino Acid as a Living Epigenetic Sensor” is on Nature Communications!
- 2025.09: One first-authored paper “Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input” is released on bioRxiv.
- 2025.09: One co-first authored paper “Tabula: A Tabular Self-Supervised Foundation Model for Single-Cell Transcriptomics” is accepted by NeurIPS 2025!
- 2025.09: One co-authored paper “Biosynthesis of Unnatural Cyclodipeptides through Genetic Code Expansion and Cyclodipeptide Synthase Evolution” is on Journal of the American Chemical Society!
- 2025.08: One co-authored paper “SaprotHub: Democratizing Protein Language Model Training, Sharing and Collaboration for the Biology Community” is accepted by Nature Biotechnology!
- 2025.07: One co-authored paper “A tri-modal protein language model enables advanced protein searches” is accepted by Nature Biotechnology!
- 2025.07: “Predicting function of evolutionarily implausible DNA sequences” is presented at Q-BIO 2025 Conference: Emergent Orders in Living Systems Across Scales, see our poster.
- 2025.06: “Sequence Display-Enabled Machine Learning for Protein Evolution” is presented at 2025 Synthetic Biology: Engineering, Evolution, & Design, see our poster.
- 2025.06: One first authored paper “Predicting function of evolutionarily implausible DNA sequences” is accepted by ICML 2025 Generative AI and Biology Workshop!
- 2025.04: I will be joining the PhD program in Computational Biology and Bioinformatics at USC QCB, looking forward to the journey.
- 2025.01: “Toward a privacy-preserving predictive foundation model of single-cell transcriptomics with federated learning and tabular modeling” is released on bioRxiv, see our post.
đź“ť Selected Publications
2026
SMARTFlexDB: a database of paired apo-holo RNA structures for analyzing conformational remodeling and small-molecule recognition
Shiyu Jiang, Zekun Yang, Amirhossein Taghavi, Jinhang Wei, Jessica L. Childs-Disney, Chenglong Li, Mattew D. Disney, Yanjun Li. 2026. (In preparation)
The landscape of single-cell foundation models: design principles, applications, and open challenges
Shiyu Jiang †, Zhaoyu Fang †, York Zhang, Xuting Zhang, Jérémie Kalfon, Weixu Wang, …, Fei Wang, Yuying Xie, Jiliang Tang, Raul Rabadan, David van Dijk, Pengtao Xie, Peng He, Emily Fox, Le Song, Fabian J. Theis, Eric Xing, Christina V. Theodoris, Xiaojie Qiu, Jiayuan Ding. 2026. (Under Review)
Jiayuan Ding †, Jianhui Lin †, Ziyang Miao †, Nils Mechtel †, Shiyu Jiang, Yixin Wang, Zhaoyu Fang, Jorge D. Martin-Rufino, Chen Weng, Reuben Saunders, Weize Xu, Jonathan S. Weissman, Wei Ouyang, Min Li, Jiliang Tang, Yuancheng Ryan Lu, Xiaojie Qiu. arXiv, 2026. (Under Review at Nature Portfolio)
Decoding the Molecular Language of Proteins with Evolla
Xibin Zhou †, Chenchen Han †, Yinqi Zhang †, Huan Du †, Jiayuan Tian †, Jin Su ‡, Renju Liu ‡, Kai Zhuang ‡, Shiyu Jiang ‡, Anthony Gitter, …, Zongze Zhao, Yang Liu, Hongyuan Lu, Fajie Yuan. bioRxiv, 2026. (Under Review at Nature Portfolio)
Shiyu Jiang †, Amirhossein Taghavi †, Tenghui Wang, Kisu Sung, Samantha M. Meyer, Noah A. Springer, Jinhang Wei, Jessica L. Childs-Disney, Chenglong Li, Mattew D. Disney, Yanjun Li. bioRxiv, 2026. (Under Review at Nature Portfolio)
Linqi Cheng †, Xinzhe Zheng †, Haoxue Ding †, Shiyu Jiang, Yu Hu, Chenhang Wang, Chen-Long Li, Zuotong Tian, Rain Jay Leeuwon, Jinyan Rui, Haoxin Ye, Teng Yuan, Yijie Liu, Kaiqiang Yang, Boyang Zhou, Xiongyi Huang, Han Xiao. Nature Communications, 2026. (Accepted in principle)
Shiyu Jiang, Xuyin Liu, Jerry Zitong Wang. ACS Synthetic Biology, 2026.
Linqi Cheng †, Xinzhe Zheng †, Shiyu Jiang †, Hu Y, Liu Y, Yang K, Rui J, Ding H, Zhang M, Yuan T, Ye H, Li C, Kevin K. Yang, Xiongyi Huang, Han Xiao. Nature Biotechnology, 2026.
Apo2Mol: 3D Molecule Generation via Dynamic Pocket-Aware Diffusion Models
Xinzhe Zheng, Shiyu Jiang, Gustavo Seabra, Chenglong Li, Yanjun Li. AAAI (poster), 2026.
2025
Tabula: A Tabular Self-Supervised Foundation Model for Single-Cell Transcriptomics
Jiayuan Ding †, Jianhui Lin †, Shiyu Jiang †, Yixin Wang, Ziyang Mao, Zhaoyu Fang, Jiliang Tang, Min Li, Xiaojie Qiu. NeurIPS (poster), 2025.
Hu Y †, Cheng L †, Liu Y, Liu R, Jiang S, Yuan T, Wang Y, Ye H, Xiao H. Journal of the American Chemical Society, 2025.
A tri-modal protein language model enables advanced protein searches
Jin Su †, Yan He †, Shiyang You †, Shiyu Jiang, Xibin Zhou, Xuting Zhang, Yuxuan Wang, Xining Su, Igor Tolstoy, Xing Chang, Hongyuan Lu, Fajie Yuan. Nature Biotechnology, 2025.
Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Fengyuan Dai, Qingyan Yuan, Yuan Gao, Tong Si, Xuting Zhang, Yuyang Zhou, Junjie Shan, Xibin Zhou, Xing Chang, Shiyu Jiang, Dacheng Ma, The OPMC, Martin Steinegger, Sergey Ovchinnikov, Fajie Yuan. Nature Biotechnology, 2025.
Predicting function of evolutionarily implausible DNA sequences
Shiyu Jiang, Xuyin Liu, Jerry Zitong Wang. ICML 2025 Generative AI and Biology Workshop, 2025.
2024
Haoxin Ye, Shiyu Jiang, Yan Yan, Bin Zhao, Edward R Grant, David D Kitts, Rickey Y Yada, Anubhav Pratap-Singh, Alberto Baldelli, Tianxi Yang. ACS Nano, 2024.
2023
Simulating Disease Spread During Disaster Scenarios
Shiyu Jiang, Heejoong Kim, Fabio Henrique Tanaka, Claus Aranha, Anna Bogdanova, Kimia Ghobadi, Anton Dahbura. The International Conference on Artificial Life, 2023.
2022
HNOXPred: a web tool for the prediction of gas-sensing H-NOX proteins from amino acid sequence
Shiyu Jiang, Hemn Barzan Abdalla, Chuyun Bi, Yi Zhu, Xuechen Tian, Yixin Yang, Aloysius Wong. Bioinformatics, 2022.
🧑‍💻 Experience
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2024.08 - 2025.06
Research Associate
Development and evaluation of protein/genomic language model | Advisor: Prof. Fajie Yuan & Dr. Zitong Jerry Wang
Westlake University, School of Engineering & Center for Interdisciplinary Studies, School of Science
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2023 - 2025
Remote Research Assistant
Protein language model driven protein evolution with sequence display | Advisor: Prof. Han Xiao
Rice University, Department of Chemistry
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2023 - 2025
Remote Research Assistant
RNA-small molecule drug discovery and protein-molecule generation | Advisor: Prof. Yanjun Li & Prof. Matthew D. Disney
University of Florida, College of Pharmacy & UF Scripps Institute, Department of Chemistry
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2023 - 2025
Remote Research Assistant
Foundation model for single-cell transcriptomics | Advisor: Prof. Xiaojie Qiu
Stanford University, Department of Genetics
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2024.01 - 2024.07
Lab Specialist
ChIP-Seq peak calling tool | Advisor: Prof. Chongzhi Zang
University of Virginia, Department of Genome Sciences
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2021 - 2022
Undergraduate Research Assistant
Bioinformatics webtool development | Advisor: Prof. Aloysius Wong
Wenzhou Kean University, Department of Biology
đź“ť Service
- Journal reviewer: IEEE Transactions on Computational Biology and Bioinformatics, PLoS Computational Biology;
- Conference reviewer: AAAI 2026 2027, NeurIPS 2026;
🌎 Miscellaneous
Outside of work, you’ll often find me at gym, playing soccer, road cycling, or go hiking. I also enjoy playing table tennis and the piano occasionally.