Publications

# co-first author; * corresponding author

  1. Zheng, L.#, Shi, D.#, Yan, Y.#, Zhou, B., Lim, J., Hou, Y., An, B., Adhinarta, J.K., Lin, M., Ko, B., Joesten, W.C., Gautam, M., Huez, E.D.M., Kim, E.C., Klyder, E.G., Chang, B., Pitchiaya, S., Roberts, M.T., Cai, D.J., Boyden, E.S., Wei, D., Liò, P., Linghu, C.* Scalable and Multiplexed Recorders of Gene Regulation Dynamics Across Weeks. Nature 2026, 652, 1038–1048.
  2. Qian, X.#, Han, D.#, Zheng, L.#, Chen, J.#, Tyagi, M., Li, Q., Du, F., Zheng, S., Huang, X., Zhang, S., Shi, J., Huang, H., Shi, X., Chen, J., Chen, L., Hong, L.*, Zhang, Q.M. High-entropy Polymer Produce a Giant Electrocaloric Effect at Low Fields. Nature 2021, 600, 664–669. 1% highly cited paper.
  3. Zheng, L.#, Zhou, B.#, Yang, Y.#, Zan, B.#, Zhong, B., Wu, B., Feng, Y., Liu, Q., Hong, L. Mn2+-Induced Structural Flexibility Enhances the Entire Catalytic Cycle and the Cleavage of Mismatches in Prokaryotic Argonaute Proteins. Chemical Science 2024, 15, 5612–5626.
  4. Zheng, L.#, Zhou, B.#, Wu, B.#, Huang, J., Tyagi, M., Sakai, V., Yamada, T., O’Neill, H., Zhang, Q., Hong, L.* Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K. eLife 2024, 13:RP95665.
  5. Zheng, L.#, Lu, H.#, Zan, B.#, Liu, H., Li, S., Huang, J., Liu, Y., Jiang, F., Liu, Q., Feng, Y., Hong, L. Loosely-packed Dynamical Structure with Partially-melted Surface Being the Key for Thermophilic Argonaute Proteins Achieving High DNA-cleavage Activity. Nucleic Acids Research 2022, 50, 7529–7544.
  6. Zheng, L.#, Liu, Z.#, Zhang, Q.#, Huang, J., Zhang, L., Yang, C., Tan, P., Zan, B., Li, S., Jiang, F., Tyagi, M., Sakai, V., Yamada, T., Zuo, T., Chen, H., Cheng, H., Zhuang, W., Hong, L. Universal Dynamical Onset in Water at Distinct Material Interfaces. Chemical Science 2022, 13, 4341–4351.
  7. Zheng, L., Liu, L., Shao, C., Wang, W., Wang, B., Pan, L., Li, Y., Ma, Z. Phase Transition from Tetragonal Form II to Hexagonal Form I of Butene-1/4-Methyl-1-pentene Random Copolymers: Molecular Factor versus Stretching Stimuli. Macromolecules 2019, 52, 1188–1199.
  8. Zheng, L., Fernandez-Ballester, L., Peters, G.W.M., Ma, Z. Concomitant Crystallization in Propylene/Ethylene Random Copolymer with Strong Flow at Elevated Temperatures. Industrial & Engineering Chemistry Research 2018, 57, 6870–6877.
  9. Zheng, L., Hong, L. Combining Neutron Scattering, Deuteration Technique, and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules. Chinese Journal of Polymer Science 2019, 37, 1083–1091.
  10. Zheng, L., Li, W., Ma, Z., Sheng, J. Influence of Co-unit and Stretching on Phase Transition in Polybutene Random Copolymers. Polymer Materials Science and Engineering 2021, 37, 33–37.
  11. Zhou, B.#, Zheng, L.#, *, Wu, B.#, Yi, K., Zhong, B., Liu, Q., Liò, P.*, Hong, L.* A Conditional Protein Diffusion Model Generates Artificial Programmable Endonuclease Sequences with Enhanced Activity. Cell Discovery 2024, 10, 95.
  12. Zhou, B.#, Zheng, L.#, *, Wu, B.#, Tan, Y.#, Lv, O., Yi, K., Fan, G., Hong, L.* Protein Engineering with Lightweight Graph Denoising Neural Networks. Journal of Chemical Information and Modeling 2024, 64, 3650–3661.
  13. Ye, Y.#, Zheng, L.#, Hong, L., Garcia-Sakai, V., Nicolas, R., Cai, J., Liu, Z. Direct Observation of Mutual Coupling Effect in Protein-water-glycerol Mixture by Combining Neutron Scattering and Selective Deuteration. Journal of Physical Chemistry B 2024, 128, 405–414.
  14. Wu, B., Zhong, B., Zheng, L.*, Huang, R., Jiang, S., Li, M., Tan, P.*, Hong, L.* Harnessing Protein Language Model for Structure-Based Discovery of Highly Efficient and Robust PET Hydrolases. Nature Communications 2025, 16, 6211. Featured article, highlighted by editor.
  15. Kang, L., Han, D., Hong, L., Zheng, L.*, Qian, X.* Statistical Mechanical Model of Giant Electrocaloric Effect in Ferroelectric Polymers. ACS Macro Letters 2023, 12, 848–853.
  16. Wu, B., Li, M., Zhang, J., Li, J., Wang, X., Zhong, B., Liu, J., Liu, Y., Wang, B., Tan, Y., Qi, W., Tan, P., Zhao, W., Zheng, L.*, Hong, L.* Deep learning-guided design of hydrolases for crystalline PET depolymerization. bioRxiv 2026, 2026.06.04.730138.
  17. Yan, Y., Wang, Y., Zheng, L., Lim, J., Xiang, N., Linghu, C. Genetically Encoded Systems for Cytosolic Activity Recording and Molecular Archiving Across Time. bioRxiv 2026, 2026.06.15.732182.
  18. Zheng, S., Du, F., Zheng, L., Li, Q., Shi, J., Chen, J., Han, D., Shi, X., Huang, H., Luo, Y., Yang, Y., O’Reilly, P., Wei, L., Souza, N., Hong, L., Qian, X. Colossal Electrocaloric Effect in An Interface-Augmented Ferroelectric Polymer. Science 2023, 382, 1020–1026.
  19. Jiang, F., Li, M., Yu, Y., Dong, J., Zheng, L., et al. A general temperature-guided language model to engineer enhanced stability and activity in proteins. Science Advances 2024, 10, eadr2641.
  20. Shi, D., Hou, Y., Yan, Y., Zhang, T.-h., Joesten, W.C., Liu, P., Wang, Y., Gautam, M., Lim, J., Zheng, L., Gould, J., Ko, B., Niu, X., Cheng, M.-C., Hsieh, J.-C., Levet, F., Cai, D., Draelos, A., Cai, D.J., Wei, D., Linghu, C. Simultaneous brain-wide single-cell recording resolves spatiotemporal memory architecture. bioRxiv 2026, 2026.05.21.726120.
  21. Tan, Y., Zhou, B., Zheng, L., Fan, G., Hong, L. Semantical and Topological Protein Encoding Toward Enhanced Bioactivity and Thermostability. eLife 2024, 13:RP98033.
  22. Tan, Y., Li, M., Zhou, B., Zhong, B., Zheng, L., Tan, P., Zhou, Z., Yu, H., Fan, G., Hong, L. Simple, efficient, and scalable structure-aware adapter boosts protein language models. Journal of Chemical Information and Modeling 2024, 64, 6338–6349.
  23. Tan, Y., Zheng, L., Zhong, B., Hong, L., Zhou, B. Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance? Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2024.
  24. Hu, Y., Tan, Y., Han, A., Zheng, L., Hong, L., Zhou, B. Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion. Proceedings of IEEE International Conference on Bioinformatics and Biomedicine 2024.
  25. Ye, Y., Chen, X., Huang, J., Zheng, L., Tang, Q., et al. A Dynamic Entity Formed by Protein and its Hydration Water. Physical Review Research 2024, 6, 033316.
  26. Zhou, B., Tan, Y., Hu, Y., Zheng, L., Zhong, B., Hong, L. Protein engineering in the deep learning era. mLife 2024, 3, 477–491.
  27. Han, D., Du, F., Zhang, Y., Zheng, L., Chen, J., Huang, X., Li, Q., Zheng, S., Shi, J., Chen, J., Dong, J., Qian, X. Molecular Interface-regulation Enables Order-disorder Synergy in Electrocaloric Nanocomposites. Joule 2023, 1, 1–17.
  28. Jiang, F., Bian, J., Liu, H., Li, S., Bai, X., Zheng, L., Jin, S., Liu, Z., Yang, G., Hong, L. Creatinase: Using Increased Entropy to Improve Activity and Thermostability. Journal of Physical Chemistry B 2023, 127, 2671–2682.
  29. Zhou, B., Lv, O., Wang, J., Xiao, X., Zhao, W., Zheng, L. A Unified View on Neural Message Passing with Opinion Dynamics for Social Networks. arXiv 2023, 2310.01272.
  30. Zhao, W., Zhong, B., Zheng, L., Tan, P., Wang, Y., Leng, H., Souza, N., Liu, Z., Hong, L., Xiao, X. Proteome-wide 3D Structure Prediction Provides Insights into the Ancestral Metabolism of Ancient Archaea and Bacteria. Nature Communications 2022, 13, 7861.
  31. Li, S., Ke, S., Yang, C., Chen, J., Xiong, Y., Zheng, L., Liu, H., Hong, L. A Ligand-and-structure Dual-driven Deep Learning Method for the Discovery of Highly Potent GnRH1R Antagonist to Treat Uterine Diseases. arXiv 2022, 2207.11547.
  32. Capaccioli, S., Zheng, L., Kyritsis, A., Paciaroni, A., Vogel, M., Ngai, K. The Dynamics of Hydrated Proteins are the Same as Highly Asymmetric Mixtures of Two Glass-Formers. ACS Omega 2021, 1, 340–347.
  33. Tan, P., Yue, J., Yu, Y., Liu, B., Liu, T., Zheng, L., He, L., Zhang, X., Suo, L., Hong, L. Solid-like Nano-Anion-Cluster Constructs Free Lithium-ion Conducting Super-Fluid Framework in Water-in-salt Electrolyte. Journal of Physical Chemistry C 2021, 125, 11838–11847.
  34. Li, W., Liu, L., Zheng, L., Lou, Y., Ma, Z., Li, Y. Interplay between Macroscopic Stretching and Microscopic Phase Transition Revealed in Butene-1/1,5-Hexadiene Random Copolymers. Macromolecules 2020, 53, 2145–2156.
  35. Wang, W., Zheng, L., Liu, L., Li, W., Li, Y., Ma, Z. Stretching Behavior of the Butene-1/Ethylene Random Copolymer: a Direct Correspondence Between Triggering of II-I Phase Transition and Mechanical Yielding. Polymer Crystallization 2019, 2, e10052.
  36. Ma, Z., Wang, W., Zheng, L., Wang, B., Pan, L., Ma, G., Li, Y. Wide Angle X-Ray Diffraction of Cyclic-Stretching Induced Phase Transition in Butene/Ethylene Copolymer. Journal of Tianjin University 2019, 3, 249–254.
  37. Wang, W., Shao, C., Zheng, L., Wang, B., Pan, L., Ma, G., Li, Y., Wang, Y., Liu, C., Ma, Z. Stretching-induced Phase Transition of the Butene-1/Ethylene Random Copolymer: Orientation and Kinetics. Journal of Polymer Science Part B: Polymer Physics 2018, 57, 116–126.