Publications by authors named "Stan Li"

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Modeling Protein-Protein and Protein-Ligand Interactions by the ClusPro Team in CASP16.
Ryota Ashizawa, Sergei Kotelnikov, Omeir Khan, Stan Xiaogang Li, Ernest Glukhov, Ayse Bekar-Cesaretli, Dmytro Kalitin, Carlos Simmerling

Proteins· January 2026

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FGeneBERT: function-driven pre-trained gene language model for metagenomics.
Chenrui Duan, Zelin Zang, Yongjie Xu, Hang He, Siyuan Li, Zihan Liu, Stan Z Li

Brief Bioinform· November 2025

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SKIP: A Prototype-Based Scalable Knowledge Graph Representation Learning Method.
Yue Liu, Ke Liang, Jun Xia, Meng Liu, Xihong Yang, Xinwang Liu, Stan Z Li

IEEE Trans Neural Netw Learn Syst· November 2025

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Conventional and non-conventional antigen-binding sites promote the development and function of chronic lymphocytic leukemia stereotyped subset #4 clones.
Yun Liu, Dzmitry Padhorny, Rosa Catera, Antonella Nicolo, Xiao-Jie Yan, Stan Xiaogang Li, Jonathan E Kolitz

Front Immunol· September 2025

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USTEP: Spatio-Temporal Predictive Learning Under a Unified View.
Cheng Tan, Jue Wang, Zhangyang Gao, Siyuan Li, Stan Z Li

IEEE Trans Pattern Anal Mach Intell· August 2025

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Modulating the Binding Kinetics of Bruton's Tyrosine Kinase Inhibitors through Transition-State Effects.
Eduardo Bravo, Yong Li, David Yin-Wei Lin, Bharath Srinivasan, Marco Barone, Stan Xiaogang Li

J Am Chem Soc· August 2025

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Learning to Model Graph Structural Information on MLPs via Graph Structure Self-Contrasting.
Lirong Wu, Haitao Lin, Guojiang Zhao, Cheng Tan, Stan Z Li

IEEE Trans Neural Netw Learn Syst· July 2025

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MuST: multiple-modality structure transformation for single-cell spatial transcriptomics.
Zelin Zang, Liangyu Li, Yongjie Xu, Chenrui Duan, Yue Shen, Stan Z Li

Brief Bioinform· July 2025

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Identification of Actionable Targeted Protein Degradation Effector Sites through Site-Specific Ligand Incorporation-Induced Proximity (SLIP).
Zhangping Xiao, Efthymios S Gavriil, Fangyuan Cao, Xinyue Zhang, Stan Xiaogang Li

J Am Chem Soc· June 2025

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Correction: DiffBP: generative diffusion of 3D molecules for target protein binding.
Haitao Lin, Yufei Huang, Odin Zhang, Siqi Ma, Meng Liu, Xuanjing Li, Lirong Wu, Stan Z Li

Chem Sci· April 2025

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Effectiveness and Efficiency: Label-Aware Hierarchical Subgraph Learning for Protein-Protein Interaction.
Yuanqing Zhou, Haitao Lin, Lianghua Xie, Yufei Huang, Lirong Wu, Stan Z Li

J Mol Biol· March 2025

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Effect of iberdomide on cutaneous manifestations in systemic lupus erythematosus: A randomized phase 2 clinical trial.
Victoria P Werth, Joan T Merrill, Richard Furie, Thomas Dörner, Ronald van Vollenhoven, Peter Lipsky, Stan Li

J Am Acad Dermatol· March 2025

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SP-DTI: subpocket-informed transformer for drug-target interaction prediction.
Sizhe Liu, Yuchen Liu, Haofeng Xu, Jun Xia, Stan Z Li

Bioinformatics· March 2025

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FGeneBERT: function-driven pre-trained gene language model for metagenomics.
Chenrui Duan, Zelin Zang, Yongjie Xu, Hang He, Siyuan Li, Zihan Liu, Stan Z Li

Brief Bioinform· March 2025

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Identification of actionable targeted protein degradation effector sites through Site-specific Ligand Incorporation-induced Proximity (SLIP).
Zhangping Xiao, Efthymios Spyridon Gavriil, Fangyuan Cao, Xinyue Zhang, Stan Xiaogang Li

bioRxiv· February 2025

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GenURL: A General Framework for Unsupervised Representation Learning.
Siyuan Li, Zicheng Liu, Zelin Zang, Di Wu, Zhiyuan Chen, Stan Z Li

IEEE Trans Neural Netw Learn Syst· January 2025

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DiffBP: generative diffusion of 3D molecules for target protein binding.
Haitao Lin, Yufei Huang, Odin Zhang, Siqi Ma, Meng Liu, Xuanjing Li, Lirong Wu, Stan Z Li

Chem Sci· January 2025

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AI-driven eyelid tumor classification in ocular oncology using proteomic data.
Linyan Wang, Xizhe Dai, Zicheng Liu, Yaxing Zhao, Yaoting Sun, Nuliqiman Maimaiti, Stan Z Li

NPJ Precis Oncol· December 2024

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R3Design: deep tertiary structure-based RNA sequence design and beyond.
Cheng Tan, Yijie Zhang, Zhangyang Gao, Hanqun Cao, Siyuan Li, Stan Z Li

Brief Bioinform· November 2024

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Complex hierarchical structures analysis in single-cell data with Poincaré deep manifold transformation.
Yongjie Xu, Zelin Zang, Bozhen Hu, Yue Yuan, Cheng Tan, Stan Z Li

Brief Bioinform· November 2024

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Aggregation Rules of Short Peptides.
Jiaqi Wang, Zihan Liu, Shuang Zhao, Yu Zhang, Tengyan Xu, Stan Z Li, Wenbin Li

JACS Au· September 2024

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Accurate ligand-protein docking in CASP15 using the ClusPro LigTBM server.
Sergei Kotelnikov, Ryota Ashizawa, Konstantin I Popov, Omeir Khan, Mikhail Ignatov, Stan Xiaogang Li

Proteins· December 2023

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Deep Learning Empowers the Discovery of Self-Assembling Peptides with Over 10 Trillion Sequences.
Jiaqi Wang, Zihan Liu, Shuang Zhao, Tengyan Xu, Huaimin Wang, Stan Z Li, Wenbin Li

Adv Sci (Weinh)· November 2023

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Efficient prediction of peptide self-assembly through sequential and graphical encoding.
Zihan Liu, Jiaqi Wang, Yun Luo, Shuang Zhao, Wenbin Li, Stan Z Li

Brief Bioinform· September 2023

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Integration of pre-trained protein language models into geometric deep learning networks.
Fang Wu, Lirong Wu, Dragomir Radev, Jinbo Xu, Stan Z Li

Commun Biol· August 2023

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