Multi-level Protein Representation Learning for Blind Mutational Effect Prediction. - Yang Tan 001; Bingxin Zhou; Yuanhong Jiang; Yu Guang Wang 001; Liang Hong (CoRR, 2023)

MedChatZH: a Better Medical Adviser Learns from Better Instructions. - Yang Tan 001; Mingchen Li; Zijie Huang 001; Huiqun Yu; Guisheng Fan (CoRR, 2023)

Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion. - Yutong Hu 008; Yang Tan 001; Andi Han; Lirong Zheng 005; Liang Hong; Bingxin Zhou (BIBM, 2024)

Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance? - Yang Tan 001; Lirong Zheng 005; Bozitao Zhong; Liang Hong; Bingxin Zhou (BIBM, 2024)

PROTSOLM: Protein Solubility Prediction with Multi-modal Features. - Yang Tan 001; Jia Zheng; Liang Hong; Bingxin Zhou (BIBM, 2024)

ProSST: Protein Language Modeling with Quantized Structure and Disentangled Attention. - Mingchen Li; Yang Tan 001; Xinzhu Ma; Bozitao Zhong; Huiqun Yu; Ziyi Zhou; Wanli Ouyang; Bingxin Zhou; Pan Tan; Liang Hong (NeurIPS, 2024)

MedChatZH: A tuning LLM for traditional Chinese medicine consultations. - Yang Tan 001; Zhixing Zhang; Mingchen Li; Fei Pan; Hao Duan; Zijie Huang 001; Hua Deng; Zhuohang Yu; Chen Yang; Guoyang Shen; Peng Qi; Chengyuan Yue; et al. (Comput. Biol. Medicine, 2024)

A PLMs based protein retrieval framework. - Yuxuan Wu; Xiao Yi; Yang Tan 001; Huiqun Yu; Guisheng Fan (CoRR, 2024)

CPE-Pro: A Structure-Sensitive Deep Learning Method for Protein Representation and Origin Evaluation. - Wenrui Gou; Wenhui Ge; Yang Tan 001; Mingchen Li; Guisheng Fan; Huiqun Yu (CoRR, 2024)

Retrieval-Enhanced Mutation Mastery: Augmenting Zero-Shot Prediction of Protein Language Model. - Yang Tan 001; Ruilin Wang; Banghao Wu; Liang Hong; Bingxin Zhou (CoRR, 2024)

Simple, Efficient, and Scalable Structure-Aware Adapter Boosts Protein Language Models. - Yang Tan 001; Mingchen Li; Bingxin Zhou; Bozitao Zhong; Lirong Zheng 005; Pan Tan; Ziyi Zhou; Huiqun Yu; Guisheng Fan; Liang Hong (J. Chem. Inf. Model., 2024)

Protein Engineering with Lightweight Graph Denoising Neural Networks. - Bingxin Zhou; Lirong Zheng 005; Banghao Wu; Yang Tan 001; Outongyi Lv; Kai Yi; Guisheng Fan; Liang Hong (J. Chem. Inf. Model., 2024)

PETA: evaluating the impact of protein transfer learning with sub-word tokenization on downstream applications. - Yang Tan 001; Mingchen Li; Ziyi Zhou; Pan Tan; Huiqun Yu; Guisheng Fan; Liang Hong (J. Cheminformatics, 2024)

Immunogenicity Prediction with Dual Attention Enables Vaccine Target Selection. - Song Li; Yang Tan 001; Song Ke; Liang Hong; Bingxin Zhou (ICLR, 2025)

Graph with Residue-Based Cross-Modal Framework Enhances Cell Function-Related Protein Properties Prediction. - Wenrui Gou; Yang Tan 001; Chen Liu; Mingchen Li; Guisheng Fan; Huiqun Yu (J. Chem. Inf. Model., 2025)

VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning. - Yang Tan 001; Chen Liu; Jingyuan Gao; Banghao Wu; Mingchen Li; Ruilin Wang; Lingrong Zhang; Huiqun Yu; Guisheng Fan; Liang Hong; Bingxin Zhou (CoRR, 2025)

VenusX: Unlocking Fine-Grained Functional Understanding of Proteins. - Yang Tan 001; Wenrui Gou; Bozitao Zhong; Liang Hong; Huiqun Yu; Bingxin Zhou (CoRR, 2025)

Sequence-Only Prediction of Binding Affinity Changes: A Robust and Interpretable Model for Antibody Engineering. - Chen Liu; Mingchen Li; Yang Tan 001; Wenrui Gou; Guisheng Fan; Bingxin Zhou (CoRR, 2025)