Publications

📅2024

• Interface-aware molecular generative framework for protein-protein interaction modulators (IF = 7.1, JCR Q1, Journal of Cheminformatics (2024))
  Jianmin Wang, Jiashun Mao, Chunyan Li, Hongxin Xiang, Xun Wang, Shuang Wang, Zixu Wang, Yangyang Chen, Yuquan Li, Kyoung Tai No*, Tao Song*, Xiangxiang Zeng*
  J. Cheminform. | bioRxiv 2023 | code

• Activity cliff-informed contrastive learning for molecular property prediction (Under Review, ChemRxiv 2024)
  Wanxiang Shen, Chao Cui, Xiaorui Su, Zaixi Zhang, Alejandro Velez-Arce, Jianmin Wang, Xiangcheng Shi, Yanbing Zhang, Jie Wu, Yuzong Chen* and Marinka Zitnik*
  ChemRxiv | code

• Diffusion-based generative drug-like molecular editing with chemical natural language (IF = 6.1, JCR Q1, Journal of Pharmaceutical Analysis (2024))
  Jianmin Wang, Peng Zhou, Zixu Wang, Wei Long, Yangyang Chen, Kyoung Tai No, Dongsheng Ouyang*，Jiashun Mao* and Xiangxiang Zeng*
  J. Pharm. Anal. | code

• Predicting mutation-disease associations through protein interactions via deep learning (Under Review, bioRxiv. 2024)
  Xue Li, Ben Cao, Jianmin Wang, Xiangyu Meng, Shuang Wang, Yu Huang, Enrico Petretto, Tao Song*
  bioRxiv | code

• Improving compound-protein interaction prediction by focusing on intra-modality and inter-modality dynamics with a multimodal tensor fusion strategy (IF = 4.4, JCR Q1, Computational and Structural Biotechnology Journal (2024))
  Meng Wang, Jianmin Wang, Zhiwei Rong, Jianxin Ji, Chenjing Ma, Hesong Wang, Jia He, Yongzhen Song, Xuan Zhang, Yong Cao, Yanyan Dai, Menglei Hua, Ruihao Qin, Kang Li* and Lei Cao*
  Comput. Struct. Biotechnol. J. | code

• Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model (Under Review)
  Peng Zhou, Jianmin Wang, Chunyan Li, Zixu Wang, Yiping Liu, Siqi Sun, Jianxin Lin, Longyue Wang*, Xiangxiang Zeng*
  ResearchSquare | code

• An Image-enhanced Molecular Graph Representation Learning Framework
  Hongxin Xiang, Shuting Jin, Jun Xia, Man Zhou, Jianmin Wang, Li Zeng, Xiangxiang Zeng*
  IJCAI2024 | code

• Introducing enzymatic cleavage features and transfer learning realizes accurate peptide half-life prediction across species and organs (IF = 6.8, JCR Q1, Briefings in Bioinformatics (2024))
  Xiaorong Tan, Qianhui Liu, Yanpeng Fang, Sen Yang, Fei Chen, Jianmin Wang , Defang Ouyang, Jie Dong*, Wenbin Zeng*
  Brief. Bioinform.

• Exploring the conformational ensembles of protein-protein complex with transformer-based generative model (IF = 5.5, JCR Q1, Journal of Chemical Theory and Computation (2024))
  Jianmin Wang, Xun Wang, Yanyi Chu, Chunyan Li, Xue Li, Xiangyu Meng, Yitian Fang, Kyoung Tai No*, Jiashun Mao*, Xiangxiang Zeng*
  J. Chem. Theory Comput. | bioRxiv | code

• FraHMT: A fragment-oriented heterogeneous graph molecular generation model for target proteins (IF = 5.6, JCR Q1, Journal of Chemical Information and Modeling (2024))
  Shuang Wang, Dingming Liang, Jianmin Wang, Kaiyu Dong, Yunjing Zhang, Huicong Liang, Ximing Xu, Tao Song*
  JCIM | code

• DockingGA: Enhancing Targeted Molecule Generation using Transformer Neural Network and Genetic Algorithm with Docking Simulation (IF = 4.0, JCR Q1, Briefings in functional genomics (2024))
  Changnan Gao, Wenjie Bao, Shuang Wang, Jianyang Zheng, Lulu Wang, Yongqi Ren, Linfang Jiao, Jianmin Wang*, Xun Wang*
  Brief. Funct. Genomics. | code

• A bidirectional interpretable compound-protein interaction prediction framework based on cross attention (IF = 7.7, JCR Q1, Computers in Biology and Medicine (2024))
  Meng Wang, Jianmin Wang, Zhiwei Rong, Liuying Wang, Zhenyi Xu, Liuchao Zhang, Jia He, Shuang Li, Lei Cao, Yan Hou, Kang Li*
  COMPUT BIOL MED | code

• Local Scaffold Diversity-Contributed Generator for Discovering Potential NLRP3 Inhibitors (IF = 5.6, JCR Q1, Journal of Chemical Information and Modeling (2024))
  Weichen Bo, Yangqin Duan, Yurong Zou, Ziyan Ma, Tao Yang, Peng Wang,Tao Guo, Zhiyuan Fu, Jianmin Wang, Linchuan Fan, Jie liu, Taijin Wang* and Lijuan Chen*
  JCIM | code

📅2023

• iupacGPT: IUPAC-based large-scale molecular pre-trained model for property prediction and molecule generation (Under Review, ChemRxiv 2023)
  Jiashun Mao, Jianmin Wang, Kwang-Hwi Cho* and Kyoung Tai No*
  ChemRxiv | code

• MOASL: Predicting drug mechanism of action through similarity learning with transcriptomic signature (IF = 7.7, JCR Q1, Computers in Biology and Medicine (2023))
  Likun Jiang, Susu Qu, Zhengqiu Yu, Jianmin Wang, Xiangrong Liu*
  COMPUT BIOL MED | code

• A Multimodal Deep Learning Framework for Predicting PPI-Modulator Interactions (IF = 5.6, JCR Q1, Journal of Chemical Information and Modeling (2023))
  Heqi Sun, Jianmin Wang*, Hongyan Wu, Shenggeng Lin, Junwei Chen, Jinghua Wei, Shuai Lv, Yi Xiong*, Dong-Qing Wei*
  JCIM | code

• Transformer-based molecular generative model for antiviral drug design (IF = 5.6, JCR Q1, Journal of Chemical Information and Modeling (2023))
  Jiashun Mao, Jianmin Wang, Amir Zeb, Kwang-Hwi Cho, Haiyan Jin, Jongwan Kim, Onju Lee, Yunyun Wang* and Kyoung Tai No*
  JCIM | code

• Deep generative model for drug design from protein target sequence (IF = 8.6, JCR Q1, Journal of Cheminformatics (2023))
  Yangyang Chen, Zixu Wang, Lei Wang, Jianmin Wang, Pengyong Li, Dongsheng Cao, Xiangxiang Zeng, Xiucai Ye & Tetsuya Sakurai
  J Cheminform | code

• Explore drug-like space with deep generative models (IF = 4.8, JCR Q1, METHODS(2023))
  Jianmin Wang, Jiashun Mao, Meng Wang, Xiangyang Le, Yunyun Wang*
  Methods | code

📅2022

• Application of a deep generative model produces novel and diverse functional peptides against microbial resistance (IF = 6.155, JCR Q1, Computational and Structural Biotechnology Journal (2022))
  Jiashun Mao, Shenghui Guan, Yongqing Chen, Amir Zeb, Qingxiang Sun, Ranlan Lu, Jie Dong*, Jianmin Wang*, Dongsheng Cao*
  CSBJ | code

• Accurate prediction of molecular properties and drug targets using a self-supervised image representation learning framework (IF = 25.898, JCR Q1, Nature Machine Intelligence. (2022))
  Xiangxiang Zeng, Hongxin Xiang, Linhui Yu, Jianmin Wang, Kenli Li, Ruth Nussinov, Feixiong Cheng
  Nat Mach Intell | code

• Development of an innovative data-driven system to generate descriptive prediction equation of dielectric constant on small sample sets (IF = 3.776, JCR Q2, Heliyon (2022))
  Jiashun Mao, AmirZeb, Min-Sung Kim, Hyeon-Nae Jeon, Jianmin Wang, Shenghui Guan, Kyoung Tai NO
  Heliyon

• Molormer: a lightweight self-attention-based method focused on spatial structure of molecular graph for drug–drug interactions prediction (IF = 13.994, JCR Q1, Briefings in Bioinformatics (2022))
  Xudong Zhang , Gan Wang, Xiangyu Meng, Shuang Wang, Ying Zhang , Alfonso Rodriguez-Paton, Jianmin Wang* and Xun Wang*
  Brief. Bioinform. | code

• De novo molecular design with deep molecular generative models for PPI inhibitors (IF = 13.994, JCR Q1, Briefings in Bioinformatics (2022))
  Jianmin Wang, Yanyi Chu , Jiashun Mao , Hyeon-Nae Jeon, Haiyan Jin, Amir Zeb, Yuil Jang, Kwang-Hwi Cho, Tao Song and Kyoung Tai No
  Brief. Bioinform. | code

• A transformer-based model to predict peptide–HLA class I binding and optimize mutated peptides for vaccine design (IF = 25.898, JCR Q1, Nature Machine Intelligence (2022))
  Yanyi Chu, Yan Zhang, Qiankun Wang, Lingfeng Zhang, Xuhong Wang, Yanjing Wang, Dennis Russell Salahub, Qin Xu, Jianmin Wang, Xue Jiang, Yi Xiong & Dong-Qing Wei
  Nat Mach Intell | code

• Geometry-Based Molecular Generation With Deep Constrained Variational Autoencoder (IF = 14.255, JCR Q1, IEEE Transactions on Neural Networks and Learning Systems (2022))
  Chunyan Li, Junfeng Yao, Wei Wei, Zhangming Niu, Xiangxiang Zeng, Jin Li, Jianmin Wang
  IEEE TNNLS | code

📅2021

• A spatial-temporal gated attention module for molecular property prediction based on molecular geometry (IF = 13.994, JCR Q1, Briefings in Bioinformatics (2021))
  Chunyan Li, Jianmin Wang, Zhangming Niu, Junfeng Yao, Xiangxiang Zeng
  Brief. Bioinform. | code

• MUFFIN: multi-scale feature fusion for drug–drug interaction prediction (IF = 6.931, JCR Q1，Bioinformatics (2021))
  Yujie Chen, Tengfei Ma, Xixi Yang, Jianmin Wang, Bosheng Song, Xiangxiang Zeng
  Bioinformatics | code

• Design and linkage optimization of ursane-thalidomide-based PROTACs and identification of their targeted-degradation properties to MDM2 protein (IF = 5.307, JCR Q1, Bioorganic Chemistry (2021))
  Zhiwen Qi, Guliang Yang, Tao Deng, Jianmin Wang, Hao Zhou, Sergey A Popov, Elvira E Shults, Chengzhang Wang
  Bioorganic Chemistry

• Pretraining model for biological sequence data (IF = 4.840, JCR Q1, Briefings in functional genomics (2021))
  Bosheng Song, Zimeng Li, Xuan Lin, Jianmin Wang, Tian Wang, Xiangzheng Fu
  bifg

📅2020

• VGG16-T: A Novel Deep Convolutional Neural Network with Boosting to Identify Pathological Type of Lung Cancer in Early Stage by CT Images (IF = 2.259, JCR Q3，International Journal of Computational Intelligence Systems (2020）)
  Shanchen Pang, Meng Fan, Xun Wang, Jianmin Wang, Tao Song, Xingguang Wang, Xiaochun Cheng
  ijcis