Jianbo Qiao (乔剑博), a Ph.D. student at the School of Software Engineering, Shandong University. I graduated from Shandong University with a bachelor’s degree in software engineering in 2022. I am currently pursuing my Ph.D. in Professor Leyi Wei(魏乐义)’s research group (WeiLab). My research interests include artificial intelligence and bioinformatics, AI drug discovery, and genome sequence analysis. In recent years, more than 30 papers have been published, of which 13 have been published as co authors, co authors, or corresponding authors, such as Nature Communications (2025, 2026), Science China Information Sciences (TOP 1, CCF-A), and other top journals in the field. The related work has been cited more than 400 times, and currently the H-factor (Google) is 10.

🔥 News

2026.08: 🎉 One paper accepted by Nature Communications [Nature子刊, 一区TOP].
2026.07: 🎉 One paper accepted by Journal of Chemical Theory and Computation [一区TOP].
2026.07: 🎉 One paper accepted by Journal of Chemical Information and Modeling.
2026.07: 🎉 One paper accepted by ACS Synthetic Biology.
2026.06: 🤗 I have been awarded the Shandong University Academic Star · Outstanding Achievement Award（学术之星·优秀成果奖）.
2026.05: 🎉 One paper accepted by Journal of Cheminformatics [一区TOP].
2025.12: 🎉 One paper accepted by ACS Synthetic Biology.
2025.10: One paper accepted by Computational Biology and Chemistry.
2025.10: 🤗 I have been awarded the National Scholarship for Graduate Students（研究生国家奖学金）.
2025.08: One paper accepted by Methods.
2025.05: 🎉 One paper accepted by Science China Information Sciences [一区TOP, CCF-A].
2025.05: 🎉 One paper accepted by Neural Networks [一区TOP, CCF-B].
2025.04: 🎉 One paper accepted by Nature Communications [Nature子刊, 一区TOP].
2024.01: 🎉 One paper accepted by Information Sciences [一区TOP, CCF-B].

📖 Educations

2022.09 - now, Artificial Intelligence, PhD student, Shandong University, Jinan, China.
2018.09 - 2022.06, Software Engineering, Bachelor’s Degree, Shandong University, Jinan, China.

📝 Publications

Nat. Commun.

A self-conformation-aware pre-training framework for molecular property prediction with substructure interpretability.
Jianbo Qiao#, Junru Jin#, Ding Wang#, Saisai Teng, Junyu Zhang, Xuetong Yang, Yuhang Liu, Yu Wang, Lizhen Cui, Quan Zou, Ran Su, Leyi Wei. Nature Communications, 2025. [Nature子刊, 一区TOP].

Nat. Commun.

Decoding the Sequence Determinants of Locus Specific DNA Methylation Across Human Tissues.
Junru Jin#, Ding Wang#, Jianbo Qiao#, Wenjia Gao, Yuhang Liu, Siqi Chen, Quan Zou, Shu Wu, Ran Su, Leyi Wei. Nature Communications, 2026. [Nature子刊, 一区TOP].

Sci. China Inf. Sci.

Molecular pretraining models towards molecular property prediction.
Jianbo Qiao, Wenjia Gao, Junru Jin, Ding Wang, Xu Guo, Balachandran Manavalan, Leyi Wei. Science China Information Sciences, 2025. [一区TOP, CCF-A].

J. Chem. Theory Comput.

Relation-Aware Pretraining and Reaction Center Modeling for Chemical Reaction Graph Representation Learning.
Jianbo Qiao#, Kefei Li#, Junru Jin, Ding Wang, Wenjia Gao, Shaoye Zhang, Shuan Liu, Leyi Wei. Journal of Chemical Theory and Computation, 2026. [一区TOP].

Neural Netw.

Taco-DDI: accurate prediction of drug-drug interaction events using graph transformers and dynamic co-attention matrices.
Jianbo Qiao, Xu Guo, Junru Jin, Ding Wang, Kefei Li, Wenjia Gao, Feifei Cui, Zilong Zhang, Hua Shi, Leyi Wei. Neural Networks, 2025. [一区TOP, CCF-B].

Inf. Sci.

Towards retraining-free RNA modification prediction with incremental learning.
Jianbo Qiao, Junru Jin, Haoqing Yu, Leyi Wei. Information Sciences, 2024. [一区TOP, CCF-B].

FGSGT-DDI: LLM-Enhanced Functional Group Semantic Graph Transformer for Drug–Drug Interaction Prediction.
Kefei Li#, Jianbo Qiao#, Yuntao Yang, Hanjun Zhao, Ding Wang, Junru Jin, Zhongmin Yan, Leyi Wei. Journal of Chemical Information and Modeling, 2026.
An Explainable Deep Learning Framework Integrating DNA Sequence and Transcription Initiation Signals for Gene Expression Prediction.
Jianbo Qiao#, Wenjia Gao#, Ding Wang#, Junru Jin#, Siqi Chen, Zhongmin, Yan, Leyi Wei. ACS Synthetic Biology, 2026.
CataCon: a contrastive graph representation learning framework for catalyst prediction.
Hua Shi, Yuzhe Wang, Shouzhen Song, Kefei Li, Wenjia Gao, Shuan Liu, Jianbo Qiao*, Leyi Wei*. Journal of Cheminformatics, 2026. [一区TOP].
FGMA: A Functional Group-enhanced Deep Learning Method for Drug Toxicity Prediction.
Yue Cheng#, Jianbo Qiao#, Siqi Chen, Leyi Wei, Guangmin Liang. Current Drug Targets, 2026.
ABT-DDI: A Graph Transformer Model with Atomic-Bond Structure Awareness for Drug–Drug Interaction Prediction.
Xu Guo#, Jianbo Qiao#, Siqi Chen, Junru Jin, Ding Wang, Wenjia Gao, Feifei Cui, Zilong Zhang, Hua Shi, Zhongmin Yan, Leyi Wei, Xinbo Jiang. ACS Synthetic Biology, 2025.
TK-DDI: Accurate and efficient drug-drug interaction prediction via token encoding.
Yue Cheng#, Jianbo Qiao#, Siqi Chen, Leyi Wei, Guangmin Liang. Computational Biology and Chemistry, 2025.
Efficient RNA nucleotide encoding enhances the accurate prediction of ac4C modifications.
Na Li*, Xiao Wang, Ming Zeng, Feng Cao, Ke Qiu, Jianbo Qiao*. Methods, 2025.

A Token-Pruning Framework Enables Efficient Representation of the Human Genome for RNA Modification Analysis.
Wenjia Gao, Junlei Yu, Junru Jin, Jiajie Cai, Ke Qiu, Shun Zhang, Jianbo Qiao, Leyi Wei. Bioinformatics, 2026. [CCF-A].
Hyp-retro: hypernetwork-guided preference-conditioned retrosynthetic planner.
Jingwen Wang, Shuan Liu, Shaoye Zhang, Jianbo Qiao, Guanhe Li, Hanjun Zhao, Xiangxiang Zeng, Jinjin Li, Changhang Lin, Chen Su, Leyi Wei. Molecular Diversity, 2026.
PeptideSGCL: Structure-enhanced graph-transformer encoding and dual-level contrastive learning for peptide property prediction.
Jiajie Cai, Shuwen Xiong, Yuntao Yang, Hanjun Zhao, Jianbo Qiao, Zhongmin Yan, Ran Su, Xinbo Jiang, Lichao Zhang, Leyi Wei. ACS Synthetic Biology, 2026.
CMA-Nano: A DNA Methylation Detection Method for Nanopore Sequencing Data Based on a Cross-Modal Attention Mechanism.
Hua Shi, Chenglin Yin, Jianbo Qiao, Wenjia Gao, Leyi Wei. ACS Omega, 2026.
Accurate and interpretable ADMET prediction: Integrating structural, geometric, and global molecular context representations.
Ke Qiu, Kefei Li, Jianbo Qiao, Ding Wang, Junru Jin, Zhongmin Yan, Ka-Chun Wong, Leyi Wei. European Journal of Medicinal Chemistry, 2026.
Structure-Aware Multimodal Learning Improves Minor-Class Signal Peptide Prediction.
Yuntao Yang, Shuwen Xiong, Siqi Chen, Jianbo Qiao, Hanjun Zhao, Zhongmin Yan, Leyi Wei. ACS Synthetic Biology, 2026.
HGCPep: Hypergraph Deep Learning Identifies Cancer-associated Non-coding Peptides.
Wentao Long, Zhongshen Li, Junru Jin, Jianbo Qiao, Yu Wang, Leyi Wei. Genomics, Proteomics & Bioinformatics, 2025. [一区TOP].
Accurate detection and quantification of single-base m6A RNA modification using nanopore signals with multi-view deep learning.
Jun Zhang, Jianbo Qiao, Zhiqun Zhao, Chenglin Yin, Junru Jin, Ding Wang, Wenjia Gao, Leyi Wei. bioRxiv, 2025.
MCAMEF-BERT: an efficient deep learning method for RNA N7-methylguanosine site prediction via multi-branch feature integration.
Junlei Yu, Wenjia Gao, Siqi Chen, Ronglin Lu, Jianbo Qiao, Junru Jin, Leyi Wei, Hua Shi, Zilong Zhang, Feifei Cui, Xinbo Jiang, Zhongmin Yan. Briefings in Bioinformatics, 2025. [二区TOP, CCF-B].
EDNTOM: An Ensemble Learning and Weight Mechanism-Based Nanopore Methylation Detection Tool.
Ge Tian, Chenglin Yin, Jianbo Qiao, Ruheng Wang, Hua Shi, Feifei Cui, Zilong Zhang, Xinbo Jiang, Leyi Wei. ACS Omega, 2025. [二区TOP].
GICL: A Cross-Modal Drug Property Prediction Framework Based on Knowledge Enhancement of Large Language Models.
Na Li, Jianbo Qiao, Fei Gao, Yanling Wang, Hua Shi, Zilong Zhang, Feifei Cui, Lichao Zhang, Leyi Wei. Journal of Chemical Information and Modeling, 2025. [二区TOP].
MC-MSTLoc: Self-supervised Pre-training for Imbalanced Multi-label Protein Subcellular Localization Prediction Using Immunofluorescence Images.
Fengsheng Wang, Jianbo Qiao, Xu Guo, Leyi Wei. IEEE Transactions on Computational Biology and Bioinformatics (TCBB), 2025. [CCF-B].
Computational models for prediction of m6A sites using deep learning.
Nan Sheng, Jianbo Qiao, Leyi Wei, Hua Shi, Huannan Guo, Changshun Yang. Methods, 2025.
ERNIE-ac4C: A novel deep learning model for effectively predicting N4-acetylcytidine sites.
Ronglin Lu, Jianbo Qiao, Kefei Li, Yanxi Zhao, Junru Jin, Feifei Cui, Zilong Zhang, Balachandran Manavalan, Leyi Wei. Journal of Molecular Biology, 2025.
Moss-m7G: A motif-based interpretable deep learning method for RNA N7-methlguanosine site prediction.
Yanxi Zhao, Junru Jin, Wenjia Gao, Jianbo Qiao, Leyi Wei. Journal of Chemical Information and Modeling, 2024. [二区TOP].
NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection.
Chenglin Yin, Ruheng Wang, Jianbo Qiao, Hua Shi, Hongliang Duan, Xinbo Jiang, Saisai Teng, Leyi Wei. Bioinformatics, 2024. [CCF-A].
Multi-CGAN: deep generative model-based multiproperty antimicrobial peptide design.
Haoqing Yu, Ruheng Wang, Jianbo Qiao, Leyi Wei. Journal of Chemical Information and Modeling, 2023. [二区TOP].
Deep Generative Models in De Novo Drug Molecule Generation.
Chao Pang, Jianbo Qiao, Xiangxiang Zeng, Quan Zou, Leyi Wei. Journal of Chemical Information and Modeling, 2023. [二区TOP].
Rm-LR: a long-range-based deep learning model for predicting multiple types of RNA modifications.
Sirui Liang, Yanxi Zhao, Junru Jin, Jianbo Qiao, Ding Wang, Yu Wang, Leyi Wei. Computers in Biology and Medicine, 2023.
Clinical Phenotyping Prediction via Auxiliary Task Selection and Adaptive Shared-Space Correction.
Xiao Yang, Ning Liu, Jianbo Qiao, Haitao Yuan, Teng Ma, Yonghui Xu, Lizhen Cui. CAAI International Conference on Artificial Intelligence (CICAI), 2022.

🎖 Honors and Awards

2026.06 Shandong University Academic Star · Outstanding Achievement Award（学术之星·优秀成果奖）.
2025.10 National Scholarship for Graduate Students（研究生国家奖学金）.

💬 Invited Talks

Predicting RNA modifications without retraining through incremental learning. The Second CCF Bioinformatics “New Future” Young Scholars (BIO-3NEW) Symposium.2024.04.

✏️ Academic Activities

Topic Coordinators

Frontiers in Neurology. See our Research Topic

Conference Reviewer

ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)

Journal Reviewer

IEEE Transactions on Neural Networks and Learning Systems (TNNLS)
Engineering Applications of Artificial Intelligence (EAAI)
IEEE Journal of Biomedical and Health Informatics (JBHI)
Molecular Diversity
Scientific Reports
Chemical Papers
International Journal of Data Science and Analytics
BMC Bioinformatics
BMC Medical Genomics
BMC Artificial Intelligence
Journal of King Saud University Computer and Information Sciences
Discover Applied Sciences
In Silico Pharmacology