[Your Name]

Yi-Heng Zhu, Ph.D.

College of Artificial Intelligence, Nanjing Agricultural University
Address: 1 Weigang Street, Nanjing, Jiangsu, China, 210095
Email: yihzhu@njau.edu.cn
GitHub: https://github.com/yiheng-zhu
Chinese Version

About Me

Yi-Heng Zhu received his Ph.D. degree in control science and engineering from Nanjing University of Science and Technology in 2023, led by Professor Dong-Jun Yu. From 2019 to 2021, he acted as a visiting Ph.D. student at University of Michigan (Ann Arbor), funded by China Scholarship Council and led by Professor Yang Zhang. He is currently a lecturer at the College of Artificial Intelligence, Nanjing Agricultural University.

Education

Research

Protein Function Prediction [Papers]

Developing computational methods to accurately predict protein functions in the context of Gene Ontology from sequence and structure data.

Enzyme Function Prediction [Papers]

Developing computational methods to annotate the functions for enzymes using Enzyme Commission Number from sequence and structure data.

Protein-Ligand Binding Sites Prediction [Papers]

Developing deep learning methods to identify and characterize binding bindings and pockets for drug discovery applications.

Protein Crystallization Prediction [Papers]

Machine learning approaches to predict crystallization propensity and optimize conditions for structural biology studies.

Protein-Drug Interaction Prediction [Papers]

Computational models to predict and analyze interactions between pharmaceutical compounds and target proteins.

Transcription Factor Binding Site Prediction [Papers]

Computational identification of transcription factor binding sites and their regulatory mechanisms.

Large Language Models in Bioinformatics [Papers]

Adapting transformer-based architectures for biological sequence analysis and knowledge extraction.

Research Projects & Grants

High-Accuracy Protein Function Prediction through Fusing Multi-Source Heterogeneous Data (2025-2027)
National Natural Science Foundation of China (Youth Program), No.62402227.
High-Accuracy Protein Function Prediction through Biological Large Language Model (2025-2026)
Fundamental Research Funds for the Central Universities, No.YDZX2025024.
High-Accuracy Protein Function Prediction through Deep Learning Methods (2019-2021)
The Award of China Scholarship Council, No.201906840041.

Publications

2025

Machine Learning for Protein Function Prediction.
Yi-Heng Zhu, Zi Liu, Yu Ding, Zhiwei Ji*, Dong-Jun Yu*.
In: Kurgan, L., Kihara, D. (eds) Protein Function Prediction. Methods in Molecular Biology, vol 2947. Humana, New York, NY.
DOI: https://doi.org/10.1007/978-1-0716-4662-5_2, [PDF]
MKFGO: Integrating Multi-Source Knowledge Fusion with Pre-Trained Language Model for High-Accuracy Protein Function Prediction.
Yi-Heng Zhu, Shuxin Zhu, Xuan Yu, He Yan, Yan Liu, Xiaojun Xie, Dong-Jun Yu*, Rui Ye*.
Briefings in Bioinformatics, [PDF], [Web Server], [Source Code].
Deep Learning-Based Single- and Multi-Domain Protein Structure Prediction with D-I-TASSER.
Wei Zheng, Qiqige Wuyun, Yang Li, Quancheng Liu, Xiaogen Zhou, Chunxiang Peng, Yi-Heng Zhu, Lydia Freddolino *, Yang Zhang *.
Nature Biotechnology.
A Comprehensive Review of Computational Methods for Protein-DNA Binding Site Prediction.
Zi Liu, Wang-Ren Qiu, Yan Liu, He Yan, Wenyi Pei*, Yi-Heng Zhu*, and Jing Qiu*.
Analytical Biochemistry, [PDF].
MutPIN: A Unified Model Architerture for Accurately Predicting the Effects of Mutations on Protein-Nucleic Acid Interactions.
Zi-Hao Yan, Fang Ge, Ying Zhang, He Yan, Yi-Heng Zhu, Jiangning Song*, and Dong-Jun Yu*.
Journal of Chemical Information and Modeling.
Identifying Protein-Nucleotide Binding Residues via Grouped Multi-Task Learning and Pre-Trained Protein Language Models.
Jia-Shun Wu, Yan Liu, Ying Zhang, Xiaoyu Wang, He Yan, Yi-Heng Zhu, Jiangning Song*, and Dong-Jun Yu*.
Journal of Chemical Information and Modeling.
A Systematic Review of Computational Methods for Protein-Translational Modification Site Prediction.
Yuan-Yuan Li, Zi Liu*, Xin Liu, Yi-Heng Zhu, Conghui Fang,Muhammad Arif, Wang-Ren Qiu *
Archives of Computational Methods in Engineering.
UniMethylNet: A Universal DNA Methylation Site Prediction Network Integrating a Neural Network and an Attention Mechanism.
Mingyue Zhang, Hongwei Wang, Yu Ding, Yi-Heng Zhu, Huanliang Xu, Honggui La, Zhenxing Wang, Zhaoyu Zhai*
Journal of Chemical Information and Modeling.

2024

ULDNA: Integrating Unsupervised Multi-Source Language Models with LSTM-Attention Network for High-Accuracy Protein-DNA Binding Site Prediction.
Yi-Heng Zhu, Zi Liu, Zhiwei Ji*, Dong-Jun Yu*.
Briefings in Bioinformatics, [PDF], [Web Server], [Source Code].
Improving Antifreeze Proteins Prediction with Protein Language Models and Hybrid Feature Extraction Network.
Jiashun Wu, Yan Liu, Yi-Heng Zhu, Dong-Jun Yu*.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.
BLAM6A-Merge: Leveraging Attention Mechanisms and Feature Fusion Strategies to Improve the Identification of RNA N6-methyladenosine Sites.
Yunpeng Xia, Ying Zhang, Dian Liu, Yi-Heng Zhu, Zhikang Wang, Jiangning Song*, and Dong-Jun Yu*.
IEEE/ACM Transactions on Computational Biology and Bioinformatics.

2023

Integrating Unsupervised Language Model with Multi-View Multiple Sequence Alignments for High-Accuracy Inter-Chain Contact Prediction.
Zi Liu#, Yi-Heng Zhu#, Long-Chen Shen, Xuan Xiao, Wang-Ren Qiu, Dong-Jun Yu.
Computers in Biology and Medicine, [PDF], [Source Code].
GCmapCrys: Integrating Graph Attention Network with Predicted Contact Map for Multi-Stage Protein Crystallization Propensity Prediction.
Peng-Hao Wang#, Yi-Heng Zhu#, Xibei Yang, Dong-Jun Yu.
Analytical Biochemistry [PDF], [Source Code].

2022

Integrating Unsupervised Language Model with Triplet Neural Networks for Protein Gene Ontology Prediction.
Yi-Heng Zhu, Chengxin Zhang, Dongjun Yu*, Yang Zhang*.
PLOS Computational Biology [PDF], [Web Server].
TripletGO: Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction.
Yi-Heng Zhu, Chengxin Zhang, Yan Liu, Gilbert Omenn, Peter Freddolino, Dongjun Yu*, Yang Zhang*.
Genomics, Proteomics & Bioinformatics [PDF], [Web Server].
MAResNet: Predicting Transcript Factor Binding Sites by Combining Multi-Scale Bottom-Up and Top-Down Attention and Residual Network.
Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song*, and Dong-Jun Yu*.
Briefings in Bioinformatics.

2021

Accurate Multi-Stage Prediction of Protein Crystallization Propensity Using Deep-Cascade Forest with Sequence-Based Features.
Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song*, Yang Zhang*, Dong-Jun Yu*.
Briefings in Bioinformatics [PDF], [Web Server].
Improving Protein Fold Recognition Using Triplet Network and Ensemble Deep Learning.
Yan Liu, Ken Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu*.
Briefings in Bioinformatics.
Why Can Deep Convolutional Neural Networks Improve Protein Fold Recognition? A visual Explanation by Interpretation.
Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song*, Dong-Jun Yu*.
Briefings in Bioinformatics.
MutTMPredictor: Robust and Accurate Cascade XGBoost Classifier for Prediction of Disease-Associated Mutations in Transmembrane Proteins.
Fang Ge, Yi-Heng Zhu, Jian Xu, Arif Muhammad, Jiangning Song*, and Dong-Jun Yu*.
Computational and Structural Biotechnology Journal.
TargetDBP+: Enhancing the Performance of Identifying DNA-Binding Proteins via Weighted Convolutional Features.
Jun Hu, Liang Rao, Yi-Heng Zhu, Gui-Jun Zhang, Dong-Jun Yu*.
Journal of Chemical Information and Modeling.

2020

MetaGOPlus: Improving Gene Ontology Prediction of Proteins Using Deep Residual Network with Hierarchical Classification.
Yi-Heng Zhu, Chengxin Zhang, Rucheng Diao, Xiaogen Zhou, Peter Freddolino*, Dongjun Yu*, Yang Zhang*.
The 28th Conference on Intelligent Systems for Molecular Biology (ISMB 2020), [PDF], [Link]
SSCpred: Single-Sequence-Based Protein Contact Prediction Using Deep Fully Convolutional Network.
Ming-Cai Chen, Yang Li, Yi-Heng Zhu, Fang Ge, Dong-Jun Yu*.
Journal of Chemical Information and Modeling.

2019

DNAPred: Accurate Identification of DNA-binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines.
Yi-Heng Zhu, Jun Hu, Xiao-Ning Song, Dong-Jun Yu*.
Journal of Chemical Information and Modeling, [PDF], [Web Server].
Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites.
Yi-Heng Zhu, Jun Hu, Yong Qi, Xiao-Ning Song, Dong-Jun Yu.
Combinatorial Chemistry & High Throughput Screening, [PDF], [Web Server].

Online Web Services/Tools

ULDNA Screenshot

MKFGO

Protein Function Prediction

Integrating Multi-Source Knowledge Fusion with Pre-Trained Language Model for High-Accuracy Protein Function Prediction

Brief. Binform. (2025) Access Tool
ULDNA Screenshot

ULDNA

Protein-DNA binding site prediction

Integrating Unsupervised Multi-Source Language Models with LSTM-Attention Network for High-Accuracy Protein-DNA Binding Site Prediction

Brief. Binform. (2024) Access Tool
ICCPred Screenshot

ICCPred

Protein-protein contact map prediction

Integrating Unsupervised Language Model with Multi-View Multiple Sequence Alignments for High-Accuracy Inter-Chain Contact Prediction

Comput. Biol. Med. (2023) Access Tool
ATGO Screenshot

ATGO

Protein function prediction

Integrating Unsupervised Language Model with Triplet Neural Networks for Protein Gene Ontology Prediction

PLOS Comp. Biol. (2022) Access Tool
TripletGO Screenshot

TripletGO

Protein function prediction

Integrating Transcript Expression Profiles with Protein Homology Inferences for Gene Function Prediction

GPB (2022) Access Tool
DCFCrystal Screenshot

DCFCrystal

Protein crystallization prediction

Accurate Multi-Stage Prediction of Protein Crystallization Propensity Using Deep-Cascade Forest with Sequence-Based Features

Brief. Binform. (2021) Access Tool
DNAPred Screenshot

DNAPred

Protein-DNA binding site prediction

Accurate Identification of DNA-binding Sites from Protein Sequence by Ensembled Hyperplane-Distance-Based Support Vector Machines

J. Chem. Inf. Model. (2019) Access Tool
BGSVM-NUC Screenshot

BGSVM-NUC

Protein-nucleotide binding sites prediction

Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites

Comb. Chem. & HTS (2019) Access Tool
GCMapCrys Screenshot

GCMapCrys

Protein crystallization prediction

Integrating Graph Attention Network with Predicted Contact Map for Multi-Stage Protein Crystallization Propensity Prediction

Anal. Biochem. (2023) Access Tool

Academic Committees

Member: China Computer Federation, Jiangsu Society of Bioinformatics.
Journal Reviewer: Briefings in Bioinformatics, IEEE-ACM Transactions on Computational Biology and Bioinformatics, Journal of Cheminformatics, BMC Bioinformatics, Science Reports, Computational and Structural Biotechnology Journal.
Reviewer Certificate: IEEE-ACM Transactions on Computational Biology and Bioinformatics [Certification].

Teaching

Algorithm Design and Analysis [Teaching Materials]
Computer Operating System [Teaching Materials]
Bioinformatics [Teaching Materials]
Python Programming [Teaching Materials]
VB.NET Programming [Teaching Materials]
IT Fundamentals [Teaching Materials]