Research Output

Publications

^* corresponding author · bold = first author

2026

Interpretable deep learning framework for mapping E3–substrate binding interfaces

Dianke Li, Yuting Zhang, Yuan Liu, Zihao Zhang, Yingjie Qu, Jiajun Li, Linyang Jiang, Lihong Diao, Ziding Zhang^*, Lingqiang Zhang^*, Chun-Ping Cui & Dong Li^*

Nature Communications, 2026.

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2025

PPEPFinder: A deep learning framework integrating sequence embeddings and structural graph representations for predicting fungal and oomycete effector proteins

Mengdi Yuan, Shaoke Zhang, Jiajun Li, Jingyan Zheng, Chenping Lei, Zhuojun Wang, Miao Zhao, Wenyu Shi^*, Ziding Zhang^*

The plant journal, 2025.

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Graph neural network integrated with pretrained protein language model for predicting human–virus protein–protein interactions

Linyang Jiang, Xiaodi Yang, Xiaokun Guo, Dianke Li, Jiajun Li, Stefan Wuchty, Wenyu Shi^*, Ziding Zhang^*

Briefings in Bioinformatics, 2025.

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2024

POOE: predicting oomycete effectors based on a pre-trained large protein language model

Miao Zhao, Chenping Lei, Kewei Zhou, Yan Huang, Chen Fu, Shiping Yang^*, Ziding Zhang^*

mSystems, 2024.

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Multi-modal features-based human-herpesvirus protein–protein interaction prediction by using LightGBM

Xiaodi Yang, Stefan Wuchty, Zeyin Liang, Li Ji, Bingjie Wang, Jialin Zhu, Ziding Zhang^*, Yujun Dong^*

Briefings in Bioinformatics, 2024.

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Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome

Pan Zhang, Biliang Zhang, Yuan‐Yuan Ji, Jian Jiao, Ziding Zhang^*, Chang‐Fu Tian^*

mLife, 2024.

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2023

SGPPI: structure-aware prediction of protein–protein interactions in rigorous conditions with graph convolutional network

Yan Huang, Stefan Wuchty, Yuan Zhou^*, Ziding Zhang^*

Briefings in Bioinformatics, 2023.

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Deep learning‐assisted prediction of protein–protein interactions in Arabidopsis thaliana

Jingyan Zheng, Xiaodi Yang, Yan Huang, Shiping Yang, Stefan Wuchty, Ziding Zhang^*

The Plant Journal, 2023.

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PlaASDB: a comprehensive database of plant alternative splicing events in response to stress

Xiaokun Guo, Tianpeng Wang^*, Linyang Jiang, Huan Qi, Ziding Zhang^*

BMC Plant Biology, 2023.

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Pre-trained protein language model sheds new light on the prediction of Arabidopsis protein–protein interactions

Kewei Zhou, Chenping Lei, Jingyan Zheng, Yan Huang, Ziding Zhang^*

Plant Methods, 2023.

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AraPathogen2.0: An Improved Prediction of Plant–Pathogen Protein–Protein Interactions Empowered by the Natural Language Processing Technique

Chenping Lei, Kewei Zhou, Jingyan Zheng, Miao Zhao, Yan Huang, Huaqin He, Shiping Yang^*, Ziding Zhang^*

Journal of Proteome Research, 2023.

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2022

Understanding the influence of AMG 510 on the structure of KRASG12C empowered by molecular dynamics simulation

Yu Li, Lei Han^*, Ziding Zhang^*

Computational and Structural Biotechnology Journal, 2022.

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ASTool: An Easy-to-Use Tool to Accurately Identify Alternative Splicing Events from Plant RNA-Seq Data

Huan Qi, Xiaokun Guo, Tianpeng Wang, Ziding Zhang^*

International Journal of Molecular Sciences, 2022.

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Deep Learning-Powered Prediction of Human-Virus Protein-Protein Interactions

Xiaodi Yang, Shiping Yang, Panyu Ren, Stefan Wuchty, Ziding Zhang^*

Frontiers in Microbiology, 2022.

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Proteome-wide prediction and analysis of the Cryptosporidium parvum protein–protein interaction network through integrative methods

Panyu Ren, Xiaodi Yang, Tianpeng Wang, Yunpeng Hou^*, Ziding Zhang^*

Computational and Structural Biotechnology Journal, 2022.

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The zinc-finger bearing xenogeneic silencer MucR in α-proteobacteria balances adaptation and regulatory integrity

Jian Jiao, Biliang Zhang, Meng-Lin Li, Ziding Zhang^*, Chang-Fu Tian^*

The ISME Journal, 2022.

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Sympatric Recombination in Zoonotic Cryptosporidium Leads to Emergence of Populations with Modified Host Preference

Tianpeng Wang, Yaqiong Guo, Dawn M Roellig, Na Li, Mónica Santín, Jason Lombard, Martin Kváč, Doaa Naguib, Ziding Zhang^*, Yaoyu Feng^*, Lihua Xiao^*

Molecular Biology and Evolution, 2022.

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AbAgIntPre: A deep learning method for predicting antibody-antigen interactions based on sequence information

Yan Huang, Ziding Zhang^*, Yuan Zhou^*

Frontiers in Immunology, 2022.

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2021

Lineage-Specific Rewiring of Core Pathways Predating Innovation of Legume Nodules Shapes Symbiotic Efficiency

Wen-Jing Cui, Biliang Zhang, Ran Zhao, Li-Xue Liu, Jian Jiao, Ziding Zhang^*, Chang-Fu Tian^*

mSystems, 2021.

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HVIDB: a comprehensive database for human–virus protein–protein interactions

Xiaodi Yang, Xianyi Lian, Chen Fu, Stefan Wuchty, Shiping Yang^*, Ziding Zhang^*

Briefings in Bioinformatics, 2021.

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Current status and future perspectives of computational studies on human–virus protein–protein interactions

Xianyi Lian, Xiaodi Yang, Shiping Yang^*, Ziding Zhang^*

Briefings in Bioinformatics, 2021.

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Transfer learning via multi-scale convolutional neural layers for human–virus protein–protein interaction prediction

Xiaodi Yang, Shiping Yang, Xianyi Lian, Stefan Wuchty^*, Ziding Zhang^*

Bioinformatics, 2021.

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2020

Enhancing thermostability of a psychrophilic alpha-amylase by the structural energy optimization in the trajectories of molecular dynamics simulations

Qingbin Li, Yaru Yan, Xiaoqing Liu, Ziding Zhang^*, Jian Tian^*, Ningfeng Wu

International Journal of Biological Macromolecules, 2020.

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PlaPPISite: a comprehensive resource for plant protein-protein interaction sites

Xiaodi Yang, Shiping Yang, Huan Qi, Tianpeng Wang, Hong Li^*, Ziding Zhang^*

BMC Plant Biology, 2020.

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Prediction of human-virus protein-protein interactions through a sequence embedding-based machine learning method

Xiaodi Yang, Shiping Yang, Qinmengge Li, Stefan Wuchty, Ziding Zhang^*

Computational and Structural Biotechnology Journal, 2020.

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The MERS-CoV Receptor DPP4 as a Candidate Binding Target of the SARS-CoV-2 Spike

Yu Li, Ziding Zhang, Li Yang, Xianyi Lian, Yan Xie, Shen Li, Shuyu Xin, Pengfei Cao, Jianhong Lu^*

iScience, 2020.

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Human Gene Functional Network-Informed Prediction of HIV-1 Host Dependency Factors

Chen Fu, Shiping Yang, Xiaodi Yang, Xianyi Lian, Yan Huang, Xiaobao Dong, Ziding Zhang^*

mSystems, 2020.

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Prediction and analysis of human‐herpes simplex virus type 1 protein‐protein interactions by integrating multiple methods

Xianyi Lian, Xiaodi Yang, Jiqi Shao, Fujun Hou, Shiping Yang^*, Dongli Pan, Ziding Zhang^*

Quantitative Biology, 2020.

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2019

Understanding Human-Virus Protein-Protein Interactions Using a Human Protein Complex-Based Analysis Framework

Shiping Yang, Chen Fu, Xianyi Lian, Xiaobao Dong, Ziding Zhang^*

mSystems, 2019.

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Machine-Learning-Based Predictor of Human–Bacteria Protein–Protein Interactions by Incorporating Comprehensive Host-Network Properties

Xianyi Lian, Shiping Yang, Hong Li, Chen Fu, Ziding Zhang^*

Journal of Proteome Research, 2019.

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The hybrid protein interactome contributes to rice heterosis as epistatic effects

Hong Li, Shuqin Jiang, Chen Li, Lei Liu, Zechuan Lin, Hang He, Xing‐Wang Deng, Ziding Zhang^*, Xiangfeng Wang^*

The Plant Journal, 2019.

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2018

PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System

Huan Qi, Zhenhong Jiang, Kang Zhang, Shiping Yang, Fei He^*, Ziding Zhang^*

Genomics, Proteomics & Bioinformatics, 2018.

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2017

Critical assessment and performance improvement of plant–pathogen protein–protein interaction prediction methods

Shiping Yang, Hong Li, Huaqin He, Yuan Zhou^*, Ziding Zhang^*

Briefings in Bioinformatics, 2017.

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Large-scale transcriptome analysis reveals arabidopsis metabolic pathways are frequently influenced by different pathogens

Zhenhong Jiang, Fei He, Ziding Zhang^*

Plant Molecular Biology, 2017.

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Network Analysis Reveals a Common Host–Pathogen Interaction Pattern in Arabidopsis Immune Responses

Hong Li, Yuan Zhou^*, Ziding Zhang^*

Frontiers in Plant Science, 2017.

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An Important Role for Purifying Selection in Archaeal Genome Evolution

Zhe Lyu, Zhi-Gang Li, Fei He, Ziding Zhang^*

mSystems, 2017.

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2016

Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections

Zhenhong Jiang, Xiaobao Dong, Ziding Zhang^*

Scientific Reports, 2016.

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Identification of WD40 repeats by secondary structure-aided profile–profile alignment

Chuan Wang, Xiaobao Dong, Lei Han, Xiao-Dong Su, Ziding Zhang^*, Jinyan Li^*, Jiangning Song^*

Journal of Theoretical Biology, 2016.

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SPAR: a random forest-based predictor for self-interacting proteins with fine-grained domain information

Xuhan Liu, Shiping Yang, Chen Li, Ziding Zhang^*, Jiangning Song^*

Amino Acids, 2016.

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Systems understanding of plant–pathogen interactions through genome-wide protein–protein interaction networks

Hong Li, Ziding Zhang^*

Frontiers of Agricultural Science and Engineering, 2016.

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AraPPISite: a database of fine-grained protein–protein interaction site annotations for Arabidopsis thaliana

Hong Li, Shiping Yang, Chuan Wang, Yuan Zhou^*, Ziding Zhang^*

Plant Molecular Biology, 2016.

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Differential Coexpression Analysis Reveals Extensive Rewiring of Arabidopsis Gene Coexpression in Response to Pseudomonas syringae Infection

Zhenhong Jiang, Xiaobao Dong, Zhi-Gang Li, Fei He^*, Ziding Zhang^*

Scientific Reports, 2016.

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2015

Computational characterization of parallel dimeric and trimeric coiled-coils using effective amino acid indices

Chen Li, Xiao-Feng Wang, Zhen Chen, Ziding Zhang^*, Jiangning Song^*

Molecular BioSystems, 2015.

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Revealing Shared and Distinct Gene Network Organization in Arabidopsis Immune Responses by Integrative Analysis

Xiaobao Dong, Zhenhong Jiang, You-Liang Peng, Ziding Zhang^*

Plant Physiology, 2015.

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Computational Identification of Protein Pupylation Sites by Using Profile-Based Composition of k-Spaced Amino Acid Pairs

Md. Mehedi Hasan, Yuan Zhou, Xiaotian Lu, Jinyan Li, Jiangning Song, Ziding Zhang^*

PLOS ONE, 2015.

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BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors

Xiaobao Dong, Xiaotian Lu, Ziding Zhang^*

Database, 2015.

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MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins

Yuan Zhou, Shiping Yang, Tonglin Mao, Ziding Zhang^*

Database, 2015.

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2014

Prediction of outer membrane proteins by combining the position- and composition-based features of sequence profiles

Renxiang Yan, Jun Lin, Zhen Chen, Xiaofeng Wang, Lanqing Huang, Weiwen Cai, Ziding Zhang^*

Molecular BioSystems, 2014.

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GPCRserver: an accurate and novel G protein-coupled receptor predictor

Renxiang Yan, Xiaofeng Wang, Lanqing Huang, Jun Lin, Weiwen Cai, Ziding Zhang^*

Mol. BioSyst., 2014.

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Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features

Yuan Li, Mingjun Wang, Huilin Wang, Hao Tan, Ziding Zhang^*, Geoffrey I. Webb^*, Jiangning Song^*

Scientific Reports, 2014.

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Operating Mechanism and Molecular Dynamics of Pheromone-Binding Protein ASP1 as Influenced by pH

Lei Han, Yong-Jun Zhang, Long Zhang, Xu Cui, Jinpu Yu, Ziding Zhang^*, Ming S. Liu^*

PLoS ONE, 2014.

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Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features

Zhen Chen, Yuan Zhou, Ziding Zhang^*, Jiangning Song^*

Briefings in Bioinformatics, 2014.

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2013

Using Weakly Conserved Motifs Hidden in Secretion Signals to Identify Type-III Effectors from Bacterial Pathogen Genomes

Xiaobao Dong, Yong-Jun Zhang, Ziding Zhang^*

PLoS ONE, 2013.

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hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties

Zhen Chen, Yuan Zhou, Jiangning Song^*, Ziding Zhang^*

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2013.

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ZincExplorer: an accurate hybrid method to improve the prediction of zinc-binding sites from protein sequences

Zhen Chen, Yanying Wang, Ya-Feng Zhai, Jiangning Song^*, Ziding Zhang^*

Molecular BioSystems, 2013.

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Structural Propensities of Human Ubiquitination Sites: Accessibility, Centrality and Local Conformation

Yuan Zhou, Sixue Liu, Jiangning Song^*, Ziding Zhang^*

PLoS ONE, 2013.

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2012

Identification of Catalytic Residues Using a Novel Feature that Integrates the Microenvironment and Geometrical Location Properties of Residues

Lei Han, Yong-Jun Zhang, Jiangning Song, Ming S. Liu^*, Ziding Zhang^*

PLoS ONE, 2012.

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Computational enzyme design approaches with significant biological outcomes: progress and challenges

Xiaoman Li, Ziding Zhang^*, Jiangning Song^*

Computational and Structural Biotechnology Journal, 2012.

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Can simple codon pair usage predict protein–protein interaction?

Yuan Zhou, Ying-Si Zhou, Fei He, Jiangning Song, Ziding Zhang^*

Molecular BioSystems, 2012.

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2011

Comprehensive analysis of tandem amino acid repeats from ten angiosperm genomes

Yuan Zhou, Jing Liu, Lei Han, Zhi-Gang Li, Ziding Zhang^*

BMC Genomics, 2011.

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Outer membrane proteins can be simply identified using secondary structure element alignment

Renxiang Yan, Zhen Chen, Ziding Zhang^*

BMC Bioinformatics, 2011.

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A predicted protein–protein interaction network of the filamentous fungus Neurospora crassa

Ting-You Wang, Fei He, Qi-Wen Hu, Ziding Zhang^*

Molecular BioSystems, 2011.

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Prediction of Ubiquitination Sites by Using the Composition of k-Spaced Amino Acid Pairs

Zhen Chen, Yongzi Chen, Xiao-Feng Wang, Chuan Wang, Renxiang Yan, Ziding Zhang^*

PLoS ONE, 2011.

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Comparison of linear gap penalties and profile-based variable gap penalties in profile–profile alignments

Chuan Wang, Renxiang Yan, Xiao-Feng Wang, Jingna Si, Ziding Zhang^*

Computational Biology and Chemistry, 2011.

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Prediction of protein–protein interactions between Ralstonia solanacearum and Arabidopsis thaliana

Zhi-Gang Li, Fei He, Ziding Zhang, You-Liang Peng

Amino Acids, 2011.

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Predicting Residue-Residue Contacts and Helix-Helix Interactions in Transmembrane Proteins Using an Integrative Feature-Based Random Forest Approach

Xiao-Feng Wang, Zhen Chen, Chuan Wang, Renxiang Yan, Ziding Zhang^*, Jiangning Song^*

PLoS ONE, 2011.

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2010

Deciphering the Arabidopsis Floral Transition Process by Integrating a Protein-Protein Interaction Network and Gene Expression Data

Fei He, Yuan Zhou, Ziding Zhang^*

Plant Physiology, 2010.

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2009

An Overview of the De Novo Prediction of Enzyme Catalytic Residues

Ziding Zhang^*, Yu-Rong Tang, Zhi-Ya Sheng, Dongbin Zhao

Current Bioinformatics, 2009.

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Binding specificity of locust odorant binding protein and its key binding site for initial recognition of alcohols

Quan-Yong Jiang, Wei-Xuan Wang, Ziding Zhang^*, Long Zhang^*

Insect Biochemistry and Molecular Biology, 2009.

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TIM-Finder: A new method for identifying TIM-barrel proteins

Jingna Si, Renxiang Yan, Chuan Wang, Ziding Zhang, Xiao-Dong Su

BMC Structural Biology, 2009.

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DescFold: A web server for protein fold recognition

Renxiang Yan, Jingna Si, Chuan Wang, Ziding Zhang^*

BMC Bioinformatics, 2009.

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2008

An improved prediction of catalytic residues in enzyme structures

Yurong Tang, Z.-Y. Sheng, Yongzi Chen, Ziding Zhang^*

Protein Engineering Design and Selection, 2008.

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Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs

Yongzi Chen, Yu-Rong Tang, Zhi-Ya Sheng, Ziding Zhang^*

BMC Bioinformatics, 2008.

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The prediction of protein-protein interaction networks in rice blast fungus

Fei He, Yan Zhang, Hao Chen, Ziding Zhang^*, You-Liang Peng

BMC Genomics, 2008.

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2007

Genome-Wide Analysis of Enzyme Structure-Function Combination Across Three Domains of Life

Ziding Zhang^*, Yu-Rong Tang

Protein & Peptide Letters, 2007.

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GANNPhos: a new phosphorylation site predictor based on a genetic algorithm integrated neural network

Yurong Tang, Yongzi Chen, C. A. Canchaya, Ziding Zhang^*

Protein Engineering Design and Selection, 2007.

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2005

Similarity networks of protein binding sites

Ziding Zhang, Martin G. Grigorov^*

Proteins: Structure, Function, and Bioinformatics, 2005.

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