Zlab Publications

2026

Protein Function Prediction

PlantPTM: A deep learning framework integrating protein language models with multi-view features for predicting diverse post-translational modification sites in plants

Gensheng Dou, Kaiyuan Wang, Zhaohui Qin, Min Zhang, Wentian Zhang, Chunbo Miao, Junzhou Li, Zhen Chen.

Molecular Plant

Open publication ↗

2026

Genome Editing

Efficient homologous replacement and deletion of large genomic fragments through template-jumping prime editing in rice

Huixia Liu, Y. Wang, S. Guan, Z. Zhang, Zhaohui Qin, D. Zhao, F. Li, Min Zhang, Wentian Zhang, Y. Du, Junzhou Li, Zhen Chen, Chunbo Miao.

New Phytologist

Open publication ↗

2026

Plant Biology

Multiplex gene editing and effect analysis of yield, fragrance, and blast resistance genes in rice

S. Guan, Y. Han, J. Zhang, Y. Du, Z. Chen, C. Miao, J. Li.

Genes

Open publication ↗

2025

Computational Biology

AI sheds new light on genome editing

Zhaohui Qin (秦兆辉)*, Zhaolong Deng (邓兆龙), Chengwei Li (李成伟), Daowen Wang (王道文), Xiang Ji (姬祥), Zhen Chen (陈震).

Trends in Biotechnology

Open publication ↗

2024

Computational Biology

SLAM: Structure-aware lysine β-hydroxybutyrylation prediction with protein language model

Zhaohui Qin, Huixia Liu, Pei Zhao, Kaiyuan Wang, Haoran Ren, Chunbo Miao, Junzhou Li, Yong-Zi Chen, Zhen Chen.

International Journal of Biological Macromolecules

Open publication ↗

2024

Computational Biology

Current computational tools for protein lysine acylation site prediction

Zhaohui Qin, Haoran Ren, Pei Zhao, Kaiyuan Wang, Huixia Liu, Chunbo Miao, Yanxiu Du, Junzhou Li, Liuji Wu, Zhen Chen

Briefings in Bioinformatics

Open publication ↗

2024

Genome Editing

CRISPR/CasΦ2-mediated gene editing in wheat and rye

S. Zhao, X. Han, Y. Zhu, Y. Han, H. Liu, Z. Chen, H. Li, D. Wang, C. Tian, et al.

Journal of Integrative Plant Biology

Open publication ↗

2023

Computational Biology

ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning

Xiaoti Jia*, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song.

Briefings in Bioinformatics

Open publication ↗

2023

Protein Function Prediction

Designing Effective Predictors of Protein Post-Translational Modifications Using iLearnPlus

Z. Chen, F. Li, X. Wang, Y. Wang, L. Kurgan, J. Song.

Machine Learning in Bioinformatics of Protein Sequences: Algorithms and Applications

Open publication ↗

2022

Computational Biology

iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets

Zhen Chen, Xuhan Liu, Pei Zhao, Chen Li, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Chris Bain, Robin B Gasser, Junzhou Li, Zuoren Yang, Xin Gao, Lukasz Kurgan, Jiangning Song.

Nucleic Acids Research

Open publication ↗

2022

Protein Function Prediction

Systematic characterization of lysine post-translational modification sites using MUscADEL

Z. Chen, X. Liu, F. Li, C. Li, T. Marquez-Lago, A. Leier, G. I. Webb, D. Xu, et al.

Computational Methods for Predicting Post-Translational Modification Sites

Open publication ↗

2021

Computational Biology

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

Zhen Chen, Pei Zhao, Chen Li, Fuyi Li, Dongxu Xiang, Yong-Zi Chen, Tatsuya Akutsu, Roger J Daly, Geoffrey I Webb, Quanzhi Zhao, Lukasz Kurgan, Jiangning Song.

Nucleic Acids Research

Open publication ↗

2021

Protein Function Prediction

nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning

Y.-Z. Chen, Z.-Z. Wang, Y. Wang, G. Ying, Z. Chen, J. Song.

Briefings in Bioinformatics

Open publication ↗

2020

Computational Biology

iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T Marquez-Lago, André Leier, Jerico Revote, Yan Zhu, David R Powell, Tatsuya Akutsu, Geoffrey I Webb, Kuo-Chen Chou, A Ian Smith, Roger J Daly, Jian Li, Jiangning Song.

Briefings in Bioinformatics

Open publication ↗

2020

Computational Biology

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, A Ian Smith, Geoffrey I Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song

Briefings in Bioinformatics

Open publication ↗

2020

Protein Function Prediction

PROSPECT: a web server for predicting protein histidine phosphorylation sites

Z. Chen, P. Zhao, F. Li, A. Leier, T. T. Marquez-Lago, G. I. Webb, A. Baggag, et al.

Journal of Bioinformatics and Computational Biology

Open publication ↗

2019

Computational Biology

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites

Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I Webb, Dakang Xu, Alexander Ian Smith

Briefings in Bioinformatics

Open publication ↗

2018

Computational Biology

Integration of A Deep Learning Classifier with A Random Forest Approach for Predicting Malonylation Sites

Zhen Chen, Ningning He, Yu Huang, Wen Tao Qin, Xuhan Liu, Lei Li

Genomics, Proteomics & Bioinformatics

Open publication ↗

2018

Computational Biology

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T Marquez-Lago, Yanan Wang, Geoffrey I Webb, A Ian Smith, Roger J Daly, Kuo-Chen Chou, Jiangning Song

Bioinformatics

Open publication ↗

2015

Protein Function Prediction

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

Z. Chen, Y. Zhou, Z. Zhang, J. Song.

Briefings in Bioinformatics

Open publication ↗

2013

Protein Function Prediction

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

Z. Chen, Y. Zhou, J. Song, Z. Zhang.

Biochimica et Biophysica Acta - Proteins and Proteomics

Open publication ↗

2013

Protein Function Prediction

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

Z. Chen, Y. Wang, Y.-F. Zhai, J. Song, Z. Zhang.

Molecular BioSystems

Open publication ↗

2011

Protein Function Prediction

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

Z. Chen, Y.-Z. Chen, X.-F. Wang, C. Wang, R.-X. Yan, Z. Zhang.

PLOS ONE

Open publication ↗