ZLab研究成果汇总

2026

蛋白质功能预测

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

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2026

基因组编辑

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

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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

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2025

计算生物学

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

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2024

计算生物学

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

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2024

计算生物学

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

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2024

基因组编辑

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

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2023

计算生物学

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

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2023

蛋白质功能预测

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

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2022

计算生物学

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

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2022

蛋白质功能预测

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

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2021

计算生物学

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

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2021

蛋白质功能预测

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

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2020

计算生物学

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

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2020

计算生物学

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

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2020

蛋白质功能预测

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

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2019

计算生物学

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

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2018

计算生物学

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

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2018

计算生物学

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

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2015

蛋白质功能预测

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

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2013

蛋白质功能预测

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

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2013

蛋白质功能预测

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

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2011

蛋白质功能预测

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

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