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Zlab Publications

Explore ZLab's recent research articles and collaborations.

2025

AI sheds new light on genome editing
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

2024

Current computational tools for protein lysine acylation site prediction
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

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

2023

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

2022

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

2021

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

2020

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences
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, Volume 21, Issue 5, Pages 1676–1696

DeepKhib: A Deep-Learning Framework for Lysine 2-Hydroxyisobutyrylation Sites Prediction
DeepKhib: A Deep-Learning Framework for Lysine 2-Hydroxyisobutyrylation Sites Prediction

Luna Zhang, Yang Zou, Ningning He, Yu Chen, Zhen Chen, Lei Li.

Front. Cell Dev. Biol.

2019

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites
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, Volume 20, Issue 6, Pages 2267–2290

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

2018

Integration of A Deep Learning Classifier with A Random Forest Approach for Predicting Malonylation Sites
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, Volume 16, Issue 6, Pages 451–459

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences
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, Volume 34, Issue 14, Pages 2499–2502