Bagging One-Class Decision Trees. - Chen Li 021; Yang Zhang 010 (FSKD (2), 2008)

OcVFDT: one-class very fast decision tree for one-class classification of data streams. - Chen Li 021; Yang Zhang 010; Xue Li 001 (KDD Workshop on Knowledge Discovery from Sensor Data, 2009)

Learning from data streams with only positive and unlabeled data. - Xiangju Qin; Yang Zhang 010; Chen Li 021; Xue Li 001 (J. Intell. Inf. Syst., 2013)

Towards Positive Unlabeled Learning for Parallel Data Mining: A Random Forest Framework. - Chen Li 021; Xue-Liang Hua (ADMA, 2014)

GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. - Fuyi Li; Chen Li 021; Mingjun Wang; Geoffrey I. Webb; Yang Zhang 010; James C. Whisstock; Jiangning Song (Bioinform., 2015)

Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. - Chen Li 021; Catherine Ching Han Chang; Jeremy Nagel; Benjamin T. Porebski; Morihiro Hayashida; Tatsuya Akutsu; Jiangning Song; Ashley M. Buckle (Briefings Bioinform., 2016)

KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. - Chen Li 021; Steve G. Androulakis; Ashley M. Buckle; Jiangning Song (Database J. Biol. Databases Curation, 2016)

PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. - Chen Li 021; Jeremy Nagel; Steve G. Androulakis; Christopher J. Lupton; Jiangning Song; Ashley M. Buckle (Database J. Biol. Databases Curation, 2016)

PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. - Chen Li 021; Jeremy Nagel; Steve G. Androulakis; Jiangning Song; Ashley M. Buckle (Database J. Biol. Databases Curation, 2016)

CNN based post-processing to improve HEVC. - Chen Li 021; Li Song 001; Rong Xie; Wenjun Zhang 001 (ICIP, 2017)

Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI. - Yi An; Jiawei Wang 002; Chen Li 021; André Leier; Tatiana T. Marquez-Lago; Jonathan Wilksch; Yang Zhang 010; Geoffrey I. Webb; Jiangning Song; Trevor Lithgow (Briefings Bioinform., 2018)

Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. - Fuyi Li; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Anthony W. Purcell; Alexander Ian Smith; Trevor Lithgow; Roger J. Daly; Jiangning Song; Kuo-Chen Chou (Bioinform., 2018)

ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features. - Bangli Lu; Chen Li 021; Qingfeng Chen; Jiangning Song (J. Bioinform. Comput. Biol., 2018)

Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. - Zhen Chen 009; Xuhan Liu; Fuyi Li; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Tatsuya Akutsu; Geoffrey I. Webb; Dakang Xu; Alexander Ian Smith; Lei Li 013; Kuo-Chen Chou; et al. (Briefings Bioinform., 2019)

Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. - Fuyi Li; Yanan Wang 003; Chen Li 021; Tatiana T. Marquez-Lago; André Leier; Neil D. Rawlings; Gholamreza Haffari; Jerico Nico De Leon Revote; Tatsuya Akutsu; Kuo-Chen Chou; Anthony W. Purcell; Robert N. Pike; et al. (Briefings Bioinform., 2019)

Positive-unlabelled learning of glycosylation sites in the human proteome. - Fuyi Li; Yang Zhang 010; Anthony W. Purcell; Geoffrey I. Webb; Kuo-Chen Chou; Trevor Lithgow; Chen Li 021; Jiangning Song (BMC Bioinform., 2019)

SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. - Xiaochuan Wang; Chen Li 021; Fuyi Li; Varun S. Sharma; Jiangning Song; Geoffrey I. Webb (BMC Bioinform., 2019)

3D-BitNet: Flow-Agnostic and Precise Network for video Bit-Depth Expansion. - Geyingjie Wen; Zhen Yang; Chen Li 021; Rong Xie; Li Song 001; Weiyong Cai (BMSB, 2021)

SimCTC: A Simple Contrast Learning Method of Text Clustering (Student Abstract). - Chen Li 021; Xiaoguang Yu; Shuangyong Song; Jia Wang; Bo Zou; Xiaodong He 001 (AAAI, 2022)

Multi-Scale Coarse-to-Fine Transformer for Frame Interpolation. - Chen Li 021; Li Song 001; Xueyi Zou; Jiaming Guo; Youliang Yan; Wenjun Zhang 001 (ACM Multimedia, 2022)

Positive-unlabeled learning in bioinformatics and computational biology: a brief review. - Fuyi Li; Shuangyu Dong; André Leier; Meiya Han; Xudong Guo; Jing Xu 008; Xiaoyu Wang 016; Shirui Pan; Cangzhi Jia; Yang Zhang 010; Geoffrey I. Webb; Lachlan J. M. Coin; et al. (Briefings Bioinform., 2022)

PCfun: a hybrid computational framework for systematic characterization of protein complex function. - Varun S. Sharma; Andrea Fossati; Rodolfo Ciuffa; Marija Buljan; Evan G. Williams; Zhen Chen 009; Wenguang Shao; Patrick G. A. Pedrioli; Anthony W. Purcell; María Rodríguez Martínez; Jiangning Song; Matteo Manica; et al. (Briefings Bioinform., 2022)

Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. - Meng Zhang 046; Cangzhi Jia; Fuyi Li; Chen Li 021; Yan Zhu 006; Tatsuya Akutsu; Geoffrey I. Webb; Quan Zou 001; Lachlan J. M. Coin; Jiangning Song (Briefings Bioinform., 2022)

L0 structure-prior assisted blur-intensity aware efficient video deblurring. - Chen Li 021; Li Song 001; Rong Xie; Wenjun Zhang 001 (Neurocomputing, 2022)

iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. - Zhen Chen 009; Xuhan Liu; Pei Zhao; Chen Li 021; Yanan Wang 003; Fuyi Li; Tatsuya Akutsu; Chris Bain; Robin B. Gasser; Junzhou Li; Zuoren Yang; Xin Gao 001; et al. (Nucleic Acids Res., 2022)

csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames. - Meng Zhang 046; Jian Zhao 034; Chen Li 021; Fang Ge; Jing Wu; Bin Jiang 001; Jiangning Song; Xiaofeng Song (Briefings Bioinform., 2022)

Link-Breakage Recovery Strategies for Tactical MANET Based on OLSR. - Lianghui Ding; Hongyu Gao; Huan Lin; Chen Li 021; Yangyang Liu; Feng Yang 006 (IFTC (1), 2023)

Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis. - Jing Xu 008; Jiarui Ou; Chen Li 021; Zheng Zhu; Jian Li 052; Hailun Zhang; Junchen Chen; Bin Yi; Wu Zhu; Weiru Zhang; Guanxiong Zhang; Qian Gao; et al. (npj Digit. Medicine, 2023)

Deep Online Video Stabilization Using IMU Sensors. - Chen Li 021; Li Song 001; Shuai Chen; Rong Xie; Wenjun Zhang 001 (IEEE Trans. Multim., 2023)

Local Bidirection Recurrent Network for Efficient Video Deblurring with the Fused Temporal Merge Module. - Chen Li 021; Li Song 001; Rong Xie; Wenjun Zhang 001 (ACM Trans. Multim. Comput. Commun. Appl., 2023)

VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. - Fang Ge; Chen Li 021; Shahid Iqbal; Muhammad Arif 012; Fuyi Li; Maha A. Thafar; Zihao Yan; Apilak Worachartcheewan; Xiaofeng Xu; Jiangning Song; Dong-Jun Yu (Briefings Bioinform., 2023)

PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. - Tong Pan; Chen Li 021; Yue Bi; Zhikang Wang; Robin B. Gasser; Anthony W. Purcell; Tatsuya Akutsu; Geoffrey I. Webb; Seiya Imoto; Jiangning Song (Bioinform., 2023)

ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. - Ruyi Chen; Fuyi Li; Xudong Guo; Yue Bi; Chen Li 021; Shirui Pan; Lachlan J. M. Coin; Jiangning Song (Briefings Bioinform., 2023)

TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level. - Yan Liu 038; Guo Wei; Chen Li 021; Long-Chen Shen; Robin B. Gasser; Jiangning Song; Dijun Chen; Dong-Jun Yu (Briefings Bioinform., 2023)

iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. - Jing Xu 008; Fuyi Li; Chen Li 021; Xudong Guo; Cornelia B. Landersdorfer; Hsin-Hui Shen; Anton Y. Peleg; Jian Li 052; Seiya Imoto; Jianhua Yao 001; Tatsuya Akutsu; Jiangning Song (Briefings Bioinform., 2023)

MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning. - Jiani Ma; Chen Li 021; Yiwen Zhang; Zhikang Wang; Shanshan Li; Yuming Guo 001; Lin Zhang 015; Hui Liu 024; Xin Gao 001; Jiangning Song (Bioinform., 2023)

DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock. - Liangwei Zhao; Ran Hao; Ziyi Chai; Weiwei Fu; Wei Yang 052; Chen Li 021; Quanzhong Liu; Yu Jiang (Comput. Biol. Chem., 2024)

CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data. - Xiao Wang; Ziyi Chai; Shaohua Li; Yan Liu 038; Chen Li 021; Yu Jiang; Quanzhong Liu (Bioinform., 2024)

scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data. - Yan Liu 038; Chen Li 021; Long-Chen Shen; He Yan; Guo Wei; Robin B. Gasser; Xiaohua Hu 001; Jiangning Song; Dong-Jun Yu (Comput. Biol. Medicine, 2025)

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence. - Yingying Sun; Jun A; Zhiwei Liu; Rui Sun; Liujia Qian; Samuel H. Payne; Wout Bittremieux; Markus Ralser; Chen Li 021; Yi Chen; Zhen Dong; Yasset Pérez-Riverol; et al. (CoRR, 2025)