Chen Li

41 papers A* 2B 1C 1Journal 33Unranked 4
YearRankTypeTitle / Venue / Authors
2026 J jnl
AGEP_TWAS: A Deep Learning-Based Framework for Predicting Gene Expression Levels in Tissues.
IEEE Trans. Comput. Biol. Bioinform.
Sizhe Wang, Zhichao Zhou, Chen Li, Yudong Cai, Jiong Wang, Zhuangbiao Zhang, Ran Li, Zhannur Niyazbekova, Yu Jiang, Quanzhong Liu
2025 J jnl
MUSIC-GCN: A Novel Multi-Tasking Pipeline for Analyzing Single-Cell Transcriptomic Data Using Residual Graph Convolution Network.
IEEE Trans. Comput. Biol. Bioinform.
Yan Liu, Guo Wei, Jia-Shun Wu, Chen Li, He Yan, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
2025 J jnl
Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence.
CoRR
Yingying Sun, Jun A, Zhiwei Liu, Rui Sun, Liujia Qian, Samuel H. Payne, Wout Bittremieux, Markus Ralser, Chen Li, Yi Chen, Zhen Dong, Yasset Pérez-Riverol, Asif Khan, Chris Sander, Ruedi Aebersold, Juan Antonio Vizcaíno, Jonathan R. Krieger, Jianhua Yao, Han Wen, Linfeng Zhang, Yunping Zhu, Yue Xuan, Benjamin Boyang Sun, Liang Qiao, Henning Hermjakob, Haixu Tang, Huanhuan Gao, Yamin Deng, Qing Zhong, Cheng Chang, Nuno Bandeira, Ming Li, Weinan E, Siqi Sun, Yuedong Yang, Gilbert S. Omenn, Yue Zhang, Ping Xu, Yan Fu, Xiaowen Liu, Christopher M. Overall, Yu Wang, Eric W. Deutsch, Luonan Chen, Jürgen Cox, Vadim Demichev, Fuchu He, Jiaxing Huang, Huilin Jin, Chao Liu, Nan Li, Zhongzhi Luan, Jiangning Song, Kaicheng Yu, Wanggen Wan, Tai Wang, Kang Zhang, Le Zhang, Peter A. Bell, Matthias Mann, Bing Zhang, Tiannan Guo
2025 J jnl
scRCA: A Siamese network-based pipeline for annotating cell types using noisy single-cell RNA-seq reference data.
Comput. Biol. Medicine
Yan Liu, Chen Li, Long-Chen Shen, He Yan, Guo Wei, Robin B. Gasser, Xiaohua Hu, Jiangning Song, Dong-Jun Yu
2024 J jnl
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data.
Bioinform.
Xiao Wang, Ziyi Chai, Shaohua Li, Yan Liu, Chen Li, Yu Jiang, Quanzhong Liu
2024 J jnl
DeepOCR: A multi-species deep-learning framework for accurate identification of open chromatin regions in livestock.
Comput. Biol. Chem.
Liangwei Zhao, Ran Hao, Ziyi Chai, Weiwei Fu, Wei Yang, Chen Li, Quanzhong Liu, Yu Jiang
2023 J jnl
ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species.
Briefings Bioinform.
Ruyi Chen, Fuyi Li, Xudong Guo, Yue Bi, Chen Li, Shirui Pan, Lachlan J. M. Coin, Jiangning Song
2023 J jnl
Deep Online Video Stabilization Using IMU Sensors.
IEEE Trans. Multim.
Chen Li, Li Song, Shuai Chen, Rong Xie, Wenjun Zhang
2023 — conf
Link-Breakage Recovery Strategies for Tactical MANET Based on OLSR.
IFTC (1)
Lianghui Ding, Hongyu Gao, Huan Lin, Chen Li, Yangyang Liu, Feng Yang
2023 J jnl
Local Bidirection Recurrent Network for Efficient Video Deblurring with the Fused Temporal Merge Module.
ACM Trans. Multim. Comput. Commun. Appl.
Chen Li, Li Song, Rong Xie, Wenjun Zhang
2023 J jnl
MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning.
Bioinform.
Jiani Ma, Chen Li, Yiwen Zhang, Zhikang Wang, Shanshan Li, Yuming Guo, Lin Zhang, Hui Liu, Xin Gao, Jiangning Song
2023 J jnl
Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis.
npj Digit. Medicine
Jing Xu, Jiarui Ou, Chen Li, Zheng Zhu, Jian Li, Hailun Zhang, Junchen Chen, Bin Yi, Wu Zhu, Weiru Zhang, Guanxiong Zhang, Qian Gao, Yehong Kuang, Jiangning Song, Xiang Chen, Hong Liu
2023 J jnl
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships.
Bioinform.
Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B. Gasser, Anthony W. Purcell, Tatsuya Akutsu, Geoffrey I. Webb, Seiya Imoto, Jiangning Song
2023 J jnl
TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level.
Briefings Bioinform.
Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
2023 J jnl
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.
Briefings Bioinform.
Fang Ge, Chen Li, Shahid Iqbal, Muhammad Arif, Fuyi Li, Maha A. Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
2023 J jnl
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities.
Briefings Bioinform.
Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Seiya Imoto, Jianhua Yao, Tatsuya Akutsu, Jiangning Song
2022 J jnl
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.
Briefings Bioinform.
Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey I. Webb, Quan Zou, Lachlan J. M. Coin, Jiangning Song
2022 J jnl
L0 structure-prior assisted blur-intensity aware efficient video deblurring.
Neurocomputing
Chen Li, Li Song, Rong Xie, Wenjun Zhang
2022 A* conf
Multi-Scale Coarse-to-Fine Transformer for Frame Interpolation.
ACM Multimedia
Chen Li, Li Song, Xueyi Zou, Jiaming Guo, Youliang Yan, Wenjun Zhang
2022 J jnl
PCfun: a hybrid computational framework for systematic characterization of protein complex function.
Briefings Bioinform.
Varun S. Sharma, Andrea Fossati, Rodolfo Ciuffa, Marija Buljan, Evan G. Williams, Zhen Chen, Wenguang Shao, Patrick G. A. Pedrioli, Anthony W. Purcell, María Rodríguez Martínez, Jiangning Song, Matteo Manica, Ruedi Aebersold, Chen Li
2022 J jnl
Positive-unlabeled learning in bioinformatics and computational biology: a brief review.
Briefings Bioinform.
Fuyi Li, Shuangyu Dong, André Leier, Meiya Han, Xudong Guo, Jing Xu, Xiaoyu Wang, Shirui Pan, Cangzhi Jia, Yang Zhang, Geoffrey I. Webb, Lachlan J. M. Coin, Chen Li, Jiangning Song
2022 A* conf
SimCTC: A Simple Contrast Learning Method of Text Clustering (Student Abstract).
AAAI
Chen Li, Xiaoguang Yu, Shuangyong Song, Jia Wang, Bo Zou, Xiaodong He
2022 J jnl
csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames.
Briefings Bioinform.
Meng Zhang, Jian Zhao, Chen Li, Fang Ge, Jing Wu, Bin Jiang, Jiangning Song, Xiaofeng Song
2021 — conf
3D-BitNet: Flow-Agnostic and Precise Network for video Bit-Depth Expansion.
BMSB
Geyingjie Wen, Zhen Yang, Chen Li, Rong Xie, Li Song, Weiyong Cai
2019 J jnl
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites.
Briefings Bioinform.
Zhen Chen, Xuhan Liu, Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Geoffrey I. Webb, Dakang Xu, Alexander Ian Smith, Lei Li, Kuo-Chen Chou, Jiangning Song
2019 J jnl
Positive-unlabelled learning of glycosylation sites in the human proteome.
BMC Bioinform.
Fuyi Li, Yang Zhang, Anthony W. Purcell, Geoffrey I. Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li, Jiangning Song
2019 J jnl
SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models.
BMC Bioinform.
Xiaochuan Wang, Chen Li, Fuyi Li, Varun S. Sharma, Jiangning Song, Geoffrey I. Webb
2019 J jnl
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods.
Briefings Bioinform.
Fuyi Li, Yanan Wang, Chen Li, 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, Geoffrey I. Webb, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, James C. Whisstock, Jiangning Song
2018 J jnl
Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI.
Briefings Bioinform.
Yi An, Jiawei Wang, Chen Li, André Leier, Tatiana T. Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I. Webb, Jiangning Song, Trevor Lithgow
2018 J jnl
ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features.
J. Bioinform. Comput. Biol.
Bangli Lu, Chen Li, Qingfeng Chen, Jiangning Song
2018 J jnl
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome.
Bioinform.
Fuyi Li, Chen Li, Tatiana T. Marquez-Lago, André Leier, Tatsuya Akutsu, Anthony W. Purcell, Alexander Ian Smith, Trevor Lithgow, Roger J. Daly, Jiangning Song, Kuo-Chen Chou
2017 B conf
CNN based post-processing to improve HEVC.
ICIP
Chen Li, Li Song, Rong Xie, Wenjun Zhang
2016 J jnl
Critical evaluation of
Briefings Bioinform.
Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T. Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M. Buckle
2016 J jnl
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins.
Database J. Biol. Databases Curation
Chen Li, Steve G. Androulakis, Ashley M. Buckle, Jiangning Song
2016 J jnl
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins.
Database J. Biol. Databases Curation
Chen Li, Jeremy Nagel, Steve G. Androulakis, Christopher J. Lupton, Jiangning Song, Ashley M. Buckle
2016 J jnl
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins.
Database J. Biol. Databases Curation
Chen Li, Jeremy Nagel, Steve G. Androulakis, Jiangning Song, Ashley M. Buckle
2015 J jnl
GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome.
Bioinform.
Fuyi Li, Chen Li, Mingjun Wang, Geoffrey I. Webb, Yang Zhang, James C. Whisstock, Jiangning Song
2014 C conf
Towards Positive Unlabeled Learning for Parallel Data Mining: A Random Forest Framework.
ADMA
Chen Li, Xue-Liang Hua
2013 J jnl
Learning from data streams with only positive and unlabeled data.
J. Intell. Inf. Syst.
Xiangju Qin, Yang Zhang, Chen Li, Xue Li
2009 — conf
OcVFDT: one-class very fast decision tree for one-class classification of data streams.
KDD Workshop on Knowledge Discovery from Sensor Data
Chen Li, Yang Zhang, Xue Li
2008 — conf
Bagging One-Class Decision Trees.
FSKD (2)
Chen Li, Yang Zhang