Chen Li

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 32

Top Topics

Ultra High Performance Liquid Chromatography

Top Venues

Briefings in bioinformatics

Bioinformatics (Oxford, England)

NPJ digital medicine

JMIR mHealth and uHealth

This page only lists publications with an associated author ORCID identifier.

Publications

Xiao Wang, Ziyi Chai, Shaohua Li, Yan Liu, Chen Li, Yu Jiang, Quanzhong Liu
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data. Bioinformatics (Oxford, England) 40 (2) (2024)
Zhijie He, Cong Wang, Xudong Guo, Heyun Sun, Yue Bi, Miranda E Pitt, Chen Li, Jiangning Song, Lachlan J M Coin, Fuyi Li
MERITS: a web-based integrated Mycobacterial PE/PPE protein database. Bioinformatics advances 4 (1) (2024)
Xiao Wang, Ziyi Chai, Shaohua Li, Yan Liu, Chen Li, Yu Jiang, Quanzhong Liu
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data. Bioinformatics (Oxford, England) 40 (2) (2024)
Asolina Braun, Louise C Rowntree, Ziyi Huang, Kirti Pandey, Nikolas Thuesen, Chen Li, Jan Petersen, Dene R Littler, Shabana Raji, Thi H O Nguyen, Emma Jappe Lange, Gry Persson, Michael Schantz Klausen, Jens V Kringelum, Shanzou Chung, Nathan Paul Croft, Pouya Faridi, Rochelle Ayala, Jamie Rossjohn, Patricia T Illing, Katherine E Scull, Sri Ramarathinam, Nicole A Mifsud, Katherine Kedzierska, Anders Bundgård Sørensen, Anthony Wayne Purcell
Mapping the immunopeptidome of seven SARS-CoV-2 antigens across common HLA haplotypes. Nature communications 15 (1) (2024)
Mohammad Shahbazy, Sri H Ramarathinam, Chen Li, Patricia T Illing, Pouya Faridi, Nathan Paul Croft, Anthony Wayne Purcell
MHCpLogics: an interactive machine learning-based tool for unsupervised data visualization and cluster analysis of immunopeptidomes. Briefings in bioinformatics 25 (2) (2024)
Zhijie He, Cong Wang, Xudong Guo, Heyun Sun, Yue Bi, Miranda E Pitt, Chen Li, Jiangning Song, Lachlan J M Coin, Fuyi Li
MERITS: a web-based integrated Mycobacterial PE/PPE protein database. Bioinformatics advances 4 (1) (2024)
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
Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis. NPJ digital medicine 6 (1) (2023)
Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B Gasser, Anthony W Purcell, Tatsuya Akutsu, Geoffrey I Webb, Seiya Imoto, Jiangning Song
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. Bioinformatics (Oxford, England) 39 (3) (2023)
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
Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis. NPJ digital medicine 6 (1) (2023)
Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B Gasser, Anthony W Purcell, Tatsuya Akutsu, Geoffrey I Webb, Seiya Imoto, Jiangning Song
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. Bioinformatics (Oxford, England) 39 (3) (2023)
Jing Xu, Fuyi Li, Chen Li, Xudong Guo, Cornelia Landersdorfer, Hsin-Hui Shen, Anton Y Peleg, Jian Li, Seiya Imoto, Jianhua Yao, Tatsuya Akutsu, Jiangning Song
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Briefings in bioinformatics (2023)
Yu Zhao, Bing He, Fan Xu, Chen Li, Zhimeng Xu, Xiaona Su, Haohuai He, Yueshan Huang, Jamie Rossjohn, Jiangning Song, Jianhua Yao
DeepAIR: A deep learning framework for effective integration of sequence and 3D structure to enable adaptive immune receptor analysis. Science advances 9 (32) (2023)
Wei Yang, Jingyuan Zhuang, Chen Li, Chen Bai, Guijuan Cheng
Insights into the Inhibitory Mechanisms of the Covalent Drugs for DNMT3A. International journal of molecular sciences 24 (16) (2023)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics 24 (1) (2023)
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
Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis. NPJ digital medicine 6 (1) (2023)
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
Multi-modality data-driven analysis of diagnosis and treatment of psoriatic arthritis. NPJ digital medicine 6 (1) (2023)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics 24 (1) (2023)
Tong Pan, Chen Li, Yue Bi, Zhikang Wang, Robin B Gasser, Anthony W Purcell, Tatsuya Akutsu, Geoffrey I Webb, Seiya Imoto, Jiangning Song
PFresGO: an attention mechanism-based deep-learning approach for protein annotation by integrating gene ontology inter-relationships. Bioinformatics (Oxford, England) 39 (3) (2023)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics (2022)
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
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. Nucleic acids research (2022)
Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu
VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants. Briefings in bioinformatics (2022)
Meng Zhang, Jian Zhao, Chen Li, Fang Ge, Jing Wu, Bin Jiang, Jiangning Song, Xiaofeng Song
csORF-finder: an effective ensemble learning framework for accurate identification of multi-species coding short open reading frames. Briefings in bioinformatics 23 (6) (2022)
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
PCfun: a hybrid computational framework for systematic characterization of protein complex function. Briefings in bioinformatics 23 (4) (2022)
Jie Zhang, Xiqian Chen, Jiaxin Zou, Chen Li, Wanying Kang, Yang Guo, Sheng Liu, Wenjing Zhao, Xiangyu Mou, Jiayuan Huang, Jia Ke
MADET: a Manually Curated Knowledge Base for Microbiomic Effects on Efficacy and Toxicity of Anticancer Treatments. Microbiology spectrum (2022)
Meng Zhang, Cangzhi Jia, Fuyi Li, Chen Li, Yan Zhu, Tatsuya Akutsu, Geoffrey I Webb, Quan Zou, Lachlan J M Coin, Jiangning Song
Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction. Briefings in bioinformatics 23 (2) (2022)
Chen Li, Jerico Revote, Sri H Ramarathinam, Shan Zou Chung, Nathan Paul Croft, Katherine E Scull, Ziyi Huang, Rochelle Ayala, Asolina Braun, Nicole A Mifsud, Patricia T Illing, Pouya Faridi, Anthony Wayne Purcell
Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies. Proteomics 21 (17-18) (2021)
Andrea Fossati, Chen Li, Federico Uliana, Fabian Wendt, Fabian Frommelt, Peter Sykacek, Moritz Heusel, Mahmoud Hallal, Isabell Bludau, Tümay Capraz, Peng Xue, Jiangning Song, Bernd Wollscheid, Anthony Wayne Purcell, Matthias Gstaiger, Ruedi Aebersold
PCprophet: a framework for protein complex prediction and differential analysis using proteomic data. Nature methods 18 (5) (2021)
Xueliang Hua, Chen Li, Jason M Pogue, Varun S Sharma, Ilias Karaiskos, Keith S Kaye, Brian T Tsuji, Phillip J Bergen, Yan Zhu, Jiangning Song, Hsin-Hui Shen
Correction: ColistinDose, a Mobile App for Determining Intravenous Dosage Regimens of Colistimethate in Critically Ill Adult Patients: Clinician-Centered Design and Development Study. JMIR mHealth and uHealth 8 (12) (2020)
Xueliang Hua, Chen Li, Jason M Pogue, Varun S Sharma, Ilias Karaiskos, Keith S Kaye, Brian T Tsuji, Phillip J Bergen, Yan Zhu, Jiangning Song, Hsin-Hui Shen
ColistinDose, a Mobile App for Determining Intravenous Dosage Regimens of Colistimethate in Critically Ill Adult Patients: Clinician-Centered Design and Development Study. JMIR mHealth and uHealth 8 (12) (2020)
Pouya Faridi, Chen Li, Sri H Ramarathinam, Patricia T Illing, Nicole A Mifsud, Rochelle Ayala, Jiangning Song, Linden J Gearing, Nathan Paul Croft, Anthony Wayne Purcell
Response to Comment on "A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands". Science immunology 4 (38) (2020)
Tatjana Sajic, Rodolfo Ciuffa, Vera Lemos, Pan Xu, Valentina Leone, Chen Li, Evan G Williams, Georgios Makris, Amir Banaei-Esfahani, Mathias F Heikenwälder, Kristina Schoonjans, Ruedi Aebersold
A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model. Scientific reports 9 (1) (2019)
Pouya Faridi, Chen Li, Sri H Ramarathinam, Julian P Vivian, Patricia T Illing, Nicole A Mifsud, Rochelle Ayala, Jiangning Song, Linden J Gearing, Paul J Hertzog, Nicola Ternette, Jamie Rossjohn, Nathan Paul Croft, Anthony Wayne Purcell
A subset of HLA-I peptides are not genomically templated: Evidence for cis- and trans-spliced peptide ligands. Science immunology 3 (28) (2019)