Jiangning Song

Scopus Author ID Loop profile ResearcherID Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 95

Top Topics

Pseudomonas Aeruginosa

Top Venues

Briefings in bioinformatics

Bioinformatics (Oxford, England)

Journal of chemical information and modeling

Nucleic acids research

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

Publications

Wenhua Yu, Wenzhong Huang, Antonio Gasparrini, Francesco Sera, Alexandra Schneider, Susanne Breitner, Jan Kyselý, Joel Schwartz, Joana Madureira, Vânia Gaio, Yue Leon Guo, Rongbin Xu, Gongbo Chen, Zhengyu Yang, Bo Wen, Yao Wu, Antonella Zanobetti, Haidong Kan, Jiangning Song, Shanshan Li, Yuming Guo, null null
Ambient fine particulate matter and daily mortality: a comparative analysis of observed and estimated exposure in 347 cities. International journal of epidemiology 53 (3) (2024)
Tulio de Lima Campos, Pasi K Korhonen, Neil David Young, Tao Wang, Jiangning Song, Richard Marhoefer, Bill C H Chang, Paul M Selzer, Robin B Gasser
Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning. International journal of molecular sciences 25 (13) (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)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling 64 (4) (2024)
Wenhua Yu, Wenzhong Huang, Antonio Gasparrini, Francesco Sera, Alexandra Schneider, Susanne Breitner, Jan Kyselý, Joel Schwartz, Joana Madureira, Vânia Gaio, Yue Leon Guo, Rongbin Xu, Gongbo Chen, Zhengyu Yang, Bo Wen, Yao Wu, Antonella Zanobetti, Haidong Kan, Jiangning Song, Shanshan Li, Yuming Guo, null null
Ambient fine particulate matter and daily mortality: a comparative analysis of observed and estimated exposure in 347 cities. International journal of epidemiology 53 (3) (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling (2024)
Hoai-An Nguyen, Anton Y Peleg, Jiangning Song, Bhavna Josephine Antony, Geoffrey I Webb, Jessica A Wisniewski, Luke V Blakeway, Gnei Z Badoordeen, Ravali Theegala, Helen Zisis, David L Dowe, Nenad Macesic
Predicting Pseudomonas aeruginosa drug resistance using artificial intelligence and clinical MALDI-TOF mass spectra. mSystems (2024)
Yue Bi, Fuyi Li, Cong Wang, Tong Pan, Chen Davidovich, Geoffrey I Webb, Jiangning Song
Advancing microRNA target site prediction with transformer and base-pairing patterns. Nucleic acids research (2024)
Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. Journal of chemical information and modeling (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling 64 (4) (2024)
Yuan-Ting Zheng, Neil David Young, Jiangning Song, Robin B Gasser
The Mitogenome of the Haecon-5 Strain of Haemonchus contortus and a Comparative Analysis of Its Nucleotide Variation with Other Laboratory Strains. International journal of molecular sciences 25 (16) (2024)
Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Briefings in bioinformatics 25 (2) (2024)
Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. Journal of chemical information and modeling 64 (15) (2024)
Tulio de Lima Campos, Pasi K Korhonen, Neil David Young, Tao Wang, Jiangning Song, Richard Marhoefer, Bill C H Chang, Paul M Selzer, Robin B Gasser
Inference of Essential Genes of the Parasite Haemonchus contortus via Machine Learning. International journal of molecular sciences 25 (13) (2024)
Liang Wang, Chenyang Hong, Jiangning Song, Jianhua Yao
CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis. Bioinformatics (Oxford, England) 40 (4) (2024)
Liang Wang, Chenyang Hong, Jiangning Song, Jianhua Yao
CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis. Bioinformatics (Oxford, England) 40 (4) (2024)
Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Briefings in bioinformatics 25 (2) (2024)
Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. Journal of chemical information and modeling 64 (4) (2024)
Xiaoyu Wang, Fuyi Li, Yiwen Zhang, Seiya Imoto, Hsin-Hui Shen, Shanshan Li, Yuming Guo, Jian Yang, Jiangning Song
Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. Briefings in bioinformatics 25 (5) (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)
Yuan-Ting Zheng, Neil David Young, Jiangning Song, Robin B Gasser
The Mitogenome of the Haecon-5 Strain of Haemonchus contortus and a Comparative Analysis of Its Nucleotide Variation with Other Laboratory Strains. International journal of molecular sciences 25 (16) (2024)
Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J Daly, Jiangning Song
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. Bioinformatics (Oxford, England) 39 (3) (2023)
Fang Wang, Chunpu Liu, Jiawei Li, Fan Yang, Jiangning Song, Tianyi Zang, Jianhua Yao, Guohua Wang
SPDB: a comprehensive resource and knowledgebase for proteomic data at the single-cell resolution. Nucleic acids research (2023)
Yu Zhao, Bing He, Zhimeng Xu, Yidan Zhang, Xuan Zhao, Zhi-An Huang, Fan Yang, Liang Wang, Lei Duan, Jiangning Song, Jianhua Yao
Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire. Briefings in bioinformatics 24 (1) (2023)
Jiangning Song, Lukasz Kurgan
Availability of web servers significantly boosts citations rates of bioinformatics methods for protein function and disorder prediction. Bioinformatics advances 3 (1) (2023)
Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song
SMG: self-supervised masked graph learning for cancer gene identification. Briefings in bioinformatics 24 (6) (2023)
Meng Wang, Guitian Liu, Meng Liu, Cui Tai, Zixin Deng, Jiangning Song, Hongping Qu
ICEberg 3.0: functional categorization and analysis of the integrative and conjugative elements in bacteria. Nucleic acids research (2023)
Yan Zhu, Fuyi Li, Xudong Guo, Xiaoyu Wang, Lachlan J M Coin, Geoffrey I Webb, Jiangning Song, Cangzhi Jia
TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. Briefings in bioinformatics (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)
Jiani Ma, Jiangning Song, Neil D Young, Bill C H Chang, Pasi K Korhonen, Tulio L Campos, Hui Liu, Robin B Gasser
'Bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data. Briefings in bioinformatics 25 (1) (2023)
Jiani Ma, Jiangning Song, Neil D Young, Bill C H Chang, Pasi K Korhonen, Tulio L Campos, Hui Liu, Robin B Gasser
'Bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data. Briefings in bioinformatics 25 (1) (2023)
Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning. Briefings in bioinformatics 24 (2) (2023)
Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning. Briefings in bioinformatics (2023)
Niwanthi Rajapakse, Haru Nomura, Melanie Wu, Jiangning Song, Andrew Hung, Shirley Tran, Hang Ta, Fahima Akther, Yuao Wu, Matt D Johansen, Keng Chew, Vinod Kumar, Trent M Woodruff, Richard J Clark, Johannes Koehbach, Bruno Lomonte, Carlos Rosado, Merlin Thomas, Marion Boudes, Cyril Reboul, Lachlan D Rash, Linda Gallo, Sumia Essid, Dominika Elmlund, Stefan Miemczyk, Nicole Hansbro, Bernadette Saunders, Warwick Britton, Peter D Sly, Ayaho Yamamoto, Julián Fernández, Peter Michael Moyle, Kirsty Short, Philip Hansbro, Sanjaya Kuruppu, Ian Smith
Development of a novel angiotensin converting enzyme 2 stimulator with broad implications in SARS-CoV2 and type 1 diabetes. Research square (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)
Yuan-Ting Zheng, Neil David Young, Jiangning Song, Robin B Gasser
Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host-Parasite Interactions. International journal of molecular sciences 24 (15) (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)
Jiangning Song, Lukasz Kurgan
Availability of web servers significantly boosts citations rates of bioinformatics methods for protein function and disorder prediction. Bioinformatics advances 3 (1) (2023)
Yu Zhao, Bing He, Zhimeng Xu, Yidan Zhang, Xuan Zhao, Zhi-An Huang, Fan Yang, Liang Wang, Lei Duan, Jiangning Song, Jianhua Yao
Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire. Briefings in bioinformatics 24 (1) (2023)
Jianfeng Zhang, Yongkui Chen, Ying-Xian Goh, Meng Wang, Cui Tai, Zixin Deng, Jiangning Song, Hong-Yu Ou
TADB 3.0: an updated database of bacterial toxin-antitoxin loci and associated mobile genetic elements. Nucleic acids research (2023)
Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song
ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning. Briefings in bioinformatics 24 (2) (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)
Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J Daly, Jiangning Song
Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. Bioinformatics (Oxford, England) 39 (3) (2023)
Jiani Ma, Jiangning Song, Neil D Young, Bill C H Chang, Pasi K Korhonen, Tulio L Campos, Hui Liu, Robin B Gasser
'Bingo'-a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data. Briefings in bioinformatics 25 (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)
Xiaoyu Wang, Fuyi Li, Jing Xu, Jia Rong, Geoffrey I Webb, Zongyuan Ge, Jian Li, Jiangning Song
ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning. Briefings in bioinformatics 23 (2) (2022)
Xinxin Peng, Xiaoyu Wang, Yuming Guo, Zongyuan Ge, Fuyi Li, Xin Gao, Jiangning Song
RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. Briefings in bioinformatics 23 (4) (2022)
Yue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I Webb, Jianhua Yao, Cangzhi Jia, Jiangning Song
Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations. Briefings in bioinformatics 23 (6) (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)
Yanan Wang, Yu Guang Wang, Changyuan Hu, Ming Li, Yanan Fan, Nina Otter, Ikuan Sam, Hongquan Gou, Yiqun Hu, Terry Kwok, John Zalcberg, Alex Boussioutas, Roger J Daly, Guido Montúfar, Pietro Lió, Dakang Xu, Geoffrey I Webb, Jiangning Song
Cell graph neural networks enable the precise prediction of patient survival in gastric cancer. NPJ precision oncology 6 (1) (2022)
Fang Ge, Ying Zhang, Jian Xu, Arif Muhammad, Jiangning Song, Dong-Jun Yu
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. Briefings in bioinformatics 23 (1) (2022)
Mengyao Li, Mohammad A K Azad, Maizbha Uddin Ahmed, Yan Zhu, Jiangning Song, Fanfan Zhou, Hak-Kim Chan, Xukai Jiang, Qi Tony Zhou, Jian Li
Polymyxin Induces Significant Transcriptomic Perturbations of Cellular Signalling Networks in Human Lung Epithelial Cells. Antibiotics (Basel, Switzerland) 11 (3) (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)
Shiqi Li, Ruohua Ren, Letian Lyu, Jiangning Song, Yajun Wang, Tsung-Wu Lin, Anton Le Brun, Hsien-Yi Hsu, Hsin-Hui Shen
Solid and Liquid Surface-Supported Bacterial Membrane Mimetics as a Platform for the Functional and Structural Studies of Antimicrobials. Membranes 12 (10) (2022)
Yu Zhao, Bing He, Zhimeng Xu, Yidan Zhang, Xuan Zhao, Zhi-An Huang, Fan Yang, Liang Wang, Lei Duan, Jiangning Song, Jianhua Yao
Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire. Briefings in bioinformatics (2022)
Wenhua Yu, Shanshan Li, Tingting Ye, Rongbin Xu, Jiangning Song, Yuming Guo
Deep Ensemble Machine Learning Framework for the Estimation of P M 2.5 Concentrations. Environmental health perspectives 130 (3) (2022)
Yuanyuan Bu, Cangzhi Jia, Xudong Guo, Fuyi Li, Jiangning Song
COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants. Briefings in functional genomics (2022)
Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinformatics (Oxford, England) 38 (23) (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)
Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data. Bioinformatics (Oxford, England) 38 (16) (2022)
Yanan Wang, Changyuan Hu, Terry Kwok, Christopher A Bain, Xiangyang Xue, Robin B Gasser, Geoffrey I Webb, Alex Boussioutas, Xian Shen, Roger J Daly, Jiangning Song
DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images. Bioinformatics (Oxford, England) 38 (17) (2022)
Ruohua Ren, Chiaxin Lim, Shiqi Li, Yajun Wang, Jiangning Song, Tsung-Wu Lin, Benjamin W Muir, Hsien-Yi Hsu, Hsin-Hui Shen
Recent Advances in the Development of Lipid-, Metal-, Carbon-, and Polymer-Based Nanomaterials for Antibacterial Applications. Nanomaterials (Basel, Switzerland) 12 (21) (2022)
Xiangfeng Lai, Mei-Ling Han, Yue Ding, Seong Hoong Chow, Anton P Le Brun, Chun-Ming Wu, Phillip J Bergen, Jhih-Hang Jiang, Hsien-Yi Hsu, Benjamin W Muir, Jacinta F White, Jiangning Song, Hsin-Hui Shen, Hsin-Hui Shen
A polytherapy based approach to combat antimicrobial resistance using cubosomes. Nature communications 13 (1) (2022)
Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites. Briefings in bioinformatics 22 (6) (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)
Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B Gasser, Dong-Jun Yu, Geoffrey I Webb, Jiangning Song
PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. Journal of chemical information and modeling 62 (17) (2022)
Quanzhong Liu, Honglin Fang, Xiao Wang, Miao Wang, Shuqin Li, Lachlan J M Coin, Fuyi Li, Jiangning Song
DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. Bioinformatics (Oxford, England) 38 (17) (2022)
Yanan Wang, Fuyi Li, Manasa Bharathwaj, Natalia C Rosas, André Leier, Tatsuya Akutsu, Geoffrey I Webb, Tatiana T Marquez-Lago, Jian Li, Trevor Lithgow, Jiangning Song
DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases. Briefings in bioinformatics 22 (4) (2021)
Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song, Dong-Jun Yu
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. Briefings in bioinformatics 22 (5) (2021)
Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-Jun Yu
MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. Briefings in bioinformatics (2021)
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
Positive-unlabeled learning in bioinformatics and computational biology: a brief review. Briefings in bioinformatics (2021)
Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hongping Qu
T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model. Briefings in bioinformatics (2021)
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
iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization. Nucleic acids research 49 (10) (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)
Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings in bioinformatics 22 (3) (2021)
Matiss Ozols, Alexander Eckersley, Christopher I Platt, Callum Stewart-McGuinness, Sarah A Hibbert, Jerico Revote, Fuyi Li, Christopher E M Griffiths, Rachel E B Watson, Jiangning Song, Mike Bell, Michael J Sherratt
Predicting Proteolysis in Complex Proteomes Using Deep Learning. International journal of molecular sciences 22 (6) (2021)
Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. Briefings in bioinformatics 22 (4) (2021)
Shutao Mei, Fuyi Li, Dongxu Xiang, Rochelle Ayala, Pouya Faridi, Geoffrey I Webb, Patricia T Illing, Jamie Rossjohn, Tatsuya Akutsu, Nathan P Croft, Anthony W Purcell, Jiangning Song
Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules. Briefings in bioinformatics 22 (5) (2021)
Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T Marquez Lago, Jian Li, Dong-Jun Yu, Jiangning Song
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. Briefings in bioinformatics 22 (5) (2021)
Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. Briefings in bioinformatics 22 (3) (2021)
Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T Marquez-Lago, Geoffrey I Webb, Abdelkader Baggag, Halima Bensmail, Jiangning Song
PROSPECT: A web server for predicting protein histidine phosphorylation sites. Journal of bioinformatics and computational biology 18 (4) (2020)
Pengyu Li, He Zhang, Xuyang Zhao, Cangzhi Jia, Fuyi Li, Jiangning Song
Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins. Journal of bioinformatics and computational biology 18 (2) (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
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)
Fuyi Li, Yang Zhang, Anthony W Purcell, Geoffrey I Webb, Kuo-Chen Chou, Trevor Lithgow, Chen Li, Jiangning Song
Positive-unlabelled learning of glycosylation sites in the human proteome. BMC bioinformatics 20 (1) (2019)
Xiuquan Ma, Luxi Zhang, Jiangning Song, Elizabeth Nguyen, Rachel S Lee, Samuel J Rodgers, Fuyi Li, Cheng Huang, Ralf B Schittenhelm, Howard Chan, Chanly Chheang, Jianmin Wu, Kristin K Brown, Christina A Mitchell, Kaylene J Simpson, Roger J Daly
Characterization of the Src-regulated kinome identifies SGK1 as a key mediator of Src-induced transformation. Nature communications 10 (1) (2019)
Xiaochuan Wang, Chen Li, Fuyi Li, Varun S Sharma, Jiangning Song, Geoffrey I Webb
SIMLIN: a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models. BMC bioinformatics 20 (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)
Ying Xu, Jiangning Song, Campbell Wilson, James C Whisstock
PhosContext2vec: a distributed representation of residue-level sequence contexts and its application to general and kinase-specific phosphorylation site prediction. Scientific reports 8 (1) (2018)
Bangli Lu, Chen Li, Qingfeng Chen, Jiangning Song
ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features. Journal of bioinformatics and computational biology 16 (4) (2018)