Jiangning Song

182 papers A* 3C 2Misc 1Journal 165Unranked 9

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	BiVAE-CPI: An Interpretable Generative Model Using a Bilateral Variational Autoencoder for Compound-Protein Interaction Prediction. J. Chem. Inf. Model. Yongxin Zhu, Jianxin Wang, Shiyue He, Xinghui Sun, Jiangning Song, Bin Yu
2025	A*	`conf`	CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction. AAAI Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang, Ting Chen
2025	J	`jnl`	Dual-Branch Contrastive Network with Deep Separable Convolution for Enhanced 6mA Site Identification. J. Chem. Inf. Model. Youwei Sun, Zhifei Wang, Ying Zhang, Jiangning Song, Dong-Jun Yu
2025	J	`jnl`	Histo-Genomic Knowledge Association for Cancer Prognosis From Histopathology Whole Slide Images. IEEE Trans. Medical Imaging Zhikang Wang, Yumeng Zhang, Yingxue Xu, Seiya Imoto, Hao Chen, Jiangning Song
2025	J	`jnl`	Identification of Protein-Nucleotide Binding Residues With Deep Multi-Task and Multi-Scale Learning. IEEE J. Biomed. Health Informatics Jiashun Wu, Fang Ge, Shanruo Xu, Yan Liu, Jiangning Song, Dong-Jun Yu
2025	J	`jnl`	Identifying Protein-Nucleotide Binding Residues via Grouped Multi-task Learning and Pre-trained Protein Language Models. J. Chem. Inf. Model. Jiashun Wu, Yan Liu, Ying Zhang, Xiaoyu Wang, He Yan, Yiheng Zhu, Jiangning Song, Dong-Jun Yu
2025	J	`jnl`	Integrating Graph Convolutional Networks for Missing Gene Expression Imputation. IEEE Trans. Comput. Biol. Bioinform. Ying Zhang, Hong-Jin Yu, Zihao Yan, Tong Pan, Yiwen Zhang, Yan Liu, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2025	J	`jnl`	MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification. Briefings Bioinform. Yuhan Wang, Zhikang Wang, Xuan Yu, Xiaoyu Wang, Jiangning Song, Dong-Jun Yu, Fang Ge
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`	Multimodal geometric learning for antimicrobial peptide identification by leveraging alphafold2-predicted structures and surface features. Briefings Bioinform. Zehua Sun, Jing Xu, Yumeng Zhang, Yiwen Zhang, Zhikang Wang, Xiaoyu Wang, Shanshan Li, Yuming Guo, Hsin Hui Shen, Jiangning Song
2025	J	`jnl`	MutPNI: A Unified Model Architecture for Accurately Predicting the Effects of Mutations on Protein-Nucleic Acid Interactions. J. Chem. Inf. Model. Zihao Yan, Fang Ge, Ying Zhang, He Yan, Yan Liu, Yi-Heng Zhu, Jiangning Song, Dong-Jun Yu
2025	J	`jnl`	PScL-SDNNMAE: Protein Subcellular Localization Prediction Using Classical and Masked Autoencoder-Based Multi-View Features With Ensemble Feature Selection. IEEE Trans. Comput. Biol. Bioinform. Shenjian Gu, Matee Ullah, Jiangning Song, Dong-Jun Yu
2025	A*	`conf`	Rethinking Cancer Gene Identification Through Graph Anomaly Analysis. AAAI Yilong Zang, Lingfei Ren, Yue Li, Zhikang Wang, David Antony Selby, Zheng Wang, Sebastian Josef Vollmer, Hongzhi Yin, Jiangning Song, Junhang Wu
2025	J	`jnl`	SCREEN: A Graph-based Contrastive Learning Tool to Infer Catalytic Residues and Assess Enzyme Mutations. Genom. Proteom. Bioinform. Tong Pan, Yue Bi, Xiaoyu Wang, Ying Zhang, Geoffrey I. Webb, Robin B. Gasser, Lukasz A. Kurgan, Jiangning Song
2025	J	`jnl`	SFM-Net: Selective Fusion of Multiway Protein Feature Network for Predicting Binding Affinity Changes upon Mutations. J. Chem. Inf. Model. Chunting Liu, Sudong Cai, Tong Pan, Hiroyuki Ogata, Jiangning Song, Tatsuya Akutsu
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`	Structure-Directed Pan-Specific T-Cell Receptor-Peptide-Major Histocompatibility Complex Interaction Prediction. J. Chem. Inf. Model. Letao Gao, Yumeng Zhang, Fang Ge, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2025	J	`jnl`	Supervised contrastive learning enhances MHC-II peptide binding affinity prediction. Expert Syst. Appl. Long-Chen Shen, Yan Liu, Zi Liu, Yumeng Zhang, Zhikang Wang, Yuming Guo, Jamie Rossjohn, Jiangning Song, Dong-Jun Yu
2025	J	`jnl`	Toward fair AI-driven medical text generation. Nat. Comput. Sci. Yumeng Zhang, Jiangning Song
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`	'Bingo' - a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data. Briefings Bioinform. Jiani Ma, Jiangning Song, Neil D. Young, Bill C. H. Chang, Pasi K. Korhonen, Tulio L. Campos, Hui Liu, Robin B. Gasser
2024	—	`conf`	A Hierarchical Hypergraph Attention Network for Survival Analysis from Pathological Images. ISBI Hongmin Cai, Weiting Yi, Weitian Huang, Zhikang Wang, Yue Zhang, Jiangning Song
2024	J	`jnl`	BLAM6A-Merge: Leveraging Attention Mechanisms and Feature Fusion Strategies to Improve the Identification of RNA N6-Methyladenosine Sites. IEEE ACM Trans. Comput. Biol. Bioinform. Yunpeng Xia, Ying Zhang, Dian Liu, Yi-Heng Zhu, Zhikang Wang, Jiangning Song, Dong-Jun Yu
2024	J	`jnl`	CTEC: a cross-tabulation ensemble clustering approach for single-cell RNA sequencing data analysis. Bioinform. Liang Wang, Chenyang Hong, Jiangning Song, Jianhua Yao
2024	J	`jnl`	CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction. CoRR Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang, Ting Chen
2024	J	`jnl`	Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects. Briefings Bioinform. Xiaoyu Wang, Fuyi Li, Yiwen Zhang, Seiya Imoto, Hsin-Hui Shen, Shanshan Li, Yuming Guo, Jian Yang, Jiangning Song
2024	J	`jnl`	DiCleave: a deep learning model for predicting human Dicer cleavage sites. BMC Bioinform. Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori
2024	J	`jnl`	Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. Medical Image Anal. Zhikang Wang, Jiani Ma, Qian Gao, Chris Bain, Seiya Imoto, Pietro Liò, Hongmin Cai, Hao Chen, Jiangning Song
2024	J	`jnl`	Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor-antigen recognition. Nat. Mac. Intell. Yumeng Zhang, Zhikang Wang, Yunzhe Jiang, Dene R. Littler, Mark Gerstein, Anthony W. Purcell, Jamie Rossjohn, Hong-Yu Ou, Jiangning Song
2024	J	`jnl`	GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference. Briefings Bioinform. Shuo Li, Yan Liu, Long-Chen Shen, He Yan, Jiangning Song, Dong-Jun Yu
2024	J	`jnl`	GraphormerDTI: A graph transformer-based approach for drug-target interaction prediction. Comput. Biol. Medicine Mengmeng Gao, Daokun Zhang, Yi Chen, Yiwen Zhang, Zhikang Wang, Xiaoyu Wang, Shanshan Li, Yuming Guo, Geoffrey I. Webb, Anh T. N. Nguyen, Lauren T. May, Jiangning Song
2024	J	`jnl`	Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images. CoRR Zhikang Wang, Yumeng Zhang, Yingxue Xu, Seiya Imoto, Hao Chen, Jiangning Song
2024	J	`jnl`	Improving Cancer Survival Prediction via Graph Convolutional Neural Network Learning on Protein-Protein Interaction Networks. IEEE J. Biomed. Health Informatics Hongmin Cai, Yi Liao, Lei Zhu, Zhikang Wang, Jiangning Song
2024	—	`conf`	Joint Segmentation of Primary Nasopharyngeal Carcinoma Tumors and Lymph Nodes via Global Attention. BIBM Guihua Tao, Ziqin Ling, Haojiang Li, Jiangning Song, Hongmin Cai
2024	J	`jnl`	MLSNet: a deep learning model for predicting transcription factor binding sites. Briefings Bioinform. Yuchuan Zhang, Zhikang Wang, Fang Ge, Xiaoyu Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
2024	J	`jnl`	MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. J. Chem. Inf. Model. Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu
2024	J	`jnl`	PLANNER: A Multi-Scale Deep Language Model for the Origins of Replication Site Prediction. IEEE J. Biomed. Health Informatics Cong Wang, ZhiJie He, Runchang Jia, Shirui Pan, Lachlan J. M. Coin, Jiangning Song, Fuyi Li
2024	J	`jnl`	PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria. Comput. Biol. Medicine Xiaoyu Wang, Nitin Patil, Fuyi Li, Zhikang Wang, Haolan Zhan, Daniel Schmidt, Philip Thompson, Yuming Guo, Cornelia B. Landersdorfer, Hsin-Hui Shen, Anton Y. Peleg, Jian Li, Jiangning Song
2024	J	`jnl`	Rethinking Cancer Gene Identification through Graph Anomaly Analysis. CoRR Yilong Zang, Lingfei Ren, Yue Li, Zhikang Wang, David Antony Selby, Zheng Wang, Sebastian J. Vollmer, Hongzhi Yin, Jiangning Song, Junhang Wu
2024	J	`jnl`	TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning. IEEE ACM Trans. Comput. Biol. Bioinform. Dian Liu, Zi Liu, Yunpeng Xia, Zhikang Wang, Jiangning Song, Dong-Jun Yu
2024	J	`jnl`	TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. J. Chem. Inf. Model. Zihao Yan, Fang Ge, Yan Liu, Yumeng Zhang, Fuyi Li, Jiangning Song, Dong-Jun Yu
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 domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling. Nat. Mac. Intell. Fang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang, Jianhua Yao
2023	J	`jnl`	Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins. Comput. Biol. Medicine Fuyi Li, Xudong Guo, Yue Bi, Runchang Jia, Miranda E. Pitt, Shirui Pan, Shuqin Li, Robin B. Gasser, Lachlan J. M. Coin, Jiangning Song
2023	J	`jnl`	Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data. BMC Bioinform. Zixuan Wang, Yi Zhou, Tatsuya Takagi, Jiangning Song, Yu-Shi Tian, Tetsuo Shibuya
2023	J	`jnl`	Interpretable artificial intelligence model for accurate identification of medical conditions using immune repertoire. Briefings Bioinform. Yu Zhao, Bing He, Zhimeng Xu, Yidan Zhang, Xuan Zhao, Zhi-An Huang, Fan Yang, Liang Wang, Lei Duan, Jiangning Song, Jianhua Yao
2023	J	`jnl`	Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues. Bioinform. Ying Zhang, Zhikang Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
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`	PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method. Bioinform. Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
2023	J	`jnl`	Prediction of Multiple Types of RNA Modifications via Biological Language Model. IEEE ACM Trans. Comput. Biol. Bioinform. Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song, Dong-Jun Yu
2023	J	`jnl`	ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning. Briefings Bioinform. Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song
2023	J	`jnl`	SMG: self-supervised masked graph learning for cancer gene identification. Briefings Bioinform. Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song
2023	J	`jnl`	Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. Comput. Methods Programs Biomed. Zhikang Wang, Qian Gao, Xiaoping Yi, Xinyu Zhang, Yiwen Zhang, Daokun Zhang, Pietro Liò, Chris Bain, Richard Bassed, Shanshan Li, Yuming Guo, Seiya Imoto, Jianhua Yao, Roger J. Daly, Jiangning Song
2023	J	`jnl`	TIMER is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters. Briefings Bioinform. Yan Zhu, Fuyi Li, Xudong Guo, Xiaoyu Wang, Lachlan J. M. Coin, Geoffrey I. Webb, Jiangning Song, Cangzhi Jia
2023	J	`jnl`	Targeting tumor heterogeneity: multiplex-detection-based multiple instance learning for whole slide image classification. Bioinform. Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Roger J. Daly, 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	—	`conf`	A Regional Multiple Instance Learning Network for Whole Slide Image Segmentation. BIBM Hongmin Cai, Weiting Yi, Yucheng Li, Wenxiong Liao, Jiangning Song
2022	J	`jnl`	A multi-channel deep convolutional neural network for multi-classifying thyroid diseases. Comput. Biol. Medicine Xinyu Zhang, Vincent C. S. Lee, Jia Rong, James C. Lee, Jiangning Song, Feng Liu
2022	J	`jnl`	ASPIRER: a new computational approach for identifying non-classical secreted proteins based on deep learning. Briefings Bioinform. Xiaoyu Wang, Fuyi Li, Jing Xu, Jia Rong, Geoffrey I. Webb, Zongyuan Ge, Jian Li, Jiangning Song
2022	J	`jnl`	Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations. Briefings Bioinform. Yue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I. Webb, Jianhua Yao, Cangzhi Jia, 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`	DEMoS: a deep learning-based ensemble approach for predicting the molecular subtypes of gastric adenocarcinomas from histopathological images. Bioinform. 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
2022	J	`jnl`	DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions. Bioinform. Quanzhong Liu, Honglin Fang, Xiao Wang, Miao Wang, Shuqin Li, Lachlan J. M. Coin, Fuyi Li, Jiangning Song
2022	J	`jnl`	Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. J. Chem. Inf. Model. Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song, Dong-Jun Yu
2022	A*	`conf`	Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CVPR Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song
2022	J	`jnl`	MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network. Briefings Bioinform. Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-Jun Yu
2022	J	`jnl`	MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinform. Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu
2022	J	`jnl`	Multi-channel deep convolutional neural networks for multi-classifying thyroid disease. CoRR Xinyu Zhang, Vincent C. S. Lee, Jia Rong, James C. Lee, Jiangning Song, Feng Liu
2022	J	`jnl`	Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification. CoRR Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Jiangning Song
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`	PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations. J. Chem. Inf. Model. Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B. Gasser, Dong-Jun Yu, Geoffrey I. Webb, Jiangning Song
2022	J	`jnl`	PScL-DDCFPred: an ensemble deep learning-based approach for characterizing multiclass subcellular localization of human proteins from bioimage data. Bioinform. Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
2022	J	`jnl`	Personalized On-Device E-Health Analytics With Decentralized Block Coordinate Descent. IEEE J. Biomed. Health Informatics Guanhua Ye, Hongzhi Yin, Tong Chen, Miao Xu, Quoc Viet Hung Nguyen, Jiangning Song
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	J	`jnl`	PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. BMC Bioinform. Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song
2022	J	`jnl`	Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. Briefings Bioinform. Fang Ge, Ying Zhang, Jian Xu, Muhammad Arif, Jiangning Song, Dong-Jun Yu
2022	J	`jnl`	RBP-TSTL is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins. Briefings Bioinform. Xinxin Peng, Xiaoyu Wang, Yuming Guo, Zongyuan Ge, Fuyi Li, Xin Gao, Jiangning Song
2022	J	`jnl`	T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model. Briefings Bioinform. Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hong-Yu Ou
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	J	`jnl`	A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction. IEEE ACM Trans. Comput. Biol. Bioinform. Menglu Li, Yanan Wang, Fuyi Li, Yun Zhao, Mengya Liu, Sijia Zhang, Yannan Bin, Alexander Ian Smith, Geoffrey I. Webb, Jian Li, Jiangning Song, Junfeng Xia
2021	J	`jnl`	Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. Briefings Bioinform. Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu
2021	J	`jnl`	Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules. Briefings Bioinform. 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
2021	J	`jnl`	Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings Bioinform. Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I. Webb, Jiangning Song
2021	J	`jnl`	BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. Nucleic Acids Res. Jiawei Wang, Jiahui Li, Yi Hou, Wei Dai, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Tieli Zhou, Von Torres, Iain Hay, Christopher Stubenrauch, Yanju Zhang, Jiangning Song, Trevor Lithgow
2021	J	`jnl`	BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. Frontiers Big Data Jinxiang Chen, Fuyi Li, Miao Wang, Junlong Li, Tatiana T. Marquez-Lago, André Leier, Jerico Revote, Shuqin Li, Quanzhong Liu, Jiangning Song
2021	J	`jnl`	Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. Briefings Bioinform. Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-Jun Yu, Jiangning Song
2021	J	`jnl`	Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. Briefings Bioinform. Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia
2021	J	`jnl`	Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. Briefings Bioinform. Fuyi Li, Jinxiang Chen, Zongyuan Ge, Ya Wen, Yanwei Yue, Morihiro Hayashida, Abdelkader Baggag, Halima Bensmail, Jiangning Song
2021	J	`jnl`	DeepBL: a deep learning-based approach for Briefings Bioinform. 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
2021	J	`jnl`	DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites. Briefings Bioinform. Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song, Fuyi Li
2021	J	`jnl`	DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. Briefings Bioinform. Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang
2021	J	`jnl`	Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CoRR Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song
2021	J	`jnl`	Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling. IEEE ACM Trans. Comput. Biol. Bioinform. Cangzhi Jia, Meng Zhang, Cunshuo Fan, Fuyi Li, Jiangning Song
2021	J	`jnl`	HEAL: an automated deep learning framework for cancer histopathology image analysis. Bioinform. Yanan Wang, Nicolas Coudray, Yun Zhao, Fuyi Li, Changyuan Hu, Yao-Zhong Zhang, Seiya Imoto, Aristotelis Tsirigos, Geoffrey I. Webb, Roger J. Daly, Jiangning Song
2021	J	`jnl`	Improving protein fold recognition using triplet network and ensemble deep learning. Briefings Bioinform. Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu
2021	J	`jnl`	Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification. Briefings Bioinform. Xiao Liang, Fuyi Li, Jinxiang Chen, Junlong Li, Hao Wu, Shuqin Li, Jiangning Song, Quanzhong Liu
2021	J	`jnl`	Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites. Briefings Bioinform. Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu
2021	J	`jnl`	OCTID: a one-class learning-based Python package for tumor image detection. Bioinform. Yanan Wang, Litao Yang, Geoffrey I. Webb, Zongyuan Ge, Jiangning Song
2021	J	`jnl`	PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection. Briefings Bioinform. Matee Ullah, Ke Han, Fazal Hadi, Jian Xu, Jiangning Song, Dong-Jun Yu
2021	J	`jnl`	Personalized On-Device E-health Analytics with Decentralized Block Coordinate Descent. CoRR Guanhua Ye, Hongzhi Yin, Tong Chen, Miao Xu, Quoc Viet Hung Nguyen, Jiangning Song
2021	J	`jnl`	Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. Briefings Bioinform. Fuyi Li, Xudong Guo, Peipei Jin, Jinxiang Chen, Dongxu Xiang, Jiangning Song, Lachlan J. M. Coin
2021	J	`jnl`	ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites. BMC Bioinform. Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu
2021	J	`jnl`	SAResNet: self-attention residual network for predicting DNA-protein binding. Briefings Bioinform. Long-Chen Shen, Yan Liu, Jiangning Song, Dong-Jun Yu
2021	J	`jnl`	Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions. Briefings Bioinform. Huaming Chen, Fuyi Li, Lei Wang, Yaochu Jin, Chi-Hung Chi, Lukasz A. Kurgan, Jiangning Song, Jun Shen
2021	J	`jnl`	Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. Briefings Bioinform. Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song, Dong-Jun Yu
2021	J	`jnl`	XRRpred: accurate predictor of crystal structure quality from protein sequence. Bioinform. Sina Ghadermarzi, Bartosz Krawczyk, Jiangning Song, Lukasz A. Kurgan
2021	J	`jnl`	nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Briefings Bioinform. Yong-Zi Chen, Zhuo-Zhi Wang, Yanan Wang, Guoguang Ying, Zhen Chen, Jiangning Song
2020	J	`jnl`	A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Briefings Bioinform. Shutao Mei, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Kailin Giam, Nathan P. Croft, Tatsuya Akutsu, Alexander Ian Smith, Jian Li, Jamie Rossjohn, Anthony W. Purcell, Jiangning Song
2020	J	`jnl`	A framework towards data analytics on host-pathogen protein-protein interactions. J. Ambient Intell. Humaniz. Comput. Huaming Chen, Jun Shen, Lei Wang, Jiangning Song
2020	J	`jnl`	Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. Briefings Bioinform. Leyi Wei, Jie Hu, Fuyi Li, Jiangning Song, Ran Su, Quan Zou
2020	J	`jnl`	Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. Briefings Bioinform. Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song
2020	J	`jnl`	DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. Bioinform. Fuyi Li, Jinxiang Chen, André Leier, Tatiana T. Marquez-Lago, Quanzhong Liu, Yanze Wang, Jerico Nico De Leon Revote, Alexander Ian Smith, Tatsuya Akutsu, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song
2020	J	`jnl`	PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs. Bioinform. Cangzhi Jia, Yue Bi, Jinxiang Chen, André Leier, Fuyi Li, Jiangning Song
2020	J	`jnl`	PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. Briefings Bioinform. Fuyi Li, Cunshuo Fan, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Cangzhi Jia, Yan Zhu, Alexander Ian Smith, Geoffrey I. Webb, Quanzhong Liu, Leyi Wei, Jian Li, Jiangning Song
2020	J	`jnl`	PROSPECT: A web server for predicting protein histidine phosphorylation sites. J. Bioinform. Comput. Biol. Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Abdelkader Baggag, Halima Bensmail, Jiangning Song
2020	J	`jnl`	PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. Bioinform. Yanju Zhang, Sha Yu, Ruopeng Xie, Jiahui Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Alexander Ian Smith, Zongyuan Ge, Jiawei Wang, Trevor Lithgow, Jiangning Song
2020	—	`conf`	PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in Hierarchy. PAKDD (2) Ying Xu, Campbell Wilson, André Leier, Tatiana T. Marquez-Lago, James C. Whisstock, Jiangning Song
2020	J	`jnl`	Pippin: A random forest-based method for identifying presynaptic and postsynaptic neurotoxins. J. Bioinform. Comput. Biol. Pengyu Li, He Zhang, Xuyang Zhao, Cangzhi Jia, Fuyi Li, Jiangning Song
2020	Misc	`conf`	Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning. AMIA Ying Xu, André Leier, Tatiana T. Marquez-Lago, Jue Xie, Antonio Jimeno-Yepes, James C. Whisstock, Campbell Wilson, Jiangning Song
2020	J	`jnl`	Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. Genom. Proteom. Bioinform. Fuyi Li, André Leier, Quanzhong Liu, Yanan Wang, Dongxu Xiang, Tatsuya Akutsu, Geoffrey I. Webb, Alexander Ian Smith, Tatiana T. Marquez-Lago, Jian Li, Jiangning Song
2020	J	`jnl`	iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings Bioinform. Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Jerico Nico De Leon Revote, Yan Zhu, David R. Powell, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Alexander Ian Smith, Roger J. Daly, Jian Li, Jiangning Song
2019	J	`jnl`	Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinform. Jiawei Wang, Jiahui Li, Bingjiao Yang, Ruopeng Xie, Tatiana T. Marquez-Lago, André Leier, Morihiro Hayashida, Tatsuya Akutsu, Yanju Zhang, Kuo-Chen Chou, Joel Selkrig, Tieli Zhou, Jiangning Song, Trevor Lithgow
2019	J	`jnl`	Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. Briefings Bioinform. Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song
2019	J	`jnl`	Deep learning with evolutionary and genomic profiles for identifying cancer subtypes. J. Bioinform. Comput. Biol. Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu
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`	MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters. Bioinform. Meng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia
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`	Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings Bioinform. Jiawei Wang, Bingjiao Yang, Yi An, Tatiana T. Marquez-Lago, André Leier, Jonathan Wilksch, Qingyang Hong, Yang Zhang, Morihiro Hayashida, Tatsuya Akutsu, Geoffrey I. Webb, Richard A. Strugnell, Jiangning Song, Trevor Lithgow
2019	J	`jnl`	Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu
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
2019	J	`jnl`	iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Briefings Bioinform. Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou
2018	J	`jnl`	ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides. Bioinform. Leyi Wei, Chen Zhou, Huangrong Chen, Jiangning Song, Ran Su
2018	J	`jnl`	Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinform. Jiawei Wang, Bingjiao Yang, André Leier, Tatiana T. Marquez-Lago, Morihiro Hayashida, Andrea Rocker, Yanju Zhang, Tatsuya Akutsu, Kuo-Chen Chou, Richard A. Strugnell, Jiangning Song, Trevor Lithgow
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`	Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE ACM Trans. Comput. Biol. Bioinform. Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu
2018	J	`jnl`	Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. Briefings Bioinform. Huilin Wang, Liubin Feng, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song, Donghai Lin
2018	J	`jnl`	PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinform. Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike
2018	—	`—`	Predicting functional sites in proteins using intelligent machine learning and data mining techniques. Jiangning Song
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
2018	J	`jnl`	Structural Principles Analysis of Host-Pathogen Protein-Protein Interactions: A Structural Bioinformatics Survey. IEEE Access Huaming Chen, William W. Guo, Jun Shen, Lei Wang, Jiangning Song
2018	J	`jnl`	iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. Bioinform. Zhen Chen, Pei Zhao, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Yanan Wang, Geoffrey I. Webb, Alexander Ian Smith, Roger J. Daly, Kuo-Chen Chou, Jiangning Song
2017	C	`conf`	Collaborative data analytics towards prediction on pathogen-host protein-protein interactions. CSCWD Huaming Chen, Jun Shen, Lei Wang, Jiangning Song
2017	J	`jnl`	Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. Briefings Bioinform. Huilin Wang, Liubin Feng, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song, Donghai Lin
2017	—	`conf`	Leveraging Stacked Denoising Autoencoder in Prediction of Pathogen-Host Protein-Protein Interactions. BigData Congress Huaming Chen, Jun Shen, Lei Wang, Jiangning Song
2017	J	`jnl`	POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. Bioinform. Jiawei Wang, Bingjiao Yang, Jerico Nico De Leon Revote, André Leier, Tatiana T. Marquez-Lago, Geoffrey I. Webb, Jiangning Song, Kuo-Chen Chou, Trevor Lithgow
2017	J	`jnl`	Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences. BMC Genom. Jing Ren, Jiangning Song, John T. Ellis, Jinyan Li
2017	—	`conf`	Towards Elucidating the Structural Principles of Host-Pathogen Protein-Protein Interaction Networks: A Bioinformatics Survey. BigData Congress Huaming Chen, Jiangning Song, Geng Sun, Jun Shen, Lei Wang
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	C	`conf`	Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network. BIBE Jira Jindalertudomdee, Morihiro Hayashida, Jiangning Song, Tatsuya Akutsu
2016	—	`ed.`	IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, December 15-18, 2016 BIBM Tianhai Tian, Qinghua Jiang, Yunlong Liu, Kevin Burrage, Jiangning Song, Yadong Wang, Xiaohua Hu, Shinichi Morishita, Qian Zhu, Guohua Wang
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
2016	—	`conf`	Preface. BIBM Yadong Wang, Kevin Burrage, Yunlong Liu, Shinichi Morishita, Tianhai Tian, Qinghua Jiang, Jiangning Song, Guohua Wang, Qian Zhu, Xiaohua Tony Hu
2016	—	`conf`	Towards Data Analytics of Pathogen-Host Protein-Protein Interaction: A Survey. BigData Congress Huaming Chen, Jun Shen, Lei Wang, Jiangning Song
2015	J	`jnl`	Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. J. Comput. Biol. Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu
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
2015	J	`jnl`	Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches. Briefings Bioinform. Catherine Ching Han Chang, Beng Ti Tey, Jiangning Song, Ramakrishnan Nagasundara Ramanan
2015	J	`jnl`	Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. Zhen Chen, Yuan Zhou, Ziding Zhang, Jiangning Song
2014	J	`jnl`	Bioinformatics approaches for improved recombinant protein production in Briefings Bioinform. Catherine Ching Han Chang, Jiangning Song, Beng Ti Tey, Ramakrishnan Nagasundara Ramanan
2014	J	`jnl`	Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinform. Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song
2013	J	`jnl`	Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. BMC Syst. Biol. Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
2012	J	`jnl`	Exploring drug combinations in genetic interaction network. BMC Bioinform. Yin-Ying Wang, Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao
2012	—	`conf`	Predicting protein-RNA residue-base contacts using two-dimensional conditional random field. ISB Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
2012	J	`jnl`	The drug cocktail network. BMC Syst. Biol. Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao
2011	J	`jnl`	Bioinformatic Approaches for Predicting substrates of Proteases. J. Bioinform. Comput. Biol. Jiangning Song, Hao Tan, Sarah E. Boyd, Hong-Bin Shen, Khalid Mahmood, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock, Robert N. Pike
2011	J	`jnl`	Conditional random field approach to prediction of protein-protein interactions using domain information. BMC Syst. Biol. Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu
2010	J	`jnl`	APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinform. Junfeng Xia, Xing-Ming Zhao, Jiangning Song, De-Shuang Huang
2010	J	`jnl`	Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinform. Jiangning Song, Hao Tan, Hong-Bin Shen, Khalid Mahmood, Sarah E. Boyd, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock
2010	J	`jnl`	EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes. Bioinform. Khalid Mahmood, Arun Siddharth Konagurthu, Jiangning Song, Ashley M. Buckle, Geoffrey I. Webb, James C. Whisstock
2010	J	`jnl`	Improving the accuracy of predicting disulfide connectivity by feature selection. J. Comput. Chem. Lin Zhu, Jie Yang, Jiangning Song, Kuo-Chen Chou, Hong-Bin Shen
2010	J	`jnl`	Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties. Inf. Media Technol. Jiangning Song, Kazuhiro Takemoto, Hongbin Shen, Hao Tan, M. Michael Gromiha, Tatsuya Akutsu
2008	J	`jnl`	HSEpred: predict half-sphere exposure from protein sequences. Bioinform. Jiangning Song, Hao Tan, Kazuhiro Takemoto, Tatsuya Akutsu
2007	J	`jnl`	Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure. Bioinform. Jiangning Song, Zheng Yuan, Hao Tan, Thomas Huber, Kevin Burrage
2006	J	`jnl`	Predicting residue-wise contact orders in proteins by support vector regression. BMC Bioinform. Jiangning Song, Kevin Burrage
2006	J	`jnl`	Prediction of BMC Bioinform. Jiangning Song, Kevin Burrage, Zheng Yuan, Thomas Huber