Jiangning Song

ORCID

Publication Activity (10 Years)

Years Active: 2006-2024
Publications (10 Years): 126

Top Venues

Publications

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 Bioinform. 25 (2) (2024)
Cong Wang, Zhijie He, Runchang Jia, Shirui Pan, Lachlan J. M. Coin, Jiangning Song, Fuyi Li
PLANNER: A Multi-Scale Deep Language Model for the Origins of Replication Site Prediction. IEEE J. Biomed. Health Informatics 28 (4) (2024)
Zhikang Wang, Jiani Ma, Qian Gao, Chris Bain, Seiya Imoto, Pietro Liò, Hongmin Cai, Hao Chen, Jiangning Song
Dual-stream multi-dependency graph neural network enables precise cancer survival analysis. Medical Image Anal. 97 (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. J. Chem. Inf. Model. 64 (4) (2024)
Hongmin Cai, Yi Liao, Lei Zhu, Zhikang Wang, Jiangning Song
Improving Cancer Survival Prediction via Graph Convolutional Neural Network Learning on Protein-Protein Interaction Networks. IEEE J. Biomed. Health Informatics 28 (2) (2024)
Zhikang Wang, Yumeng Zhang, Yingxue Xu, Seiya Imoto, Hao Chen, Jiangning Song
Histo-Genomic Knowledge Distillation For Cancer Prognosis From Histopathology Whole Slide Images. CoRR (2024)
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
PmxPred: A data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria. Comput. Biol. Medicine 168 (2024)
Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori
DiCleave: a deep learning model for predicting human Dicer cleavage sites. BMC Bioinform. 25 (1) (2024)
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
GraphormerDTI: A graph transformer-based approach for drug-target interaction prediction. Comput. Biol. Medicine 173 (2024)
Fuyi Li, Xudong Guo, Yue Bi, Runchang Jia, Miranda E. Pitt, Shirui Pan, Shuqin Li, Robin B. Gasser, Lachlan J. M. Coin, Jiangning Song
Digerati - A multipath parallel hybrid deep learning framework for the identification of mycobacterial PE/PPE proteins. Comput. Biol. Medicine 163 (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 Bioinform. 24 (4) (2023)
Yan Liu, Guo Wei, Chen Li, Long-Chen Shen, Robin B. Gasser, Jiangning Song, Dijun Chen, Dong-Jun Yu
TripletCell: a deep metric learning framework for accurate annotation of cell types at the single-cell level. Briefings Bioinform. 24 (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 Digit. Medicine 6 (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. Bioinform. 39 (3) (2023)
Fang Ge, Chen Li, Shahid Iqbal, Muhammad Arif, 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 Bioinform. 24 (1) (2023)
Zixuan Wang, Yi Zhou, Tatsuya Takagi, Jiangning Song, Yu-Shi Tian, Tetsuo Shibuya
Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data. BMC Bioinform. 24 (1) (2023)
Ying Zhang, Fang Ge, Fuyi Li, Xibei Yang, Jiangning Song, Dong-Jun Yu
Prediction of Multiple Types of RNA Modifications via Biological Language Model. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (5) (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 Bioinform. 24 (2) (2023)
Ruyi Chen, Fuyi Li, Xudong Guo, Yue Bi, Chen Li, Shirui Pan, Lachlan J. M. Coin, Jiangning Song
ATTIC is an integrated approach for predicting A-to-I RNA editing sites in three species. Briefings Bioinform. 24 (3) (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. Bioinform. 39 (3) (2023)
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
Surformer: An interpretable pattern-perceptive survival transformer for cancer survival prediction from histopathology whole slide images. Comput. Methods Programs Biomed. 241 (2023)
Ying Zhang, Zhikang Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu
Interpretable prediction models for widespread m6A RNA modification across cell lines and tissues. Bioinform. 39 (12) (2023)
Matee Ullah, Fazal Hadi, Jiangning Song, Dong-Jun Yu
PScL-2LSAESM: bioimage-based prediction of protein subcellular localization by integrating heterogeneous features with the two-level SAE-SM and mean ensemble method. Bioinform. 39 (1) (2023)
Fang Wang, Fan Yang, Longkai Huang, Wei Li, Jiangning Song, Robin B. Gasser, Ruedi Aebersold, Guohua Wang, Jianhua Yao
Deep domain adversarial neural network for the deconvolution of cell type mixtures in tissue proteome profiling. Nat. Mac. Intell. 5 (11) (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 Bioinform. 24 (1) (2023)
Jiani Ma, Chen Li, Yiwen Zhang, Zhikang Wang, Shanshan Li, Yuming Guo, Lin Zhang, Hui Liu, Xin Gao, Jiangning Song
MULGA, a unified multi-view graph autoencoder-based approach for identifying drug-protein interaction and drug repositioning. Bioinform. 39 (9) (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 Bioinform. 24 (4) (2023)
Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hong-Yu Ou
T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model. Briefings Bioinform. 23 (1) (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 Bioinform. 23 (2) (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 Bioinform. 23 (4) (2022)
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 Bioinform. 23 (1) (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 Bioinform. 23 (6) (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. Bioinform. 38 (16) (2022)
Xinyu Zhang, Vincent C. S. Lee, Jia Rong, James C. Lee, Jiangning Song, Feng Liu
A multi-channel deep convolutional neural network for multi-classifying thyroid diseases. Comput. Biol. Medicine 148 (2022)
Zhikang Wang, Yue Bi, Tong Pan, Xiaoyu Wang, Chris Bain, Richard Bassed, Seiya Imoto, Jianhua Yao, Jiangning Song
Multiplex-detection Based Multiple Instance Learning Network for Whole Slide Image Classification. CoRR (2022)
Fang Ge, Ying Zhang, Jian Xu, Muhammad Arif, Jiangning Song, Dong-Jun Yu
Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion. Briefings Bioinform. 23 (1) (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. Bioinform. 38 (17) (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 Bioinform. 23 (4) (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. Bioinform. 38 (17) (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. J. Chem. Inf. Model. 62 (17) (2022)
Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song
Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CVPR (2022)
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 Bioinform. 23 (1) (2022)
Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. BMC Bioinform. 23 (1) (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 A. Kurgan, Jiangning Song
an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. Nucleic Acids Res. 50 (W1) (2022)
Lu-Xing Zhang, He Yan, Yan Liu, Jian Xu, Jiangning Song, Dong-Jun Yu
Enhancing Characteristic Gene Selection and Tumor Classification by the Robust Laplacian Supervised Discriminative Sparse PCA. J. Chem. Inf. Model. 62 (7) (2022)
Guanhua Ye, Hongzhi Yin, Tong Chen, Miao Xu, Quoc Viet Hung Nguyen, Jiangning Song
Personalized On-Device E-Health Analytics With Decentralized Block Coordinate Descent. IEEE J. Biomed. Health Informatics 26 (6) (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 Bioinform. 23 (2) (2022)
Hongmin Cai, Weiting Yi, Yucheng Li, Wenxiong Liao, Jiangning Song
A Regional Multiple Instance Learning Network for Whole Slide Image Segmentation. BIBM (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 Bioinform. 23 (6) (2022)
Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinform. 38 (23) (2022)
Xinyu Zhang, Vincent CS. Lee, Jia Rong, James C. Lee, Jiangning Song, Feng Liu
Multi-channel deep convolutional neural networks for multi-classifying thyroid disease. CoRR (2022)
Yanan Wang, Litao Yang, Geoffrey I. Webb, Zongyuan Ge, Jiangning Song
OCTID: a one-class learning-based Python package for tumor image detection. Bioinform. 37 (21) (2021)
Fuyi Li, Xudong Guo, Peipei Jin, Jinxiang Chen, Dongxu Xiang, Jiangning Song, Lachlan J. M. Coin
Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. Briefings Bioinform. 22 (6) (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 Bioinform. 22 (3) (2021)
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 Bioinform. 22 (6) (2021)
Xiao Liang, Fuyi Li, Jinxiang Chen, Junlong Li, Hao Wu, Shuqin Li, Jiangning Song, Quanzhong Liu
Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification. Briefings Bioinform. 22 (4) (2021)
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
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. Nucleic Acids Res. 49 (Database-Issue) (2021)
Matee Ullah, Ke Han, Fazal Hadi, Jian Xu, Jiangning Song, Dong-Jun Yu
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. 22 (6) (2021)
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
HEAL: an automated deep learning framework for cancer histopathology image analysis. Bioinform. 37 (22) (2021)
Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I Webb, Jiangning Song
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. Briefings Bioinform. 22 (6) (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 Bioinform. 22 (5) (2021)
Pengyu Liu, Jiangning Song, Chun-Yu Lin, Tatsuya Akutsu
ReCGBM: a gradient boosting-based method for predicting human dicer cleavage sites. BMC Bioinform. 22 (1) (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 Bioinform. 22 (5) (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 Bioinform. 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 Bioinform. 22 (5) (2021)
Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song
Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CoRR (2021)
Fuyi Li, Jinxiang Chen, Zongyuan Ge, Ya Wen, Yanwei Yue, Morihiro Hayashida, Abdelkader Baggag, Halima Bensmail, Jiangning Song
Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. Briefings Bioinform. 22 (2) (2021)
Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song, Fuyi Li
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites. Briefings Bioinform. 22 (3) (2021)
Yong-Zi Chen, Zhuo-Zhi Wang, Yanan Wang, Guoguang Ying, Zhen Chen, Jiangning Song
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. Briefings Bioinform. 22 (6) (2021)
Sina Ghadermarzi, Bartosz Krawczyk, Jiangning Song, Lukasz A. Kurgan
XRRpred: accurate predictor of crystal structure quality from protein sequence. Bioinform. 37 (23) (2021)
Huaming Chen, Fuyi Li, Lei Wang, Yaochu Jin, Chi-Hung Chi, Lukasz A. Kurgan, Jiangning Song, Jun Shen
Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions. Briefings Bioinform. 22 (3) (2021)
Cangzhi Jia, Meng Zhang, Cunshuo Fan, Fuyi Li, Jiangning Song
Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (5) (2021)
Jinxiang Chen, Fuyi Li, Miao Wang, Junlong Li, Tatiana T. Marquez-Lago, André Leier, Jerico Revote, Shuqin Li, Quanzhong Liu, Jiangning Song
BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data. Frontiers Big Data 4 (2021)
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
A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction. IEEE ACM Trans. Comput. Biol. Bioinform. 18 (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 Bioinform. 22 (3) (2021)
Long-Chen Shen, Yan Liu, Jiangning Song, Dong-Jun Yu
SAResNet: self-attention residual network for predicting DNA-protein binding. Briefings Bioinform. 22 (5) (2021)
Guanhua Ye, Hongzhi Yin, Tong Chen, Miao Xu, Quoc Viet Hung Nguyen, Jiangning Song
Personalized On-Device E-health Analytics with Decentralized Block Coordinate Descent. CoRR (2021)
Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu
Improving protein fold recognition using triplet network and ensemble deep learning. Briefings Bioinform. 22 (6) (2021)
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
PRISMOID: a comprehensive 3D structure database for post-translational modifications and mutations with functional impact. Briefings Bioinform. 21 (3) (2020)
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
Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information. Genom. Proteom. Bioinform. 18 (1) (2020)
Huaming Chen, Jun Shen, Lei Wang, Jiangning Song
A framework towards data analytics on host-pathogen protein-protein interactions. J. Ambient Intell. Humaniz. Comput. 11 (11) (2020)
Ying Xu, Campbell Wilson, André Leier, Tatiana T. Marquez-Lago, James C. Whisstock, Jiangning Song
PhosTransfer: A Deep Transfer Learning Framework for Kinase-Specific Phosphorylation Site Prediction in Hierarchy. PAKDD (2) (2020)
Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, Alexander Ian Smith, Geoffrey I. Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song
Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences. Briefings Bioinform. 21 (5) (2020)
Cangzhi Jia, Yue Bi, Jinxiang Chen, André Leier, Fuyi Li, Jiangning Song
PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs. Bioinform. 36 (15) (2020)
Ying Xu, André Leier, Tatiana T. Marquez-Lago, Jue Xie, Antonio Jimeno-Yepes, James C. Whisstock, Campbell Wilson, Jiangning Song
Prediction of secondary structure population and intrinsic disorder of proteins using multitask deep learning. AMIA (2020)
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
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins. Bioinform. 36 (3) (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. J. Bioinform. Comput. Biol. 18 (2) (2020)
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
A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Briefings Bioinform. 21 (4) (2020)
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
DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites. Bioinform. 36 (4) (2020)
Leyi Wei, Jie Hu, Fuyi Li, Jiangning Song, Ran Su, Quan Zou
Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms. Briefings Bioinform. 21 (1) (2020)
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
iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data. Briefings Bioinform. 21 (3) (2020)
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. J. Bioinform. Comput. Biol. 18 (4) (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 Bioinform. 20 (1) (2019)
Jiangning Song, Yanan Wang, Fuyi Li, Tatsuya Akutsu, Neil D. Rawlings, Geoffrey I. Webb, Kuo-Chen Chou
iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites. Briefings Bioinform. 20 (2) (2019)
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
Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods. Briefings Bioinform. 20 (6) (2019)
Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu
Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. 20 (5) (2019)
Meng Zhang, Fuyi Li, Tatiana T. Marquez-Lago, André Leier, Cunshuo Fan, Chee Keong Kwoh, Kuo-Chen Chou, Jiangning Song, Cangzhi Jia
MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters. Bioinform. 35 (17) (2019)
Yanju Zhang, Ruopeng Xie, Jiawei Wang, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Geoffrey I. Webb, Kuo-Chen Chou, Jiangning Song
Computational analysis and prediction of lysine malonylation sites by exploiting informative features in an integrative machine-learning framework. Briefings Bioinform. 20 (6) (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 Bioinform. 20 (1) (2019)
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
Systematic analysis and prediction of type IV secreted effector proteins by machine learning approaches. Briefings Bioinform. 20 (3) (2019)

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Publication Activity (10 Years)

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Jiangning Song