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2020 – today
- 2023
[j102]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)- [j101]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) - 2022
- [j100]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) - [j99]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) - [j98]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) - [j97]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) - [j96]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) - [j95]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) - [j94]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) - [j93]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) - [j92]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) - [j91]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): 4019-4026 (2022) - [j90]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): 4053-4061 (2022) - [j89]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): 4206-4213 (2022) - [j88]Chunting Liu, Jiangning Song, Hiroyuki Ogata, Tatsuya Akutsu:
MSNet-4mC: learning effective multi-scale representations for identifying DNA N4-methylcytosine sites. Bioinform. 38(23): 5160-5167 (2022) - [j87]Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song:
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. BMC Bioinform. 23(1): 444 (2022) - [j86]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: 105961 (2022) - [j85]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): 1794-1807 (2022) - [j84]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): 4270-4282 (2022) - [j83]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:
iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets. Nucleic Acids Res. 50(W1): 434-447 (2022) - [j82]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): 2778-2786 (2022) - [c11]Hongmin Cai, Weiting Yi, Yucheng Li, Wenxiong Liao, Jiangning Song:
A Regional Multiple Instance Learning Network for Whole Slide Image Segmentation. BIBM 2022: 922-928 - [c10]Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song:
Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CVPR 2022: 4744-4753 - [i4]Xinyu Zhang, Vincent C. S. Lee, Jia Rong, James C. Lee, Jiangning Song, Feng Liu:
Multi-channel deep convolutional neural networks for multi-classifying thyroid disease. CoRR abs/2203.03627 (2022) - [i3]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 abs/2208.03526 (2022) - 2021
- [j81]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): 2126-2140 (2021) - [j80]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) - [j79]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) - [j78]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) - [j77]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) - [j76]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) - [j75]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) - [j74]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) - [j73]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) - [j72]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) - [j71]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) - [j70]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) - [j69]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) - [j68]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) - [j67]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) - [j66]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): 3986-3988 (2021) - [j65]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): 4291-4295 (2021) - [j64]Sina Ghadermarzi, Bartosz Krawczyk, Jiangning Song, Lukasz A. Kurgan:
XRRpred: accurate predictor of crystal structure quality from protein sequence. Bioinform. 37(23): 4366-4374 (2021) - [j63]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): 63 (2021) - [j62]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): D651-D659 (2021) - [j61]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): 1801-1810 (2021) - [j60]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): 1937-1945 (2021) - [i2]Zhikang Wang, Feng Zhu, Shixiang Tang, Rui Zhao, Lihuo He, Jiangning Song:
Feature Erasing and Diffusion Network for Occluded Person Re-Identification. CoRR abs/2112.08740 (2021) - [i1]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 abs/2112.09341 (2021) - 2020
- [j59]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): 106-119 (2020) - [j58]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): 1047-1057 (2020) - [j57]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): 1069-1079 (2020) - [j56]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): 1119-1135 (2020) - [j55]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): 1676-1696 (2020) - [j54]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): 704-712 (2020) - [j53]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): 1057-1065 (2020) - [j52]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): 4276-4282 (2020) - [j51]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): 52-64 (2020) - [j50]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): 4667-4679 (2020) - [j49]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): 2050008:1-2050008:21 (2020) - [j48]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): 2050018:1-2050018:17 (2020) - [c9]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 - [c8]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: 384-395
2010 – 2019
- 2019
- [j47]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): 638-658 (2019) - [j46]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): 931-951 (2019) - [j45]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): 1669-1684 (2019) - [j44]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): 2150-2166 (2019) - [j43]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): 2185-2199 (2019) - [j42]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:
Large-scale comparative assessment of computational predictors for lysine post-translational modification sites. Briefings Bioinform. 20(6): 2267-2290 (2019) - [j41]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:
Bastion3: a two-layer ensemble predictor of type III secreted effectors. Bioinform. 35(12): 2017-2028 (2019) - [j40]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): 2957-2965 (2019) - [j39]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): 112:1-112:17 (2019) - [j38]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): 602:1-602:12 (2019) - [j37]Chun-Yu Lin, Peiying Ruan, Ruiming Li, Jinn-Moon Yang, Simon See, Jiangning Song, Tatsuya Akutsu:
Deep learning with evolutionary and genomic profiles for identifying cancer subtypes. J. Bioinform. Comput. Biol. 17(3): 1940005:1-1940005:15 (2019) - 2018
- [b1]Jiangning Song:
Predicting functional sites in proteins using intelligent machine learning and data mining techniques. Monash University, Australia, 2018 - [j36]Huaming Chen, William W. Guo, Jun Shen, Lei Wang, Jiangning Song:
Structural Principles Analysis of Host-Pathogen Protein-Protein Interactions: A Structural Bioinformatics Survey. IEEE Access 6: 11760-11771 (2018) - [j35]Yi An, Jiawei Wang, Chen Li, André Leier, Tatiana T. Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I. Webb, Jiangning Song, Trevor Lithgow:
Comprehensive assessment and performance improvement of effector protein predictors for bacterial secretion systems III, IV and VI. Briefings Bioinform. 19(1): 148-161 (2018) - [j34]Huilin Wang, Liubin Feng, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song, Donghai Lin:
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. Briefings Bioinform. 19(5): 838-852 (2018) - [j33]Jiangning Song, Fuyi Li, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Gholamreza Haffari, Kuo-Chen Chou, Geoffrey I. Webb, Robert N. Pike:
PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy. Bioinform. 34(4): 684-687 (2018) - [j32]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:
iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences. Bioinform. 34(14): 2499-2502 (2018) - [j31]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:
Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors. Bioinform. 34(15): 2546-2555 (2018) - [j30]Leyi Wei, Chen Zhou, Huangrong Chen, Jiangning Song, Ran Su:
ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides. Bioinform. 34(23): 4007-4016 (2018) - [j29]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:
Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome. Bioinform. 34(24): 4223-4231 (2018) - [j28]Bangli Lu, Chen Li, Qingfeng Chen, Jiangning Song:
ProBAPred: Inferring protein-protein binding affinity by incorporating protein sequence and structural features. J. Bioinform. Comput. Biol. 16(4): 1850011:1-1850011:18 (2018) - [j27]Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu:
Computing Minimum Reaction Modifications in a Boolean Metabolic Network. IEEE ACM Trans. Comput. Biol. Bioinform. 15(6): 1853-1862 (2018) - 2017
- [j26]Huilin Wang, Liubin Feng, Geoffrey I. Webb, Lukasz A. Kurgan, Jiangning Song, Donghai Lin:
Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity. Briefings Bioinform. 18(6): 1092 (2017) - [j25]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:
POSSUM: a bioinformatics toolkit for generating numerical sequence feature descriptors based on PSSM profiles. Bioinform. 33(17): 2756-2758 (2017) - [j24]Jing Ren, Jiangning Song, John T. Ellis, Jinyan Li:
Staged heterogeneity learning to identify conformational B-cell epitopes from antigen sequences. BMC Genom. 18(S2) (2017) - [c7]Huaming Chen, Jiangning Song, Geng Sun, Jun Shen, Lei Wang:
Towards Elucidating the Structural Principles of Host-Pathogen Protein-Protein Interaction Networks: A Bioinformatics Survey. BigData Congress 2017: 177-184 - [c6]Huaming Chen, Jun Shen, Lei Wang, Jiangning Song:
Leveraging Stacked Denoising Autoencoder in Prediction of Pathogen-Host Protein-Protein Interactions. BigData Congress 2017: 368-375 - [c5]Huaming Chen, Jun Shen, Lei Wang, Jiangning Song:
Collaborative data analytics towards prediction on pathogen-host protein-protein interactions. CSCWD 2017: 269-274 - 2016
- [j23]Chen Li, Catherine Ching Han Chang, Jeremy Nagel, Benjamin T. Porebski, Morihiro Hayashida, Tatsuya Akutsu, Jiangning Song, Ashley M. Buckle:
Critical evaluation of in silico methods for prediction of coiled-coil domains in proteins. Briefings Bioinform. 17(2): 270-282 (2016) - [j22]Chen Li, Steve G. Androulakis, Ashley M. Buckle, Jiangning Song:
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. Database J. Biol. Databases Curation 2016 (2016) - [j21]Chen Li, Jeremy Nagel, Steve G. Androulakis, Christopher J. Lupton, Jiangning Song, Ashley M. Buckle:
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. Database J. Biol. Databases Curation 2016 (2016) - [j20]Chen Li, Jeremy Nagel, Steve G. Androulakis, Jiangning Song,