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2020 – today
- 2024
[j138]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)- [j137]Yuchuan Zhang, Zhikang Wang, Fang Ge, Xiaoyu Wang, Yiwen Zhang, Shanshan Li, Yuming Guo, Jiangning Song, Dong-Jun Yu:
MLSNet: a deep learning model for predicting transcription factor binding sites. Briefings Bioinform. 25(6) (2024) - [j136]Yuhan Wang, Zhikang Wang, Xuan Yu, Xiaoyu Wang, Jiangning Song, Dong-Jun Yu, Fang Ge:
MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification. Briefings Bioinform. 26(1) (2024) - [j135]Lixuan Mu, Jiangning Song, Tatsuya Akutsu, Tomoya Mori:
DiCleave: a deep learning model for predicting human Dicer cleavage sites. BMC Bioinform. 25(1): 13 (2024) - [j134]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: 107681 (2024) - [j133]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: 108339 (2024) - [j132]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): 1407-1418 (2024) - [j131]Ming Zhang, Xiaohua Wang, Shanruo Xu, Fang Ge, Ian Costa Paixao, Jiangning Song, Dong-Jun Yu:
MetalTrans: A Biological Language Model-Based Approach for Predicting Disease-Associated Mutations in Protein Metal-Binding Sites. J. Chem. Inf. Model. 64(15): 6216-6229 (2024) - [j130]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: 103252 (2024) - [j129]Dian Liu, Zi Liu, Yunpeng Xia, Zhikang Wang, Jiangning Song, Dong-Jun Yu:
TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 21(5): 1403-1412 (2024) - [j128]Yunpeng Xia, Ying Zhang, Dian Liu, Yi-Heng Zhu, Zhikang Wang, Jiangning Song, Dong-Jun Yu:
BLAM6A-Merge: Leveraging Attention Mechanisms and Feature Fusion Strategies to Improve the Identification of RNA N6-Methyladenosine Sites. IEEE ACM Trans. Comput. Biol. Bioinform. 21(6): 1803-1815 (2024) - [j127]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): 1134-1143 (2024) - [j126]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): 2445-2454 (2024) - [c12]Hongmin Cai, Weiting Yi, Weitian Huang, Zhikang Wang, Yue Zhang, Jiangning Song:
A Hierarchical Hypergraph Attention Network for Survival Analysis from Pathological Images. ISBI 2024: 1-4 - [i7]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 abs/2403.10040 (2024) - [i6]Rong Han, Xiaohong Liu, Tong Pan, Jing Xu, Xiaoyu Wang, Wuyang Lan, Zhenyu Li, Zixuan Wang, Jiangning Song, Guangyu Wang, Ting Chen:
CoPRA: Bridging Cross-domain Pretrained Sequence Models with Complex Structures for Protein-RNA Binding Affinity Prediction. CoRR abs/2409.03773 (2024) - [i5]Yilong Zang, Lingfei Ren, Yue Li, Zhikang Wang, David Antony Selby, Zheng Wang, Sebastian Vollmer, Hongzhi Yin, Jiangning Song, Junhang Wu:
Rethinking Cancer Gene Identification through Graph Anomaly Analysis. CoRR abs/2412.17240 (2024) - 2023
- [j125]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) - [j124]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) - [j123]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) - [j122]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) - [j121]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) - [j120]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:
iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities. Briefings Bioinform. 24(4) (2023) - [j119]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) - [j118]Yan Cui, Zhikang Wang, Xiaoyu Wang, Yiwen Zhang, Ying Zhang, Tong Pan, Zhe Zhang, Shanshan Li, Yuming Guo, Tatsuya Akutsu, Jiangning Song:
SMG: self-supervised masked graph learning for cancer gene identification. Briefings Bioinform. 24(6) (2023) - [j117]Fuyi Li, Cong Wang, Xudong Guo, Tatsuya Akutsu, Geoffrey I. Webb, Lachlan J. M. Coin, Lukasz A. Kurgan, Jiangning Song:
ProsperousPlus: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction. Briefings Bioinform. 24(6) (2023) - [j116]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) - [j115]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) - [j114]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) - [j113]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) - [j112]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) - [j111]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): 139 (2023) - [j110]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: 107155 (2023) - [j109]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: 107733 (2023) - [j108]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): 1236-1249 (2023) - [j107]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) - [j106]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): 3205-3214 (2023) - 2022
- [j105]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) - [j104]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) - [j103]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) - [j102]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) - [j101]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) - [j100]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) - [j99]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) - [j98]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) - [j97]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) - [j96]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) - [j95]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) - [j94]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) - [j93]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) - [j92]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) - [j91]Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song:
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. BMC Bioinform. 23(1): 444 (2022) - [j90]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) - [j89]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) - [j88]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) - [j87]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) - [j86]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
- [j85]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) - [j84]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) - [j83]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) - [j82]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) - [j81]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) - [j80]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) - [j79]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) - [j78]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) - [j77]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) - [j76]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) - [j75]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) - [j74]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) - [j73]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) - [j72]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) - [j71]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) - [j70]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) - [j69]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) - [j68]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) - [j67]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) - [j66]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) - [j65]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) - [j64]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) - [j63]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) - [j62]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) - [j61]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
- [j60]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) - [j59]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) - [j58]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) - [j57]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) - [j56]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) - [j55]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) - [j54]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) - [j53]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) - [j52]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) - [j51]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) - [j50]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) - [j49]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
- [j48]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) - [j47]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) - [j46]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) - [j45]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) - [j44]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) - [j43]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) - [j42]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) - [j41]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) - [j40]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) - [j39]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) - [j38]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 - [j37]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) - [j36]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) - [j35]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) - [j34]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) - [j33]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) - [j32]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) - [j31]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) - [j30]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) - [j29]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) - [j28]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
- [j27]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) - [j26]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) - [j25]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
- [j24]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) - [j23]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) - [j22]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) - [j21]Chen Li, Jeremy Nagel, Steve G. Androulakis, 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) - [c4]Jira Jindalertudomdee, Morihiro Hayashida, Jiangning Song, Tatsuya Akutsu:
Host-Pathogen Protein Interaction Prediction Based on Local Topology Structures of a Protein Interaction Network. BIBE 2016: 7-12 - [c3]Yadong Wang, Kevin Burrage, Yunlong Liu, Shinichi Morishita, Tianhai Tian, Qinghua Jiang, Jiangning Song, Guohua Wang, Qian Zhu, Xiaohua Tony Hu:
Preface. BIBM 2016: 1-2 - [c2]Huaming Chen, Jun Shen, Lei Wang, Jiangning Song:
Towards Data Analytics of Pathogen-Host Protein-Protein Interaction: A Survey. BigData Congress 2016: 377-388 - [e1]Tianhai Tian, Qinghua Jiang, Yunlong Liu, Kevin Burrage, Jiangning Song, Yadong Wang, Xiaohua Hu, Shinichi Morishita, Qian Zhu, Guohua Wang:
IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, December 15-18, 2016. IEEE Computer Society 2016, ISBN 978-1-5090-1611-2 [contents] - 2015
- [j20]Catherine Ching Han Chang, Beng Ti Tey, Jiangning Song, Ramakrishnan Nagasundara Ramanan:
Towards more accurate prediction of protein folding rates: a review of the existing web-based bioinformatics approaches. Briefings Bioinform. 16(2): 314-324 (2015) - [j19]Zhen Chen, Yuan Zhou, Ziding Zhang, Jiangning Song:
Towards more accurate prediction of ubiquitination sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. 16(4): 640-657 (2015) - [j18]Fuyi Li, Chen Li, Mingjun Wang, Geoffrey I. Webb, Yang Zhang, James C. Whisstock, Jiangning Song:
GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome. Bioinform. 31(9): 1411-1419 (2015) - [j17]Wei Lu, Takeyuki Tamura, Jiangning Song, Tatsuya Akutsu:
Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a Boolean Model. J. Comput. Biol. 22(2): 85-110 (2015) - 2014
- [j16]Catherine Ching Han Chang, Jiangning Song, Beng Ti Tey, Ramakrishnan Nagasundara Ramanan:
Bioinformatics approaches for improved recombinant protein production in Escherichia coli: protein solubility prediction. Briefings Bioinform. 15(6): 953-962 (2014) - [j15]Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu, James C. Whisstock, Jiangning Song:
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. Bioinform. 30(1): 71-80 (2014) - 2013
- [j14]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Prediction of protein-RNA residue-base contacts using two-dimensional conditional random field with the lasso. BMC Syst. Biol. 7(S-2): S15 (2013) - 2012
- [j13]Yin-Ying Wang, Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao:
Exploring drug combinations in genetic interaction network. BMC Bioinform. 13(S-7): S7 (2012) - [j12]Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao:
The drug cocktail network. BMC Syst. Biol. 6(S-1): S5 (2012) - [c1]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Predicting protein-RNA residue-base contacts using two-dimensional conditional random field. ISB 2012: 152-157 - 2011
- [j11]Morihiro Hayashida, Mayumi Kamada, Jiangning Song, Tatsuya Akutsu:
Conditional random field approach to prediction of protein-protein interactions using domain information. BMC Syst. Biol. 5(S-1): S8 (2011) - [j10]Jiangning Song, Hao Tan, Sarah E. Boyd, Hong-Bin Shen, Khalid Mahmood, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock, Robert N. Pike:
Bioinformatic Approaches for Predicting substrates of Proteases. J. Bioinform. Comput. Biol. 9(1): 149-178 (2011) - 2010
- [j9]Jiangning Song, Hao Tan, Hong-Bin Shen, Khalid Mahmood, Sarah E. Boyd, Geoffrey I. Webb, Tatsuya Akutsu, James C. Whisstock:
Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinform. 26(6): 752-760 (2010) - [j8]Khalid Mahmood, Arun Siddharth Konagurthu, Jiangning Song, Ashley M. Buckle, Geoffrey I. Webb, James C. Whisstock:
EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes. Bioinform. 26(17): 2076-2084 (2010) - [j7]Junfeng Xia, Xing-Ming Zhao, Jiangning Song, De-Shuang Huang:
APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility. BMC Bioinform. 11: 174 (2010) - [j6]Jiangning Song, Kazuhiro Takemoto, Hongbin Shen, Hao Tan, M. Michael Gromiha, Tatsuya Akutsu:
Prediction of Protein Folding Rates from Structural Topology and Complex Network Properties. Inf. Media Technol. 5(3): 980-993 (2010) - [j5]Lin Zhu, Jie Yang, Jiangning Song, Kuo-Chen Chou, Hong-Bin Shen:
Improving the accuracy of predicting disulfide connectivity by feature selection. J. Comput. Chem. 31(7): 1478-1485 (2010)
2000 – 2009
- 2008
- [j4]Jiangning Song, Hao Tan, Kazuhiro Takemoto, Tatsuya Akutsu:
HSEpred: predict half-sphere exposure from protein sequences. Bioinform. 24(13): 1489-1497 (2008) - 2007
- [j3]Jiangning Song, Zheng Yuan, Hao Tan, Thomas Huber, Kevin Burrage:
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure. Bioinform. 23(23): 3147-3154 (2007) - 2006
- [j2]Jiangning Song, Kevin Burrage, Zheng Yuan, Thomas Huber:
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information. BMC Bioinform. 7: 124 (2006) - [j1]Jiangning Song, Kevin Burrage:
Predicting residue-wise contact orders in proteins by support vector regression. BMC Bioinform. 7: 425 (2006)
Coauthor Index
Lachlan James M. Coin
aka: Lachlan J. M. Coin
aka: Lachlan J. M. Coin
[j134] [j132] [j126] [j125] [j123] [j122] [j120] [j119] [j117] [j110] [j106] [j103] [j101] [j100] [j99] [j97] [j94] [j91] [j88] [j87] [j85] [j84] [j83] [j81] [j80] [j79] [j77] [j75] [j72] [j71] [j67] [j64] [j62] [j61] [j60] [j59] [j58] [j57] [j56] [j54] [j53] [j52] [j50] [j49] [j48] [j45] [j43] [j41] [j40] [j39] [j34] [j33] [j30] [j18]
Dongjun Yu
aka: Dong-Jun Yu
aka: Dong-Jun Yu
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