Fuyi Li

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 60

Top Topics

Features Extraction

Escherichia Coli

Top Venues

Briefings Bioinform.

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Zexing Zhao, Guangsi Shi, Xiaopeng Wu, Ruohua Ren, Xiaojun Gao, Fuyi Li
Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction. CoRR (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)
Wei Mao, Fuyi Li, Jun Liu, Rui Xiao, Kejie Huang, Yongfu Li, Hao Yu, Yan Liu, Genquan Han
A Low-Power Charge-Domain Bit-Scalable Readout System for Fully-Parallel Computing-in-Memory Accelerators. IEEE Trans. Circuits Syst. II Express Briefs 71 (6) (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)
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)
Luzhi Wang, Yizhen Zheng, Di Jin, Fuyi Li, Yongliang Qiao, Shirui Pan
Contrastive Graph Similarity Networks. ACM Trans. Web 18 (2) (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)
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)
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)
Yixin Liu, Kaize Ding, Qinghua Lu, Fuyi Li, Leo Yu Zhang, Shirui Pan
Towards Self-Interpretable Graph-Level Anomaly Detection. NeurIPS (2023)
Yixin Liu, Kaize Ding, Qinghua Lu, Fuyi Li, Leo Yu Zhang, Shirui Pan
Towards Self-Interpretable Graph-Level Anomaly Detection. CoRR (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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
Yongyan Huang, Fuyi Li, Junping Shi
Stability of synchronized steady state solution of diffusive Lotka-Volterra predator-prey model. Appl. Math. Lett. 105 (2020)
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)
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)
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)
Ting Rong, Fuyi Li, Zhanping Liang
Existence of nontrivial solutions for Kirchhoff-type problems with jumping nonlinearities. Appl. Math. Lett. 95 (2019)
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)
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)
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)
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) (2019)
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) (2018)
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) (2018)
Xiaoli Zhu, Fuyi Li, Yuhua Li
Global solutions and blow up solutions to a class of pseudo-parabolic equations with nonlocal term. Appl. Math. Comput. 329 (2018)
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) (2018)
Qi Zhang, Fuyi Li, Zhanping Liang
Existence of multiple positive solutions to nonhomogeneous Schrödinger-Poisson system. Appl. Math. Comput. 259 (2015)
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) (2015)
Qi Zhang, Fuyi Li, Xiaoli Zhu
Multiple sign-changing solutions to the Sturm-Liouville boundary value problem with resonance. Appl. Math. Comput. 219 (3) (2012)
Fuyi Li, Zhanping Liang
Existence of positive periodic solutions to nonlinear second order differential equations. Appl. Math. Lett. 18 (11) (2005)
Fuyi Li, Yajing Zhang
Multiple symmetric nonnegative solutions of second-order ordinary differential equations. Appl. Math. Lett. 17 (3) (2004)