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BibTeX records: Fuyi Li
@article{DBLP:journals/bib/GuoRL25, author = {Xudong Guo and Zixu Ran and Fuyi Li}, title = {Kinase-inhibitor binding affinity prediction with pretrained graph encoder and language model}, journal = {Briefings Bioinform.}, volume = {26}, number = {4}, year = {2025}, url = {https://doi.org/10.1093/bib/bbaf338}, doi = {10.1093/BIB/BBAF338}, timestamp = {Sun, 10 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GuoRL25.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcasI/MaoLZLLWYCZY25, author = {Wei Mao and Dingbang Liu and Haoxiang Zhou and Fuyi Li and Kai Li and Qiuping Wu and Jiaqi Yang and Quan Cheng and Liuyang Zhang and Hao Yu}, title = {A 28-nm 135.19 {TOPS/W} Bootstrapped-SRAM Compute-in-Memory Accelerator With Layer-Wise Precision and Sparsity}, journal = {{IEEE} Trans. Circuits Syst. {I} Regul. Pap.}, volume = {72}, number = {7}, pages = {3236--3246}, year = {2025}, url = {https://doi.org/10.1109/TCSI.2024.3486322}, doi = {10.1109/TCSI.2024.3486322}, timestamp = {Sat, 09 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcasI/MaoLZLLWYCZY25.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/titb/ZhaoSWRGL25, author = {Zexing Zhao and Guangsi Shi and Xiaopeng Wu and Ruohua Ren and Xiaojun Gao and Fuyi Li}, title = {DIG-Mol: {A} Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction}, journal = {{IEEE} J. Biomed. Health Informatics}, volume = {29}, number = {3}, pages = {1735--1746}, year = {2025}, url = {https://doi.org/10.1109/JBHI.2024.3464674}, doi = {10.1109/JBHI.2024.3464674}, timestamp = {Tue, 01 Apr 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/titb/ZhaoSWRGL25.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/aaai/Pan0ZZLLP25, author = {Junjun Pan and Yixin Liu and Xin Zheng and Yizhen Zheng and Alan Wee{-}Chung Liew and Fuyi Li and Shirui Pan}, editor = {Toby Walsh and Julie Shah and Zico Kolter}, title = {A Label-free Heterophily-guided Approach for Unsupervised Graph Fraud Detection}, booktitle = {AAAI-25, Sponsored by the Association for the Advancement of Artificial Intelligence, February 25 - March 4, 2025, Philadelphia, PA, {USA}}, pages = {12443--12451}, publisher = {{AAAI} Press}, year = {2025}, url = {https://doi.org/10.1609/aaai.v39i12.33356}, doi = {10.1609/AAAI.V39I12.33356}, timestamp = {Fri, 22 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/aaai/Pan0ZZLLP25.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-2502-13308, author = {Junjun Pan and Yixin Liu and Xin Zheng and Yizhen Zheng and Alan Wee{-}Chung Liew and Fuyi Li and Shirui Pan}, title = {A Label-Free Heterophily-Guided Approach for Unsupervised Graph Fraud Detection}, journal = {CoRR}, volume = {abs/2502.13308}, year = {2025}, url = {https://doi.org/10.48550/arXiv.2502.13308}, doi = {10.48550/ARXIV.2502.13308}, eprinttype = {arXiv}, eprint = {2502.13308}, timestamp = {Wed, 19 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/corr/abs-2502-13308.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SongSLLW24, author = {Renhua Song and Gavin J. Sutton and Fuyi Li and Qian Liu and Justin J.{-}L. Wong}, title = {Variable calling of m6A and associated features in databases: a guide for end-users}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae434}, doi = {10.1093/BIB/BBAE434}, timestamp = {Sun, 10 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SongSLLW24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLZISLGYS24, author = {Xiaoyu Wang and Fuyi Li and Yiwen Zhang and Seiya Imoto and Hsin{-}Hui Shen and Shanshan Li and Yuming Guo and Jian Yang and Jiangning Song}, title = {Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects}, journal = {Briefings Bioinform.}, volume = {25}, number = {3}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae446}, doi = {10.1093/BIB/BBAE446}, timestamp = {Mon, 11 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLZISLGYS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuJBGZL24, author = {Tianxiang Liu and Cangzhi Jia and Yue Bi and Xudong Guo and Quan Zou and Fuyi Li}, title = {scDFN: enhancing single-cell RNA-seq clustering with deep fusion networks}, journal = {Briefings Bioinform.}, volume = {25}, number = {6}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae486}, doi = {10.1093/BIB/BBAE486}, timestamp = {Sat, 30 Nov 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuJBGZL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangLXWHBYL24, author = {Zhenhao Zhang and Yuxi Liu and Meichen Xiao and Kun Wang and Yu Huang and Jiang Bian and Ruolin Yang and Fuyi Li}, title = {Graph contrastive learning as a versatile foundation for advanced scRNA-seq data analysis}, journal = {Briefings Bioinform.}, volume = {25}, number = {6}, year = {2024}, url = {https://doi.org/10.1093/bib/bbae558}, doi = {10.1093/BIB/BBAE558}, timestamp = {Thu, 07 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ZhangLXWHBYL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/cbm/WangPLWZSTGLSPLS24, author = {Xiaoyu Wang and Nitin Patil and Fuyi Li and Zhikang Wang and Haolan Zhan and Daniel Schmidt and Philip Thompson and Yuming Guo and Cornelia B. Landersdorfer and Hsin{-}Hui Shen and Anton Y. Peleg and Jian Li and Jiangning Song}, title = {PmxPred: {A} data-driven approach for the identification of active polymyxin analogues against gram-negative bacteria}, journal = {Comput. Biol. Medicine}, volume = {168}, pages = {107681}, year = {2024}, url = {https://doi.org/10.1016/j.compbiomed.2023.107681}, doi = {10.1016/J.COMPBIOMED.2023.107681}, timestamp = {Wed, 11 Jun 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/cbm/WangPLWZSTGLSPLS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcisd/YanGLZLSY24, author = {Zihao Yan and Fang Ge and Yan Liu and Yumeng Zhang and Fuyi Li and Jiangning Song and Dong{-}Jun Yu}, title = {TransEFVP: {A} Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion}, journal = {J. Chem. Inf. Model.}, volume = {64}, number = {4}, pages = {1407--1418}, year = {2024}, url = {https://doi.org/10.1021/acs.jcim.3c02019}, doi = {10.1021/ACS.JCIM.3C02019}, timestamp = {Mon, 03 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/jcisd/YanGLZLSY24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcasII/MaoLLXHLYLH24, author = {Wei Mao and Fuyi Li and Jun Liu and Rui Xiao and Kejie Huang and Yongfu Li and Hao Yu and Yan Liu and Genquan Han}, title = {A Low-Power Charge-Domain Bit-Scalable Readout System for Fully-Parallel Computing-in-Memory Accelerators}, journal = {{IEEE} Trans. Circuits Syst. {II} Express Briefs}, volume = {71}, number = {6}, pages = {2916--2920}, year = {2024}, url = {https://doi.org/10.1109/TCSII.2023.3330080}, doi = {10.1109/TCSII.2023.3330080}, timestamp = {Sat, 31 May 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcasII/MaoLLXHLYLH24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcbb/JiaHWGL24, author = {Runchang Jia and Zhijie He and Cong Wang and Xudong Guo and Fuyi Li}, title = {MetalPrognosis: {A} Biological Language Model-Based Approach for Disease-Associated Mutations in Metal-Binding Site Prediction}, journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.}, volume = {21}, number = {6}, pages = {2340--2348}, year = {2024}, url = {https://doi.org/10.1109/TCBB.2024.3467093}, doi = {10.1109/TCBB.2024.3467093}, timestamp = {Sat, 16 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcbb/JiaHWGL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/titb/WangHJPCSL24, author = {Cong Wang and Zhijie He and Runchang Jia and Shirui Pan and Lachlan J. M. Coin and Jiangning Song and Fuyi Li}, title = {{PLANNER:} {A} Multi-Scale Deep Language Model for the Origins of Replication Site Prediction}, journal = {{IEEE} J. Biomed. Health Informatics}, volume = {28}, number = {4}, pages = {2445--2454}, year = {2024}, url = {https://doi.org/10.1109/JBHI.2024.3349584}, doi = {10.1109/JBHI.2024.3349584}, timestamp = {Sat, 16 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/titb/WangHJPCSL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/titb/RanWSPL24, author = {Zixu Ran and Cong Wang and Heyun Sun and Shirui Pan and Fuyi Li}, title = {Characterizing Secretion System Effector Proteins With Structure-Aware Graph Neural Networks and Pre-Trained Language Models}, journal = {{IEEE} J. Biomed. Health Informatics}, volume = {28}, number = {9}, pages = {5649--5657}, year = {2024}, url = {https://doi.org/10.1109/JBHI.2024.3413146}, doi = {10.1109/JBHI.2024.3413146}, timestamp = {Sun, 17 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/titb/RanWSPL24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tweb/WangZJLQP24, author = {Luzhi Wang and Yizhen Zheng and Di Jin and Fuyi Li and Yongliang Qiao and Shirui Pan}, title = {Contrastive Graph Similarity Networks}, journal = {{ACM} Trans. Web}, volume = {18}, number = {2}, pages = {17:1--17:20}, year = {2024}, url = {https://doi.org/10.1145/3580511}, doi = {10.1145/3580511}, timestamp = {Sun, 19 Jan 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/tweb/WangZJLQP24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/pkdd/ZhangLBJSLLS24, author = {Zhenhao Zhang and Yuxi Liu and Jiang Bian and Antonio Jimeno{-}Yepes and Jun Shen and Fuyi Li and Guodong Long and Flora D. Salim}, editor = {Albert Bifet and Tomas Krilavicius and Ioanna Miliou and Slawomir Nowaczyk}, title = {Boosting Patient Representation Learning via Graph Contrastive Learning}, booktitle = {Machine Learning and Knowledge Discovery in Databases. Applied Data Science Track - European Conference, {ECML} {PKDD} 2024, Vilnius, Lithuania, September 9-13, 2024, Proceedings, Part {IX}}, series = {Lecture Notes in Computer Science}, volume = {14949}, pages = {335--350}, publisher = {Springer}, year = {2024}, url = {https://doi.org/10.1007/978-3-031-70378-2\_21}, doi = {10.1007/978-3-031-70378-2\_21}, timestamp = {Mon, 03 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/pkdd/ZhangLBJSLLS24.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/socc/LiXXYZLZH024, author = {Fuyi Li and Yu Xia and Shuai Xiao and Pengcheng Yang and Xingyu Zhu and Bo Li and Jiuren Zhou and Genquan Han and Wei Mao}, editor = {Diana G{\"{o}}hringer and Uwe G{\"{a}}bler and Tanja Harbaum and Klaus Hofmann}, title = {Accurate Charge-Domain Bootstrapped Computing-in-Memory {SRAM} Design with Wide Programmable Output Voltage Range}, booktitle = {37th {IEEE} International System-on-Chip Conference, {SOCC} 2024, Dresden, Germany, September 16-19, 2024}, pages = {1--6}, publisher = {{IEEE}}, year = {2024}, url = {https://doi.org/10.1109/SOCC62300.2024.10737831}, doi = {10.1109/SOCC62300.2024.10737831}, timestamp = {Tue, 19 Nov 2024 13:29:26 +0100}, biburl = {https://dblp.org/rec/conf/socc/LiXXYZLZH024.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-2405-02628, author = {Zexing Zhao and Guangsi Shi and Xiaopeng Wu and Ruohua Ren and Xiaojun Gao and Fuyi Li}, title = {Contrastive Dual-Interaction Graph Neural Network for Molecular Property Prediction}, journal = {CoRR}, volume = {abs/2405.02628}, year = {2024}, url = {https://doi.org/10.48550/arXiv.2405.02628}, doi = {10.48550/ARXIV.2405.02628}, eprinttype = {arXiv}, eprint = {2405.02628}, timestamp = {Fri, 07 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/corr/abs-2405-02628.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/GeLIALTYWXSY23, author = {Fang Ge and Chen Li and Shahid Iqbal and Muhammad Arif and Fuyi Li and Maha A. Thafar and Zihao Yan and Apilak Worachartcheewan and Xiaofeng Xu and Jiangning Song and Dong{-}Jun Yu}, title = {VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants}, journal = {Briefings Bioinform.}, volume = {24}, number = {1}, year = {2023}, url = {https://doi.org/10.1093/bib/bbac535}, doi = {10.1093/BIB/BBAC535}, timestamp = {Sun, 06 Oct 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/GeLIALTYWXSY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/JiaZLQRLMZADCS23, author = {Xiaoti Jia and Pei Zhao and Fuyi Li and Zhaohui Qin and Haoran Ren and Junzhou Li and Chunbo Miao and Quanzhi Zhao and Tatsuya Akutsu and Gensheng Dou and Zhen Chen and Jiangning Song}, title = {ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning}, journal = {Briefings Bioinform.}, volume = {24}, number = {2}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad063}, doi = {10.1093/BIB/BBAD063}, timestamp = {Mon, 03 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/JiaZLQRLMZADCS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLGBLPCS23, author = {Ruyi Chen and Fuyi Li and Xudong Guo and Yue Bi and Chen Li and Shirui Pan and Lachlan J. M. Coin and Jiangning Song}, title = {{ATTIC} is an integrated approach for predicting A-to-I {RNA} editing sites in three species}, journal = {Briefings Bioinform.}, volume = {24}, number = {3}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad170}, doi = {10.1093/BIB/BBAD170}, timestamp = {Mon, 03 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ChenLGBLPCS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuLLGLSPLIYAS23, author = {Jing Xu and Fuyi Li and Chen Li and Xudong Guo and Cornelia B. Landersdorfer and Hsin{-}Hui Shen and Anton Y. Peleg and Jian Li and Seiya Imoto and Jianhua Yao and Tatsuya Akutsu and Jiangning Song}, title = {iAMPCN: a deep-learning approach for identifying antimicrobial peptides and their functional activities}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad240}, doi = {10.1093/BIB/BBAD240}, timestamp = {Fri, 19 Jul 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/XuLLGLSPLIYAS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuLGWCWSJ23, author = {Yan Zhu and Fuyi Li and Xudong Guo and Xiaoyu Wang and Lachlan J. M. Coin and Geoffrey I. Webb and Jiangning Song and Cangzhi Jia}, title = {{TIMER} is a Siamese neural network-based framework for identifying both general and species-specific bacterial promoters}, journal = {Briefings Bioinform.}, volume = {24}, number = {4}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad209}, doi = {10.1093/BIB/BBAD209}, timestamp = {Thu, 27 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhuLGWCWSJ23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWGAWCKS23, author = {Fuyi Li and Cong Wang and Xudong Guo and Tatsuya Akutsu and Geoffrey I. Webb and Lachlan J. M. Coin and Lukasz A. Kurgan and Jiangning Song}, title = {\emph{ProsperousPlus}: a one-stop and comprehensive platform for accurate protease-specific substrate cleavage prediction and machine-learning model construction}, journal = {Briefings Bioinform.}, volume = {24}, number = {6}, year = {2023}, url = {https://doi.org/10.1093/bib/bbad372}, doi = {10.1093/BIB/BBAD372}, timestamp = {Sat, 16 Aug 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiWGAWCKS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/cbm/LiGBJPPLGCS23, author = {Fuyi Li and Xudong Guo and Yue Bi and Runchang Jia and Miranda E. Pitt and Shirui Pan and Shuqin Li and Robin B. Gasser and Lachlan J. M. Coin and Jiangning Song}, title = {Digerati - {A} multipath parallel hybrid deep learning framework for the identification of mycobacterial {PE/PPE} proteins}, journal = {Comput. Biol. Medicine}, volume = {163}, pages = {107155}, year = {2023}, url = {https://doi.org/10.1016/j.compbiomed.2023.107155}, doi = {10.1016/J.COMPBIOMED.2023.107155}, timestamp = {Sun, 24 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/cbm/LiGBJPPLGCS23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcbb/ZhangGLYSY23, author = {Ying Zhang and Fang Ge and Fuyi Li and Xibei Yang and Jiangning Song and Dong{-}Jun Yu}, title = {Prediction of Multiple Types of {RNA} Modifications via Biological Language Model}, journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.}, volume = {20}, number = {5}, pages = {3205--3214}, year = {2023}, url = {https://doi.org/10.1109/TCBB.2023.3283985}, doi = {10.1109/TCBB.2023.3283985}, timestamp = {Sun, 19 Jan 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/tcbb/ZhangGLYSY23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/nips/LiuD0LZP23, author = {Yixin Liu and Kaize Ding and Qinghua Lu and Fuyi Li and Leo Yu Zhang and Shirui Pan}, editor = {Alice Oh and Tristan Naumann and Amir Globerson and Kate Saenko and Moritz Hardt and Sergey Levine}, title = {Towards Self-Interpretable Graph-Level Anomaly Detection}, booktitle = {Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, NeurIPS 2023, New Orleans, LA, USA, December 10 - 16, 2023}, year = {2023}, url = {http://papers.nips.cc/paper\_files/paper/2023/hash/1c6f06863df46de009a7a41b41c95cad-Abstract-Conference.html}, timestamp = {Sun, 02 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/conf/nips/LiuD0LZP23.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-2310-16520, author = {Yixin Liu and Kaize Ding and Qinghua Lu and Fuyi Li and Leo Yu Zhang and Shirui Pan}, title = {Towards Self-Interpretable Graph-Level Anomaly Detection}, journal = {CoRR}, volume = {abs/2310.16520}, year = {2023}, url = {https://doi.org/10.48550/arXiv.2310.16520}, doi = {10.48550/ARXIV.2310.16520}, eprinttype = {arXiv}, eprint = {2310.16520}, timestamp = {Sun, 02 Jun 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/corr/abs-2310-16520.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiDLHGXWPJZWCLS22, author = {Fuyi Li and Shuangyu Dong and Andr{\'{e}} Leier and Meiya Han and Xudong Guo and Jing Xu and Xiaoyu Wang and Shirui Pan and Cangzhi Jia and Yang Zhang and Geoffrey I. Webb and Lachlan J. M. Coin and Chen Li and Jiangning Song}, title = {Positive-unlabeled learning in bioinformatics and computational biology: a brief review}, journal = {Briefings Bioinform.}, volume = {23}, number = {1}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab461}, doi = {10.1093/BIB/BBAB461}, timestamp = {Thu, 27 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiDLHGXWPJZWCLS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WangLXRWGLS22, author = {Xiaoyu Wang and Fuyi Li and Jing Xu and Jia Rong and Geoffrey I. Webb and Zongyuan Ge and Jian Li and Jiangning Song}, title = {{ASPIRER:} a new computational approach for identifying non-classical secreted proteins based on deep learning}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac031}, doi = {10.1093/BIB/BBAC031}, timestamp = {Tue, 01 Apr 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/WangLXRWGLS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhangJLLZAWZCS22, author = {Meng Zhang and Cangzhi Jia and Fuyi Li and Chen Li and Yan Zhu and Tatsuya Akutsu and Geoffrey I. Webb and Quan Zou and Lachlan J. M. Coin and Jiangning Song}, title = {Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction}, journal = {Briefings Bioinform.}, volume = {23}, number = {2}, year = {2022}, url = {https://doi.org/10.1093/bib/bbab551}, doi = {10.1093/BIB/BBAB551}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhangJLLZAWZCS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/PengWGGLGS22, author = {Xinxin Peng and Xiaoyu Wang and Yuming Guo and Zongyuan Ge and Fuyi Li and Xin Gao and Jiangning Song}, title = {{RBP-TSTL} is a two-stage transfer learning framework for genome-scale prediction of RNA-binding proteins}, journal = {Briefings Bioinform.}, volume = {23}, number = {4}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac215}, doi = {10.1093/BIB/BBAC215}, timestamp = {Wed, 11 Jun 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/PengWGGLGS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/BiLGWPGWYJS22, author = {Yue Bi and Fuyi Li and Xudong Guo and Zhikang Wang and Tong Pan and Yuming Guo and Geoffrey I. Webb and Jianhua Yao and Cangzhi Jia and Jiangning Song}, title = {Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations}, journal = {Briefings Bioinform.}, volume = {23}, number = {6}, year = {2022}, url = {https://doi.org/10.1093/bib/bbac467}, doi = {10.1093/BIB/BBAC467}, timestamp = {Wed, 11 Jun 2025 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/BiLGWPGWYJS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LiuFWWLCLS22, author = {Quanzhong Liu and Honglin Fang and Xiao Wang and Miao Wang and Shuqin Li and Lachlan J. M. Coin and Fuyi Li and Jiangning Song}, title = {DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions}, journal = {Bioinform.}, volume = {38}, number = {17}, pages = {4053--4061}, year = {2022}, url = {https://doi.org/10.1093/bioinformatics/btac454}, doi = {10.1093/BIOINFORMATICS/BTAC454}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/LiuFWWLCLS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/ZhuWLS22, author = {Lin Zhu and Xiaoyu Wang and Fuyi Li and Jiangning Song}, title = {PreAcrs: a machine learning framework for identifying anti-CRISPR proteins}, journal = {{BMC} Bioinform.}, volume = {23}, number = {1}, pages = {444}, year = {2022}, url = {https://doi.org/10.1186/s12859-022-04986-3}, doi = {10.1186/S12859-022-04986-3}, timestamp = {Thu, 27 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/ZhuWLS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jcisd/IqbalGLAZGYWS22, author = {Shahid Iqbal and Fang Ge and Fuyi Li and Tatsuya Akutsu and Yuanting Zheng and Robin B. Gasser and Dong{-}Jun Yu and Geoffrey I. Webb and Jiangning Song}, title = {{PROST:} AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations}, journal = {J. Chem. Inf. Model.}, volume = {62}, number = {17}, pages = {4270--4282}, year = {2022}, url = {https://doi.org/10.1021/acs.jcim.2c00799}, doi = {10.1021/ACS.JCIM.2C00799}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jcisd/IqbalGLAZGYWS22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/ChenLZLWLABGLYG22, author = {Zhen Chen and Xuhan Liu and Pei Zhao and Chen Li and Yanan Wang and Fuyi Li and Tatsuya Akutsu and Chris Bain and Robin B. Gasser and Junzhou Li and Zuoren Yang and Xin Gao and Lukasz A. Kurgan and Jiangning Song}, title = {\emph{iFeatureOmega: } an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets}, journal = {Nucleic Acids Res.}, volume = {50}, number = {{W1}}, pages = {434--447}, year = {2022}, url = {https://doi.org/10.1093/nar/gkac351}, doi = {10.1093/NAR/GKAC351}, timestamp = {Mon, 03 Mar 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/nar/ChenLZLWLABGLYG22.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiCGWYHBBS21, author = {Fuyi Li and Jinxiang Chen and Zongyuan Ge and Ya Wen and Yanwei Yue and Morihiro Hayashida and Abdelkader Baggag and Halima Bensmail and Jiangning Song}, title = {Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework}, journal = {Briefings Bioinform.}, volume = {22}, number = {2}, pages = {2126--2140}, year = {2021}, url = {https://doi.org/10.1093/bib/bbaa049}, doi = {10.1093/BIB/BBAA049}, timestamp = {Tue, 01 Jun 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiCGWYHBBS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLWJCKSS21, author = {Huaming Chen and Fuyi Li and Lei Wang and Yaochu Jin and Chi{-}Hung Chi and Lukasz A. Kurgan and Jiangning Song and Jun Shen}, title = {Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions}, journal = {Briefings Bioinform.}, volume = {22}, number = {3}, year = {2021}, url = {https://doi.org/10.1093/bib/bbaa068}, doi = {10.1093/BIB/BBAA068}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenLWJCKSS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiuCWLJSL21, author = {Quanzhong Liu and Jinxiang Chen and Yanze Wang and Shuqin Li and Cangzhi Jia and Jiangning Song and Fuyi Li}, title = {DeepTorrent: a deep learning-based approach for predicting {DNA} N4-methylcytosine sites}, journal = {Briefings Bioinform.}, volume = {22}, number = {3}, year = {2021}, url = {https://doi.org/10.1093/bib/bbaa124}, doi = {10.1093/BIB/BBAA124}, timestamp = {Tue, 21 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiuCWLJSL21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuHGLSZY21, author = {Yi{-}Heng Zhu and Jun Hu and Fang Ge and Fuyi Li and Jiangning Song and Yang Zhang and Dong{-}Jun Yu}, title = {Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features}, journal = {Briefings Bioinform.}, volume = {22}, number = {3}, year = {2021}, url = {https://doi.org/10.1093/bib/bbaa076}, doi = {10.1093/BIB/BBAA076}, timestamp = {Tue, 21 Jan 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhuHGLSZY21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiangLCLWLSL21, author = {Xiao Liang and Fuyi Li and Jinxiang Chen and Junlong Li and Hao Wu and Shuqin Li and Jiangning Song and Quanzhong Liu}, title = {Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification}, journal = {Briefings Bioinform.}, volume = {22}, number = {4}, year = {2021}, url = {https://doi.org/10.1093/bib/bbaa312}, doi = {10.1093/BIB/BBAA312}, timestamp = {Sun, 19 Jan 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/LiangLCLWLSL21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ZhuLXASJ21, author = {Yan Zhu and Fuyi Li and Dongxu Xiang and Tatsuya Akutsu and Jiangning Song and Cangzhi Jia}, title = {Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks}, journal = {Briefings Bioinform.}, volume = {22}, number = {4}, year = {2021}, url = {https://doi.org/10.1093/bib/bbaa299}, doi = {10.1093/BIB/BBAA299}, timestamp = {Sun, 19 Jan 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/ZhuLXASJ21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MeiLXAFWIRACPS21, author = {Shutao Mei and Fuyi Li and Dongxu Xiang and Rochelle Ayala and Pouya Faridi and Geoffrey I. Webb and Patricia T. Illing and Jamie Rossjohn and Tatsuya Akutsu and Nathan P. Croft and Anthony W. Purcell and Jiangning Song}, title = {Anthem: a user customised tool for fast and accurate prediction of binding between peptides and {HLA} class {I} molecules}, journal = {Briefings Bioinform.}, volume = {22}, number = {5}, year = {2021}, url = {https://doi.org/10.1093/bib/bbaa415}, doi = {10.1093/BIB/BBAA415}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MeiLXAFWIRACPS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/XuLLXSMLYS21, author = {Jing Xu and Fuyi Li and Andr{\'{e}} Leier and Dongxu Xiang and Hsin{-}Hui Shen and Tatiana T. Marquez{-}Lago and Jian Li and Dong{-}Jun Yu and Jiangning Song}, title = {Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides}, journal = {Briefings Bioinform.}, volume = {22}, number = {5}, year = {2021}, url = {https://doi.org/10.1093/bib/bbab083}, doi = {10.1093/BIB/BBAB083}, timestamp = {Fri, 22 Mar 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/XuLLXSMLYS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/IqbalLAAWS21, author = {Shahid Iqbal and Fuyi Li and Tatsuya Akutsu and David B. Ascher and Geoffrey I. Webb and Jiangning Song}, title = {Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations}, journal = {Briefings Bioinform.}, volume = {22}, number = {6}, year = {2021}, url = {https://doi.org/10.1093/bib/bbab184}, doi = {10.1093/BIB/BBAB184}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/IqbalLAAWS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiGJCXSC21, author = {Fuyi Li and Xudong Guo and Peipei Jin and Jinxiang Chen and Dongxu Xiang and Jiangning Song and Lachlan J. M. Coin}, title = {Porpoise: a new approach for accurate prediction of {RNA} pseudouridine sites}, journal = {Briefings Bioinform.}, volume = {22}, number = {6}, year = {2021}, url = {https://doi.org/10.1093/bib/bbab245}, doi = {10.1093/BIB/BBAB245}, timestamp = {Thu, 23 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiGJCXSC21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/WangCZLHZITWDS21, author = {Yanan Wang and Nicolas Coudray and Yun Zhao and Fuyi Li and Changyuan Hu and Yao{-}Zhong Zhang and Seiya Imoto and Aristotelis Tsirigos and Geoffrey I. Webb and Roger J. Daly and Jiangning Song}, title = {{HEAL:} an automated deep learning framework for cancer histopathology image analysis}, journal = {Bioinform.}, volume = {37}, number = {22}, pages = {4291--4295}, year = {2021}, url = {https://doi.org/10.1093/bioinformatics/btab380}, doi = {10.1093/BIOINFORMATICS/BTAB380}, timestamp = {Sun, 06 Oct 2024 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/WangCZLHZITWDS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/fdata/ChenLWLMLRLLS21, author = {Jinxiang Chen and Fuyi Li and Miao Wang and Junlong Li and Tatiana T. Marquez{-}Lago and Andr{\'{e}} Leier and Jerico Revote and Shuqin Li and Quanzhong Liu and Jiangning Song}, title = {BigFiRSt: {A} Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data}, journal = {Frontiers Big Data}, volume = {4}, year = {2021}, url = {https://doi.org/10.3389/fdata.2021.727216}, doi = {10.3389/FDATA.2021.727216}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/fdata/ChenLWLMLRLLS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcbb/LiWLZLZBSWLSX21, author = {Menglu Li and Yanan Wang and Fuyi Li and Yun Zhao and Mengya Liu and Sijia Zhang and Yannan Bin and Alexander Ian Smith and Geoffrey I. Webb and Jian Li and Jiangning Song and Junfeng Xia}, title = {A Deep Learning-Based Method for Identification of Bacteriophage-Host Interaction}, journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.}, volume = {18}, number = {5}, pages = {1801--1810}, year = {2021}, url = {https://doi.org/10.1109/TCBB.2020.3017386}, doi = {10.1109/TCBB.2020.3017386}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcbb/LiWLZLZBSWLSX21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/tcbb/JiaZFLS21, author = {Cangzhi Jia and Meng Zhang and Cunshuo Fan and Fuyi Li and Jiangning Song}, title = {Formator: Predicting Lysine Formylation Sites Based on the Most Distant Undersampling and Safe-Level Synthetic Minority Oversampling}, journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.}, volume = {18}, number = {5}, pages = {1937--1945}, year = {2021}, url = {https://doi.org/10.1109/TCBB.2019.2957758}, doi = {10.1109/TCBB.2019.2957758}, timestamp = {Mon, 03 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/tcbb/JiaZFLS21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@phdthesis{DBLP:phd/au/Li20, author = {Fuyi Li}, title = {A data-driven bioinformatic investigation into protein post-translational modifications}, school = {Monash University, Australia}, year = {2020}, url = {https://doi.org/10.26180/5ec76ca14d030}, doi = {10.26180/5EC76CA14D030}, timestamp = {Tue, 28 Feb 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/phd/au/Li20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/appml/HuangLS20, author = {Yongyan Huang and Fuyi Li and Junping Shi}, title = {Stability of synchronized steady state solution of diffusive Lotka-Volterra predator-prey model}, journal = {Appl. Math. Lett.}, volume = {105}, pages = {106331}, year = {2020}, url = {https://doi.org/10.1016/j.aml.2020.106331}, doi = {10.1016/J.AML.2020.106331}, timestamp = {Mon, 28 Aug 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/appml/HuangLS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/WeiHLSSZ20, author = {Leyi Wei and Jie Hu and Fuyi Li and Jiangning Song and Ran Su and Quan Zou}, title = {Comparative analysis and prediction of quorum-sensing peptides using feature representation learning and machine learning algorithms}, journal = {Briefings Bioinform.}, volume = {21}, number = {1}, pages = {106--119}, year = {2020}, url = {https://doi.org/10.1093/bib/bby107}, doi = {10.1093/BIB/BBY107}, timestamp = {Wed, 07 Dec 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bib/WeiHLSSZ20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZLMLRZPAWCS20, author = {Zhen Chen and Pei Zhao and Fuyi Li and Tatiana T. Marquez{-}Lago and Andr{\'{e}} Leier and Jerico Nico De Leon Revote and Yan Zhu and David R. Powell and Tatsuya Akutsu and Geoffrey I. Webb and Kuo{-}Chen Chou and Alexander Ian Smith and Roger J. Daly and Jian Li and Jiangning Song}, title = {iLearn : an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, {RNA} and protein sequence data}, journal = {Briefings Bioinform.}, volume = {21}, number = {3}, pages = {1047--1057}, year = {2020}, url = {https://doi.org/10.1093/bib/bbz041}, doi = {10.1093/BIB/BBZ041}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZLMLRZPAWCS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiFMLRJZSWLWLS20, author = {Fuyi Li and Cunshuo Fan and Tatiana T. Marquez{-}Lago and Andr{\'{e}} Leier and Jerico Nico De Leon Revote and Cangzhi Jia and Yan Zhu and Alexander Ian Smith and Geoffrey I. Webb and Quanzhong Liu and Leyi Wei and Jian Li and Jiangning Song}, title = {{PRISMOID:} a comprehensive 3D structure database for post-translational modifications and mutations with functional impact}, journal = {Briefings Bioinform.}, volume = {21}, number = {3}, pages = {1069--1079}, year = {2020}, url = {https://doi.org/10.1093/bib/bbz050}, doi = {10.1093/BIB/BBZ050}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiFMLRJZSWLWLS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/MeiLLMGCASLRPS20, author = {Shutao Mei and Fuyi Li and Andr{\'{e}} Leier and Tatiana T. Marquez{-}Lago and Kailin Giam and Nathan P. Croft and Tatsuya Akutsu and Alexander Ian Smith and Jian Li and Jamie Rossjohn and Anthony W. Purcell and Jiangning Song}, title = {A comprehensive review and performance evaluation of bioinformatics tools for {HLA} class {I} peptide-binding prediction}, journal = {Briefings Bioinform.}, volume = {21}, number = {4}, pages = {1119--1135}, year = {2020}, url = {https://doi.org/10.1093/bib/bbz051}, doi = {10.1093/BIB/BBZ051}, timestamp = {Thu, 16 Jun 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/MeiLLMGCASLRPS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenZLWSWABBS20, author = {Zhen Chen and Pei Zhao and Fuyi Li and Yanan Wang and Alexander Ian Smith and Geoffrey I. Webb and Tatsuya Akutsu and Abdelkader Baggag and Halima Bensmail and Jiangning Song}, title = {Comprehensive review and assessment of computational methods for predicting {RNA} post-transcriptional modification sites from {RNA} sequences}, journal = {Briefings Bioinform.}, volume = {21}, number = {5}, pages = {1676--1696}, year = {2020}, url = {https://doi.org/10.1093/bib/bbz112}, doi = {10.1093/BIB/BBZ112}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenZLWSWABBS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LiCLMLWRSAWKS20, author = {Fuyi Li and Jinxiang Chen and Andr{\'{e}} Leier and Tatiana T. Marquez{-}Lago and Quanzhong Liu and Yanze Wang and Jerico Nico De Leon Revote and Alexander Ian Smith and Tatsuya Akutsu and Geoffrey I. Webb and Lukasz A. Kurgan and Jiangning Song}, title = {DeepCleave: a deep learning predictor for caspase and matrix metalloprotease substrates and cleavage sites}, journal = {Bioinform.}, volume = {36}, number = {4}, pages = {1057--1065}, year = {2020}, url = {https://doi.org/10.1093/bioinformatics/btz721}, doi = {10.1093/BIOINFORMATICS/BTZ721}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/LiCLMLWRSAWKS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/JiaBCLLS20, author = {Cangzhi Jia and Yue Bi and Jinxiang Chen and Andr{\'{e}} Leier and Fuyi Li and Jiangning Song}, title = {{PASSION:} an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs}, journal = {Bioinform.}, volume = {36}, number = {15}, pages = {4276--4282}, year = {2020}, url = {https://doi.org/10.1093/bioinformatics/btaa522}, doi = {10.1093/BIOINFORMATICS/BTAA522}, timestamp = {Fri, 25 Dec 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/JiaBCLLS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/gpb/LiLLWXAWSM0S20, author = {Fuyi Li and Andr{\'{e}} Leier and Quanzhong Liu and Yanan Wang and Dongxu Xiang and Tatsuya Akutsu and Geoffrey I. Webb and Alexander Ian Smith and Tatiana T. Marquez{-}Lago and Jian Li and Jiangning Song}, title = {Procleave: Predicting Protease-specific Substrate Cleavage Sites by Combining Sequence and Structural Information}, journal = {Genom. Proteom. Bioinform.}, volume = {18}, number = {1}, pages = {52--64}, year = {2020}, url = {https://doi.org/10.1016/j.gpb.2019.08.002}, doi = {10.1016/J.GPB.2019.08.002}, timestamp = {Mon, 17 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/gpb/LiLLWXAWSM0S20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jbcb/LiZZJLS20, author = {Pengyu Li and He Zhang and Xuyang Zhao and Cangzhi Jia and Fuyi Li and Jiangning Song}, title = {Pippin: {A} random forest-based method for identifying presynaptic and postsynaptic neurotoxins}, journal = {J. Bioinform. Comput. Biol.}, volume = {18}, number = {2}, pages = {2050008:1--2050008:21}, year = {2020}, url = {https://doi.org/10.1142/S0219720020500080}, doi = {10.1142/S0219720020500080}, timestamp = {Tue, 01 Jun 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jbcb/LiZZJLS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/jbcb/0009ZLLMWBBS20, author = {Zhen Chen and Pei Zhao and Fuyi Li and Andr{\'{e}} Leier and Tatiana T. Marquez{-}Lago and Geoffrey I. Webb and Abdelkader Baggag and Halima Bensmail and Jiangning Song}, title = {{PROSPECT:} {A} web server for predicting protein histidine phosphorylation sites}, journal = {J. Bioinform. Comput. Biol.}, volume = {18}, number = {4}, pages = {2050018:1--2050018:17}, year = {2020}, url = {https://doi.org/10.1142/S0219720020500183}, doi = {10.1142/S0219720020500183}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/jbcb/0009ZLLMWBBS20.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/appml/RongLL19, author = {Ting Rong and Fuyi Li and Zhanping Liang}, title = {Existence of nontrivial solutions for Kirchhoff-type problems with jumping nonlinearities}, journal = {Appl. Math. Lett.}, volume = {95}, pages = {137--142}, year = {2019}, url = {https://doi.org/10.1016/j.aml.2019.03.035}, doi = {10.1016/J.AML.2019.03.035}, timestamp = {Sun, 19 Jan 2025 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/appml/RongLL19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/SongWLARWC19, author = {Jiangning Song and Yanan Wang and Fuyi Li and Tatsuya Akutsu and Neil D. Rawlings and Geoffrey I. Webb and Kuo{-}Chen Chou}, title = {iProt-Sub: a comprehensive package for accurately mapping and predicting protease-specific substrates and cleavage sites}, journal = {Briefings Bioinform.}, volume = {20}, number = {2}, pages = {638--658}, year = {2019}, url = {https://doi.org/10.1093/bib/bby028}, doi = {10.1093/BIB/BBY028}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/SongWLARWC19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/LiWLMLRHRACPPWS19, author = {Fuyi Li and Yanan Wang and Chen Li and Tatiana T. Marquez{-}Lago and Andr{\'{e}} Leier and Neil D. Rawlings and Gholamreza Haffari and Jerico Nico De Leon Revote and Tatsuya Akutsu and Kuo{-}Chen Chou and Anthony W. Purcell and Robert N. Pike and Geoffrey I. Webb and Alexander Ian Smith and Trevor Lithgow and Roger J. Daly and James C. Whisstock and Jiangning Song}, title = {Twenty years of bioinformatics research for protease-specific substrate and cleavage site prediction: a comprehensive revisit and benchmarking of existing methods}, journal = {Briefings Bioinform.}, volume = {20}, number = {6}, pages = {2150--2166}, year = {2019}, url = {https://doi.org/10.1093/bib/bby077}, doi = {10.1093/BIB/BBY077}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/LiWLMLRHRACPPWS19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/ChenLLLMLAWXSLC19, author = {Zhen Chen and Xuhan Liu and Fuyi Li and Chen Li and Tatiana T. Marquez{-}Lago and Andr{\'{e}} Leier and Tatsuya Akutsu and Geoffrey I. Webb and Dakang Xu and Alexander Ian Smith and Lei Li and Kuo{-}Chen Chou and Jiangning Song}, title = {Large-scale comparative assessment of computational predictors for lysine post-translational modification sites}, journal = {Briefings Bioinform.}, volume = {20}, number = {6}, pages = {2267--2290}, year = {2019}, url = {https://doi.org/10.1093/bib/bby089}, doi = {10.1093/BIB/BBY089}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/ChenLLLMLAWXSLC19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/ZhangLMLFKCSJ19, author = {Meng Zhang and Fuyi Li and Tatiana T. Marquez{-}Lago and Andr{\'{e}} Leier and Cunshuo Fan and Chee Keong Kwoh and Kuo{-}Chen Chou and Jiangning Song and Cangzhi Jia}, title = {MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters}, journal = {Bioinform.}, volume = {35}, number = {17}, pages = {2957--2965}, year = {2019}, url = {https://doi.org/10.1093/bioinformatics/btz016}, doi = {10.1093/BIOINFORMATICS/BTZ016}, timestamp = {Sun, 02 Oct 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangLMLFKCSJ19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/LiZPWCLLS19, author = {Fuyi Li and Yang Zhang and Anthony W. Purcell and Geoffrey I. Webb and Kuo{-}Chen Chou and Trevor Lithgow and Chen Li and Jiangning Song}, title = {Positive-unlabelled learning of glycosylation sites in the human proteome}, journal = {{BMC} Bioinform.}, volume = {20}, number = {1}, pages = {112:1--112:17}, year = {2019}, url = {https://doi.org/10.1186/s12859-019-2700-1}, doi = {10.1186/S12859-019-2700-1}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/LiZPWCLLS19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/WangLLSSW19, author = {Xiaochuan Wang and Chen Li and Fuyi Li and Varun S. Sharma and Jiangning Song and Geoffrey I. Webb}, title = {{SIMLIN:} a bioinformatics tool for prediction of S-sulphenylation in the human proteome based on multi-stage ensemble-learning models}, journal = {{BMC} Bioinform.}, volume = {20}, number = {1}, pages = {602:1--602:12}, year = {2019}, url = {https://doi.org/10.1186/s12859-019-3178-6}, doi = {10.1186/S12859-019-3178-6}, timestamp = {Mon, 26 Jun 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/WangLLSSW19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/amc/ZhuLL18, author = {Xiaoli Zhu and Fuyi Li and Yuhua Li}, title = {Global solutions and blow up solutions to a class of pseudo-parabolic equations with nonlocal term}, journal = {Appl. Math. Comput.}, volume = {329}, pages = {38--51}, year = {2018}, url = {https://doi.org/10.1016/j.amc.2018.02.003}, doi = {10.1016/J.AMC.2018.02.003}, timestamp = {Fri, 21 Feb 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/amc/ZhuLL18.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/SongLLMAHCWP18, author = {Jiangning Song and Fuyi Li and Andr{\'{e}} Leier and Tatiana T. Marquez{-}Lago and Tatsuya Akutsu and Gholamreza Haffari and Kuo{-}Chen Chou and Geoffrey I. Webb and Robert N. Pike}, title = {PROSPERous: high-throughput prediction of substrate cleavage sites for 90 proteases with improved accuracy}, journal = {Bioinform.}, volume = {34}, number = {4}, pages = {684--687}, year = {2018}, url = {https://doi.org/10.1093/bioinformatics/btx670}, doi = {10.1093/BIOINFORMATICS/BTX670}, timestamp = {Fri, 09 Apr 2021 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/SongLLMAHCWP18.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/ChenZLLMWWSDCS18, author = {Zhen Chen and Pei Zhao and Fuyi Li and Andr{\'{e}} Leier and Tatiana T. Marquez{-}Lago and Yanan Wang and Geoffrey I. Webb and Alexander Ian Smith and Roger J. Daly and Kuo{-}Chen Chou and Jiangning Song}, title = {iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences}, journal = {Bioinform.}, volume = {34}, number = {14}, pages = {2499--2502}, year = {2018}, url = {https://doi.org/10.1093/bioinformatics/bty140}, doi = {10.1093/BIOINFORMATICS/BTY140}, timestamp = {Mon, 17 Apr 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/ChenZLLMWWSDCS18.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LiLMLAPSLDSC18, author = {Fuyi Li and Chen Li and Tatiana T. Marquez{-}Lago and Andr{\'{e}} Leier and Tatsuya Akutsu and Anthony W. Purcell and Alexander Ian Smith and Trevor Lithgow and Roger J. Daly and Jiangning Song and Kuo{-}Chen Chou}, title = {Quokka: a comprehensive tool for rapid and accurate prediction of kinase family-specific phosphorylation sites in the human proteome}, journal = {Bioinform.}, volume = {34}, number = {24}, pages = {4223--4231}, year = {2018}, url = {https://doi.org/10.1093/bioinformatics/bty522}, doi = {10.1093/BIOINFORMATICS/BTY522}, timestamp = {Mon, 03 Jan 2022 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/LiLMLAPSLDSC18.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/amc/ZhangLL15b, author = {Qi Zhang and Fuyi Li and Zhanping Liang}, title = {Existence of multiple positive solutions to nonhomogeneous Schr{\"{o}}dinger-Poisson system}, journal = {Appl. Math. Comput.}, volume = {259}, pages = {353--363}, year = {2015}, url = {https://doi.org/10.1016/j.amc.2015.02.044}, doi = {10.1016/J.AMC.2015.02.044}, timestamp = {Fri, 21 Feb 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/amc/ZhangLL15b.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LiLWWZWS15, author = {Fuyi Li and Chen Li and Mingjun Wang and Geoffrey I. Webb and Yang Zhang and James C. Whisstock and Jiangning Song}, title = {GlycoMine: a machine learning-based approach for predicting N-, {C-} and O-linked glycosylation in the human proteome}, journal = {Bioinform.}, volume = {31}, number = {9}, pages = {1411--1419}, year = {2015}, url = {https://doi.org/10.1093/bioinformatics/btu852}, doi = {10.1093/BIOINFORMATICS/BTU852}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/LiLWWZWS15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/amc/ZhangLZ12, author = {Qi Zhang and Fuyi Li and Xiaoli Zhu}, title = {Multiple sign-changing solutions to the Sturm-Liouville boundary value problem with resonance}, journal = {Appl. Math. Comput.}, volume = {219}, number = {3}, pages = {1061--1072}, year = {2012}, url = {https://doi.org/10.1016/j.amc.2012.07.012}, doi = {10.1016/J.AMC.2012.07.012}, timestamp = {Fri, 21 Feb 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/amc/ZhangLZ12.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/appml/LiL05, author = {Fuyi Li and Zhanping Liang}, title = {Existence of positive periodic solutions to nonlinear second order differential equations}, journal = {Appl. Math. Lett.}, volume = {18}, number = {11}, pages = {1256--1264}, year = {2005}, url = {https://doi.org/10.1016/j.aml.2005.02.014}, doi = {10.1016/J.AML.2005.02.014}, timestamp = {Fri, 26 May 2017 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/appml/LiL05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/appml/LiZ04, author = {Fuyi Li and Yajing Zhang}, title = {Multiple symmetric nonnegative solutions of second-order ordinary differential equations}, journal = {Appl. Math. Lett.}, volume = {17}, number = {3}, pages = {261--267}, year = {2004}, url = {https://doi.org/10.1016/S0893-9659(04)90061-4}, doi = {10.1016/S0893-9659(04)90061-4}, timestamp = {Fri, 26 May 2017 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/appml/LiZ04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }

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