Fuyi Li

Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides.

Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T Marquez Lago, Jian Li, Dong-Jun Yu, Jiangning Song

Journal article  |  2021  |  Briefings in Bioinformatics

Antimicrobial peptides (AMPs) are a unique and diverse group of molecules that play a crucial role in a myriad of biological proce..

Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework.

Fuyi Li, Jinxiang Chen, Zongyuan Ge, Ya Wen, Yanwei Yue, Morihiro Hayashida, Abdelkader Baggag, Halima Bensmail, Jiangning Song

Journal article  |  2021  |  Briefings in Bioinformatics

Promoters are short consensus sequences of DNA, which are responsible for transcription activation or the repression of all genes...

Predicting Proteolysis in Complex Proteomes Using Deep Learning.

Matiss Ozols, Alexander Eckersley, Christopher I Platt, Callum Stewart-McGuinness, Sarah A Hibbert, Jerico Revote, Fuyi Li, Christopher EM Griffiths, Rachel EB Watson, Jiangning Song, Mike Bell, Michael J Sherratt

Journal article  |  2021  |  International Journal of Molecular Sciences

Both protease- and reactive oxygen species (ROS)-mediated proteolysis are thought to be key effectors of tissue remodeling. We hav..

Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules.

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

Journal article  |  2021  |  Briefings in Bioinformatics

Neopeptide-based immunotherapy has been recognised as a promising approach for the treatment of cancers. For neopeptides to be rec..

Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification.

Xiao Liang, Fuyi Li, Jinxiang Chen, Junlong Li, Hao Wu, Shuqin Li, Jiangning Song, Quanzhong Liu

Journal article  |  2020  |  Briefings in Bioinformatics

Anti-cancer peptides (ACPs) are known as potential therapeutics for cancer. Due to their unique ability to target cancer cells wit..

An Interpretable Prediction Model for Identifying N-7-Methylguanosine Sites Based on XGBoost and SHAP

Yue Bi, Dongxu Xiang, Zongyuan Ge, Fuyi Li, Cangzhi Jia, Jiangning Song

Journal article  |  2020  |  Molecular Therapy : Nucleic Acids

Recent studies have increasingly shown that the chemical modification of mRNA plays an important role in the regulation of gene ex..

Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks.

Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia

Journal article  |  2020  |  Briefings in Bioinformatics

A promoter is a region in the DNA sequence that defines where the transcription of a gene by RNA polymerase initiates, which is ty..

DeepBL: a deep learning-based approach for in silico discovery of beta-lactamases.

Yanan Wang, Fuyi Li, Manasa Bharathwaj, Natalia C Rosas, André Leier, Tatsuya Akutsu, Geoffrey I Webb, Tatiana T Marquez-Lago, Jian Li, Trevor Lithgow, Jiangning Song

Journal article  |  2020  |  Briefings in Bioinformatics

Beta-lactamases (BLs) are enzymes localized in the periplasmic space of bacterial pathogens, where they confer resistance to beta-..

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

Zhen Chen, Pei Zhao, Fuyi Li, Yanan Wang, A Ian Smith, Geoffrey Webb, Tatsuya Akutsu, Abdelkader Baggag, Halima Bensmail, Jiangning Song

Journal article  |  2020  |  Briefings in Bioinformatics

RNA post-transcriptional modifications play a crucial role in a myriad of biological processes and cellular functions. To date, mo..

PASSION: an ensemble neural network approach for identifying the binding sites of RBPs on circRNAs

Cangzhi Jia, Yue Bi, Jinxiang Chen, Andre Leier, Fuyi Li, Jiangning Song

Journal article  |  2020  |  Bioinformatics

MOTIVATION: Different from traditional linear RNAs (containing 5' and 3' ends), circular RNAs (circRNAs) are a special type of RNA..