Fuyi Li

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  |  2021  |  Brief Bioinform

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

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  |  2021  |  Brief Bioinform

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

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  |  2021  |  Brief Bioinform

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

Porpoise: a new approach for accurate prediction of RNA pseudouridine sites.

Fuyi Li, Xudong Guo, Peipei Jin, Jinxiang Chen, Dongxu Xiang, Jiangning Song, Lachlan JM Coin

Journal article  |  2021  |  Brief Bioinform

Pseudouridine is a ubiquitous RNA modification type present in eukaryotes and prokaryotes, which plays a vital role in various bio..

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization.

Zhen Chen, Pei Zhao, Chen Li, Fuyi Li, Dongxu Xiang, Yong-Zi Chen, Tatsuya Akutsu, Roger J Daly, Geoffrey I Webb, Quanzhi Zhao, Lukasz Kurgan, Jiangning Song

Journal article  |  2021  |  Nucleic Acids Res

Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structur..

Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations.

Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B Ascher, Geoffrey I Webb, Jiangning Song

Journal article  |  2021  |  Brief Bioinform

Understanding how a mutation might affect protein stability is of significant importance to protein engineering and for understand..

Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions.

Huaming Chen, Fuyi Li, Lei Wang, Yaochu Jin, Chi-Hung Chi, Lukasz Kurgan, Jiangning Song, Jun Shen

Journal article  |  2021  |  Brief Bioinform

In recent years, high-throughput experimental techniques have significantly enhanced the accuracy and coverage of protein-protein ..

Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features.

Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu

Journal article  |  2021  |  Brief Bioinform

X-ray crystallography is the major approach for determining atomic-level protein structures. Because not all proteins can be easil..

DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites.

Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song, Fuyi Li

Journal article  |  2021  |  Brief Bioinform

DNA N4-methylcytosine (4mC) is an important epigenetic modification that plays a vital role in regulating DNA replication and expr..

HEAL: an automated deep learning framework for cancer histopathology image analysis.

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

Journal article  |  2021  |  Bioinformatics

MOTIVATION: Digital pathology supports analysis of histopathological images using deep learning methods at a large-scale. However,..