Fuyi Li

An Interpretable Prediction Model for Identifying N7-Methylguanosine Sites Based on XGBoost and SHAP

Y Bi, D Xiang, Z Ge, F Li, C Jia, J Song

Journal article  |  2020  |  Molecular Therapy - Nucleic Acids

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 I 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, André 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..

A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction

Shutao Mei, Fuyi Li, Andre Leier, Tatiana T Marquez-Lago, Kailin Giam, Nathan P Croft, Tatsuya Akutsu, A Ian Smith, Jian Li, Jamie Rossjohn, Anthony W Purcell, Jiangning Song

Journal article  |  2020  |  Briefings in Bioinformatics

Human leukocyte antigen class I (HLA-I) molecules are encoded by major histocompatibility complex (MHC) class I loci in humans. Th..

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  |  2020  |  Briefings in Bioinformatics

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

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  |  2020  |  Briefings in Bioinformatics

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  |  2020  |  Briefings in Bioinformatics

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

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  |  2020  |  Briefings in Bioinformatics

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

iLearn: an integrated platform and meta-learner for feature engineering, machine-learning analysis and modeling of DNA, RNA and protein sequence data

Zhen Chen, Pei Zhao, Fuyi Li, Tatiana T Marquez-Lago, Andre Leier, Jerico Revote, Yan Zhu, David R Powell, Tatsuya Akutsu, Geoffrey Webb, Kuo-Chen Chou, A Ian Smith, Roger J Daly, Jian Li, Jiangning Song

Journal article  |  2020  |  Briefings in Bioinformatics