Fuyi Li

ResNetKhib: a novel cell type-specific tool for predicting lysine 2-hydroxyisobutylation sites via transfer learning.

Xiaoti Jia, Pei Zhao, Fuyi Li, Zhaohui Qin, Haoran Ren, Junzhou Li, Chunbo Miao, Quanzhi Zhao, Tatsuya Akutsu, Gensheng Dou, Zhen Chen, Jiangning Song

Journal article  |  2023  |  Brief Bioinform

Lysine 2-hydroxyisobutylation (Khib), which was first reported in 2014, has been shown to play vital roles in a myriad of biologic..

MSINGB: A Novel Computational Method Based on NGBoost for Identifying Microsatellite Instability Status from Tumor Mutation Annotation Data.

Jinxiang Chen, Miao Wang, Defeng Zhao, Fuyi Li, Hao Wu, Quanzhong Liu, Shuqin Li

Journal article  |  2023  |  Interdiscip Sci

Microsatellite instability (MSI), a vital mutator phenotype caused by DNA mismatch repair deficiency, is frequently observed in se..

VPatho: a deep learning-based two-stage approach for accurate prediction of gain-of-function and loss-of-function variants.

Fang Ge, Chen Li, Shahid Iqbal, Arif Muhammad, Fuyi Li, Maha A Thafar, Zihao Yan, Apilak Worachartcheewan, Xiaofeng Xu, Jiangning Song, Dong-Jun Yu

Journal article  |  2023  |  Brief Bioinform

Determining the pathogenicity and functional impact (i.e. gain-of-function; GOF or loss-of-function; LOF) of a variant is vital fo..

Predicting Pseudouridine Sites with Porpoise.

Xudong Guo, Fuyi Li, Jiangning Song

Journal article  |  2023  |  Methods Mol Biol

Pseudouridine is a ubiquitous RNA modification and plays a crucial role in many biological processes. However, it remains a challe..

Designing Effective Predictors of Protein Post-Translational Modifications Using iLearnPlus

Zhen Chen, Fuyi Li, Xiaoyu Wang, Yanan Wang, Lukasz Kurgan, Jiangning Song

Book Chapter  |  2023

COPPER: an ensemble deep-learning approach for identifying exclusive virus-derived small interfering RNAs in plants

Yuanyuan Bu, Cangzhi Jia, Xudong Guo, Fuyi Li, Jiangning Song

Journal article  |  2022  |  BRIEFINGS IN FUNCTIONAL GENOMICS

Antiviral defenses are one of the significant roles of RNA interference (RNAi) in plants. It has been reported that the host RNAi ..

Clarion is a multi-label problem transformation method for identifying mRNA subcellular localizations.

Yue Bi, Fuyi Li, Xudong Guo, Zhikang Wang, Tong Pan, Yuming Guo, Geoffrey I Webb, Jianhua Yao, Cangzhi Jia, Jiangning Song

Journal article  |  2022  |  Brief Bioinform

Subcellular localization of messenger RNAs (mRNAs) plays a key role in the spatial regulation of gene activity. The functions of m..

PreAcrs: a machine learning framework for identifying anti-CRISPR proteins.

Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song

Journal article  |  2022  |  BMC Bioinformatics

BACKGROUND: Anti-CRISPR proteins are potent modulators that inhibit the CRISPR-Cas immunity system and have huge potential in gene..

PredPromoter-MF(2L): A Novel Approach of Promoter Prediction Based on Multi-source Feature Fusion and Deep Forest.

Miao Wang, Fuyi Li, Hao Wu, Quanzhong Liu, Shuqin Li

Journal article  |  2022  |  Interdiscip Sci

Promoters short DNA sequences play vital roles in initiating gene transcription. However, it remains a challenge to identify promo..

PROST: AlphaFold2-aware Sequence-Based Predictor to Estimate Protein Stability Changes upon Missense Mutations

Shahid Iqbal, Fang Ge, Fuyi Li, Tatsuya Akutsu, Yuanting Zheng, Robin B Gasser, Dong-Jun Yu, Geoffrey Webb, Jiangning Song

Journal article  |  2022  |  JOURNAL OF CHEMICAL INFORMATION AND MODELING

An essential step in engineering proteins and understanding disease-causing missense mutations is to accurately model protein stab..