Shanfeng Zhu

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 20

Top Topics

Artificial Intelligence

Binding Protein

Electronic Health Record

Top Venues

Nature communications

Bioinformatics (Oxford, England)

NAR genomics and bioinformatics

This page only lists publications with an associated author ORCID identifier.

Publications

Ziye Wang, Ronghui You, Haitao Han, Wei Liu, Fengzhu Sun, Shanfeng Zhu
Effective binning of metagenomic contigs using contrastive multi-view representation learning. Nature communications 15 (1) (2024)
Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang, Shanfeng Zhu
Author Correction: PLMSearch: Protein language model powers accurate and fast sequence search for remote homology. Nature communications 15 (1) (2024)
Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang, Shanfeng Zhu
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology. Nature communications 15 (1) (2024)
Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang, Shanfeng Zhu
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology. Nature communications 15 (1) (2024)
Ziye Wang, Ronghui You, Haitao Han, Wei Liu, Fengzhu Sun, Shanfeng Zhu
Effective binning of metagenomic contigs using contrastive multi-view representation learning. Nature communications 15 (1) (2024)
Wei Liu, Ziye Wang, Ronghui You, Chenghan Xie, Hong Wei, Yi Xiong, Jianyi Yang, Shanfeng Zhu
PLMSearch: Protein language model powers accurate and fast sequence search for remote homology. Nature communications 15 (1) (2024)
Ziye Wang, Ronghui You, Haitao Han, Wei Liu, Fengzhu Sun, Shanfeng Zhu
Effective binning of metagenomic contigs using contrastive multi-view representation learning. Nature communications 15 (1) (2024)
Huiying Yan, Shaojun Wang, Hancheng Liu, Hiroshi Mamitsuka, Shanfeng Zhu
GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation. Bioinformatics (Oxford, England) 40 (Supplement_2) (2024)
Zhirui Liao, Lei Xie, Hiroshi Mamitsuka, Shanfeng Zhu
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer. Bioinformatics (Oxford, England) 39 (1) (2023)
Ziye Wang, Pingqin Huang, Ronghui You, Fengzhu Sun, Shanfeng Zhu
MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome biology 24 (1) (2023)
Zhirui Liao, Lei Xie, Hiroshi Mamitsuka, Shanfeng Zhu
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer. Bioinformatics (Oxford, England) 39 (1) (2023)
Ziye Wang, Pingqin Huang, Ronghui You, Fengzhu Sun, Shanfeng Zhu
MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome biology 24 (1) (2023)
Zhirui Liao, Lei Xie, Hiroshi Mamitsuka, Shanfeng Zhu
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer. Bioinformatics (Oxford, England) 39 (1) (2023)
Ziye Wang, Pingqin Huang, Ronghui You, Fengzhu Sun, Shanfeng Zhu
MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome biology 24 (1) (2023)
Ziye Wang, Pingqin Huang, Ronghui You, Fengzhu Sun, Shanfeng Zhu
MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities. Genome biology 24 (1) (2023)
Jing Yan, Weiqi Zhai, Zhaoxia Li, LingLing Ding, Jia You, Jiayi Zeng, Xin Yang, Chunjuan Wang, Xia Meng, Yong Jiang, Xiaodi Huang, Shouyan Wang, Yilong Wang, Zixiao Li, Shanfeng Zhu, Yongjun Wang, Xingquan Zhao, Jianfeng Feng
ICH-LR2S2: a new risk score for predicting stroke-associated pneumonia from spontaneous intracerebral hemorrhage. Journal of translational medicine 20 (1) (2022)
Ronghui You, Wei Qu, Hiroshi Mamitsuka, Shanfeng Zhu
DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction. Bioinformatics (Oxford, England) 38 (Suppl 1) (2022)
Shuwei Yao, Ronghui You, Shaojun Wang, Yi Xiong, Xiaodi Huang, Shanfeng Zhu
NetGO 2.0: improving large-scale protein function prediction with massive sequence, text, domain, family and network information. Nucleic acids research 49 (W1) (2021)
Ronghui You, Shuwei Yao, Hiroshi Mamitsuka, Shanfeng Zhu
DeepGraphGO: graph neural network for large-scale, multispecies protein function prediction. Bioinformatics (Oxford, England) 37 (Suppl_1) (2021)
Ziye Wang, Shuo Li, Ronghui You, Shanfeng Zhu, Xianghong Jasmine Zhou, Fengzhu Sun
ARG-SHINE: improve antibiotic resistance class prediction by integrating sequence homology, functional information and deep convolutional neural network. NAR genomics and bioinformatics 3 (3) (2021)