Author

Fan Xu

Peng Cheng LaboratoryORCID 0000-0002-1504-2356Unclaimed ORCID profile · follow to get notified of new preprints

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Fan Xu2 papers · Chongqing University

Biology Disciplines

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Bioinformatics· 3

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Approach:transformer / foundation model· 3 Assay:proteomics· 2 Research Focus:benchmarking· 1 Research Focus:deconvolution· 1 Assay:DNA methylation· 1 Research Focus:gene regulatory network inference· 1 Assay:long-read sequencing· 1

Frequent Co-Authors

Xiansong Huang· 3 shared Boyan SuniD· 1 shared Cheng ChangiD· 1 shared Daixi LiiD· 1 shared Feng YiniD· 1 shared Fuchu HeiD· 1 shared Guoli SongiD· 1 shared Hongyu Zhang· 1 shared

Activity by Year

2023-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 18 mutual co-author links

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3 shared papersBioinformatics

Xiansong Huang

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3 papers

Recent·Most cited

Peptide generative design with weakly order-dependent autoregressive language model and lifelong learning

Zhiwei Nie, Daixi Li, Yutian Liu, Fan Xu, Hongyu Zhang, Xiansong Huang, Xudong Liu, Zhennan Wang, Yiming Ma, Yuxin Ye, Feng Yin, Wen-Bin Zhang, Zhixiang Ren, Zhihong Liu, Zigang Li, Jie Chen

This paper introduces PepGenWOA, a generative model for bioactive peptide design that outperforms existing methods and enables efficient virtual screening.

bioRxiv · Dec 31, 2023 · PreprintBioinformatics

Multiple sequence-alignment-based RNA language model and its application to structural inference

Yikun Zhang, Mei Lang, Jiuhong Jiang, Zhiqiang Gao, Fan Xu, Thomas Litfin, Ke Chen, Jaswinder Singh, Xiansong Huang, Guoli Song, Yonghong Tian, Jian Zhan, Jie Chen, Yaoqi Zhou

This paper introduces an RNA language model based on multiple sequence alignment, showing it can accurately predict RNA structure from sequence data.

Nucleic Acids Research · Oct 21, 2023Peer-reviewedBioinformatics

Introducing π-HelixNovo for practical large-scale de novo peptide sequencing

Tingpeng Yang, Tianze Ling, Boyan Sun, Zhendong Liang, Fan Xu, Xiansong Huang, Linhai Xie, Yonghong He, Leyuan Li, Fuchu He, Yu Wang, Cheng Chang

The paper introduces π-HelixNovo, a Transformer-based model for de novo peptide sequencing that outperforms existing methods and improves taxonomic resolution in gut metaproteomes.

bioRxiv · Jul 15, 2023 · PreprintBioinformatics