Author

Yi Chen

Westlake UniversityORCID 0009-0005-5826-0600Unclaimed ORCID profile · follow to get notified of new preprints

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Yi Chen11 papers · Baylor College of Medicine

Biology Disciplines

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Bioinformatics· 1 Systems Biology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:human· 2 Assay:proteomics· 2 Research Focus:software / tool· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Pu‐Kun LiuiD· 2 shared Tiannan GuoiD· 2 shared Xiaofan ZhangiD· 2 shared Yingying SuniD· 2 shared Yuqi ZhangiD· 2 shared Zongxiang Nie· 2 shared A. S. Jun· 1 shared Jiaying Lin· 1 shared

Activity by Year

2024-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 42 mutual co-author links

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2 shared papersSystems Biology

Pu‐Kun LiuORCID

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2 papers

Recent·Most cited

Systems BiologyNature CommunicationsPeer-reviewedApr 14, 2025

DIA-BERT: pre-trained end-to-end transformer models for enhanced DIA proteomics data analysis

Zhiwei Liu, Pu‐Kun Liu, Yingying Sun…·Tiannan Guo

DIA-BERT improves DIA proteomics analysis by using pre-trained transformer models, achieving higher protein and peptide identifications than DIA-NN in cancer samples.

17 citationstop 4%

humanproteomics

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BioinformaticsbioRxivPreprintNov 13, 2024

DDA-BERT: leveraging transformer architecture pre-training for data-dependent acquisition mass spectrometry-based proteomics

A. S. Jun, Pu‐Kun Liu, Yingying Sun…·Tiannan Guo

DDA-BERT improves PSM rescoring in proteomics using a transformer-based model trained on 95 million human spectra, outperforming existing methods across species and sample types.

1 citation

humanproteomics

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