Author

Yiqi Chen

Northwestern Polytechnical UniversityORCID 0009-0008-3163-3018Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Approach:deep learning· 3 Research Focus:cell type annotation· 2 Organism:mouse· 2 Research Focus:spatial domain detection· 2 Assay:spatial transcriptomics· 2 Approach:contrastive learning· 1 Approach:graph neural network· 1 Approach:transformer / foundation model· 1

Frequent Co-Authors

Xuequn ShangiD· 4 shared Yingfu WuiD· 3 shared Dongmin ZhaoiD· 2 shared Fuhao ZhangiD· 2 shared Gaoyuan Du· 2 shared Jialuo XuiD· 2 shared Junnan ZhuiD· 2 shared Xiangting Jia· 2 shared

Activity by Year

2024-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

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4 shared papersBioinformatics

Xuequn ShangORCID

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4 papers

Recent·Most cited

BioinformaticsbioRxivPreprintMay 11, 2025

A Multimodal Graph Learning Framework for Versatile Spatial Transcriptomics Analysis with SpatialModal

Xingyi Li, Dongmin Zhao, Xiangting Jia…·Xuequn Shang

SpatialModal integrates gene expression and histological images in spatial transcriptomics to improve spatial analysis and domain identification.

DOI 10.1101/2025.05.11.653070

mousespatial transcriptomics

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BioinformaticsbioRxivPreprintMay 11, 2025

Spatial geometry-aware deep learning for deciphering tissue structure from spatially resolved transcriptomics

Xingyi Li, Xiangting Jia, Dongmin Zhao…·Xuequn Shang

SpatialGEO improves identification of spatial regions in spatial transcriptomics data and reveals biological insights in tumor microenvironments and mouse development.

DOI 10.1101/2025.05.11.652625

mousespatial transcriptomics

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BioinformaticsbioRxivPreprintJan 28, 2024

BERTE：High-precision hierarchical classification of transposable elements by a transfer learning method with BERT pre-trained model and convolutional neural network

Yiqi Chen, Yang Qi, Yingfu Wu…·Xuequn Shang

BERTE improves TE classification accuracy using BERT and CNN, achieving up to 21% higher F1-score than existing methods.

4 citations

deep learningtransformer / foundation model

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BioinformaticsbioRxivPreprintJan 27, 2024

Comprehensive Hierarchical Classification of Transposable Elements based on Deep Learning

Yang Qi, Yiqi Chen, Yingfu Wu…·Xuequn Shang

This paper introduces CREATE, a deep learning framework for TE classification, and WebDLTE, a web platform for real-time TE annotation, showing improved performance over existing tools.

3 citations

deep learningcell type annotation

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