Publications

Yu Xu 许煜, Lu Zhang, et al (2025). TRAFICA: An Open Chromatin Language Model to Improve Transcription Factor Binding Affinity Prediction. Bioinformatics.

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Zeming Li, Yu Xu 许煜, Debajyoti Chowdhury, Hip Fung Yip, Chonghao Wang, Lu Zhang (2025). Causal Transformer for Learning Embeddings from Structured Medical History Records and Multi-Source Data Integration for Complex Disease Risk Prediction. Interdisciplinary Sciences: Computational Life Sciences.

Zirui Wang, Ke Xu, Yang Liu, Yu Xu 许煜, Lu Zhang (2025). Mitigation of Multi-scale Biases in Cell-type Deconvolution for Spatially Resolved Transcriptomics Using HarmoDecon. Bioinformatics.

Ke Xu, Yu Xu 许煜, Zirui Wang, Xin Maizie Zhou, Lu Zhang (2025). stDyer enables spatial domain clustering with dynamic graph embedding. Genome Biol.

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Zeming Li, Yu Xu 许煜, Debajyoti Chowdhury, Hip Fung Yip, Chonghao Wang, Lu Zhang (2024). Med-PRSIMD: Enhanced Complex Disease Risk Prediction through Integrative Analysis of Multi-Type Data and Medical History Records. ACM BCB 2024.

Yu Xu 许煜, Lu Zhang, et al (2022). A machine learning model for disease risk prediction by integrating genetic and non-genetic factors. IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2022.

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Yu Xu 许煜, JiaxingCheng, Aiping Lyu, William K. Cheung, Lu Zhang (2022). dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data. Briefings in Bioinformatics.

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