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Bioinformatics (Oxford, England)|June 30, 2023
UNADON: transformer-based model to predict genome-wide chromosome spatial positionMuyu Yang, Jian MaJournal of Molecular Biology|June 6, 2022
Machine Learning Methods for Exploring Sequence Determinants of 3D Genome OrganizationMuyu Yang, Jian MaArxiv|May 10, 2023
UNADON: Transformer-based model to predict genome-wide chromosome spatial positionMuyu Yang, Jian MaBioinformatics (Oxford, England)|July 14, 2020
Cancer mutational signatures representation by large-scale context embeddingYang Zhang, Yunxuan Xiao, Muyu Yang, et al.Nature Reviews. Genetics|September 6, 2023
Computational methods for analysing multiscale 3D genome organizationYang Zhang, Lorenzo Boninsegna, Muyu Yang, et al.Nature Methods|August 9, 2024
Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developmentsValerie Chen, Muyu Yang, Wenbo Cui, et al.Biorxiv : the Preprint Server for Biology|January 20, 2025
DNALongBench: A Benchmark Suite for Long-Range DNA Prediction TasksWenduo Cheng, Zhenqiao Song, Yang Zhang, et al.Nature Communications|November 18, 2025
DNALONGBENCH: a benchmark suite for long-range DNA prediction tasksWenduo Cheng, Zhenqiao Song, Yang Zhang, et al.Biorxiv : the Preprint Server for Biology|November 26, 2025
Heimdall: A Modular Framework for Tokenization in Single-Cell Foundation ModelsEllie Haber, Shahul Alam, Nicholas Ho, et al.Sensors (Basel, Switzerland)|September 27, 2025
FCP-Former: Enhancing Long-Term Multivariate Time Series Forecasting with Frequency CompensationMing Li, Muyu Yang, Shaolong Chen, et al.Pageof 171