Shijie XU

About

Since April 2025, Shijie Xu is a postdoctoral researcher in Onoda Lab at Hokkaido University. His research focuses on bioinformatics, computational chemistry, and deep learning. Check his CV.

E-mail: c2hpamllLnh1QGVlcy5ob2t1ZGFpLmFjLmpw

News

• タンパク質の金属イオン結合部位を高精度･高速に予測する深層学習法を新規開発 · A better way to find where metals bind in a protein
• 分子系統解析に役立つ高精度な新手法を開発 · Streamlining genetic analysis for phylogenetic studies · PsiPartition: improved site partitioning with parameterized sorting indices and Bayesian optimization

Publications & preprints

1. Shijie Xu, Akira Onoda*, “Probe-Based Identification of Metal-Binding Sites Using Deep Learning Representations”, Nat. Commun. 17: 8146, 2026In the news(IF: 18.1)
2. Shijie Xu, Ke Xu, Akira Onoda*, “Accurate Prediction of Enzymatic Degradation of Plastics by Language Models”, Chem. Lett. 55(2): upag022, 2026(IF: 1.1)
3. Shijie Xu, Akira Onoda*, “Accurate and Rapid Prediction of Protein pK_a: Protein Language Models Reveal the Sequence-pK_a Relationship”, J. Chem. Theory Comput. 21(7): 3752-3764, 2025(TC: 6Citations per year6’26, IF: 5.8)
4. Shijie Xu, Akira Onoda*, “PsiPartition: Improved Site Partitioning for Genomic Data by Parameterized Sorting Indices and Bayesian Optimization”, J. Mol. Evol. 92: 874-890, 2024In the news(IF: 2.0)
5. Shijie Xu, Akira Onoda*, “Accurate and Fast Prediction of Intrinsically Disordered Protein by Multiple Protein Language Models and Ensemble Learning”, J. Chem. Inf. Model. 64(7): 2901-2911, 2024(TC: 25Citations per year5’2416’254’26, IF: 6.4)

*Citation counts sourced from OpenAlex and automatically updated via script. Hover “TC” for a per-year breakdown.

Academic Services

(Co-)Reviewer: J. Chem. Inf. Model., J. Chem. Theory Comput., Bioinformatics, Appl. Math. Comput., Curr. Opin. Struct. Biol.

Thanks to

EXEX Fellowship for supporting my research.