Author

Ziwei Xie

Toyota Technological Institute at ChicagoORCID 0000-0002-5986-1150Unclaimed 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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Research Focus:benchmarking· 2 Approach:deep learning· 2 Assay:protein structure· 2 Research Focus:protein structure prediction· 2 Approach:statistical model· 2 Approach:contrastive learning· 1 Research Focus:deconvolution· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Jinbo XuiD· 3 shared Aocheng Ji· 1 shared Bo CheniD· 1 shared Hao XiongiD· 1 shared Jie TangiD· 1 shared Jiezhong QiuiD· 1 shared Jing Yan· 1 shared Li ZhongiD· 1 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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3 shared papersBioinformatics

Jinbo XuORCID

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4 papers

Recent·Most cited

PRISMA: A tensor-based framework for deconstructing the genetic architecture of complex diseases, with application to diabetic retinopathy

Hao Xiong, Wenbin Xu, Aocheng Ji, Li Zhong, Siyan Liu, Ziwei Xie, Jing Yan, Zhengzheng Wu

PRISMA decomposes GWAS signals into tissue-specific genetic axes for diabetic retinopathy, revealing novel targets and regulatory patterns.

bioRxiv · May 29, 2026 · PreprintBioinformatics

Redesign selective protein binders using contrastive decoding

Ziwei Xie, Jinbo Xu

RedNet improves protein binder design by incorporating side-chain information and contrastive decoding to enhance binding affinity, folding stability, and selectivity.

bioRxiv · May 13, 2026 · PreprintBioinformatics

Improve the Protein Complex Prediction with Protein Language Models

Bo Chen, Ziwei Xie, Jiezhong Qiu, Zhaofeng Ye, Jinbo Xu, Jie Tang

This paper introduces ESMPair, a method using protein language models to improve interolog identification, leading to better protein complex structure prediction than AlphaFold-Multimer.

bioRxiv · Sep 15, 2022 · PreprintBioinformatics

Deep graph learning of inter-protein contacts

Ziwei Xie, Jinbo Xu

GLINTER improves inter-protein contact prediction for dimers using graph learning and MSA language models, achieving higher precision than existing methods.

Bioinformatics · Nov 5, 2021Peer-reviewedBioinformatics