Author

Zhanghan Ni

University of Illinois Urbana-Champaign

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:contrastive learning· 1 Approach:deep learning· 1 Research Focus:phylogenetics / evolution· 1 Research Focus:protein design· 1 Assay:protein structure· 1 Research Focus:protein structure prediction· 1 Approach:statistical model· 1

Frequent Co-Authors

Adrian Gonzalez· 1 shared Alec Leonetti· 1 shared Aya S. KlosiD· 1 shared Bernhard SchölkopfiD· 1 shared Bryan Le· 1 shared Eva E. StüekeniD· 1 shared Hongyu Guo· 1 shared Joanne Sarah BodeniD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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1 shared paperBioinformatics

Adrian Gonzalez

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2 papers

Recent·Most cited

Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

Zhanghan Ni, Yanjing Li, Zeju Qiu, Bernhard Schölkopf, Hongyu Guo, Zhifeng Li, Shengchao Liu

This paper introduces RigidSSL, a geometric pretraining framework for protein design and conformational modeling, improving designability and capturing realistic dynamics.

bioRxiv · Mar 6, 2026 · PreprintBioinformatics

Time-resolved phylogenomics analysis reveals patterns in biosphere nutrient limitation through Earth history

Zhanghan Ni, Troy Osborn, Juntao Zhong, Adrian Gonzalez, Will Puzella, Aya S. Klos, Bryan Le, Alec Leonetti, Joanne Sarah Boden, Eva E. Stüeken, Rika E. Anderson

This study uses phylogenomic analysis to trace the timing of nutrient limitation genes across Earth's history, showing phosphorus genes emerged early, nitrogen later, and iron-related siderophores possibly as early as the Archean.

bioRxiv · Nov 13, 2025 · PreprintBioinformatics