Author

Yu Shi

Purdue University West LafayetteORCID 0000-0002-2538-0295Unclaimed ORCID profile · follow to get notified of new preprints

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Yu Shi3 papers · National University of Singapore

Biology Disciplines

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Biochemistry· 1 Biophysics· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Research Focus:benchmarking· 1 Approach:deep learning· 1 Assay:DNA methylation· 1 Research Focus:drug response / drug discovery· 1 Research Focus:protein structure prediction· 1

Frequent Co-Authors

Jianing LiiD· 2 shared Yutong ShiiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

2 top collaborators · 1 mutual co-author link

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2 shared papersBiophysics

Jianing LiORCID

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2 papers

Recent·Most cited

BiophysicsbioRxivPreprintFeb 19, 2026

A Non-Alchemical Absolute Binding Free Energy Framework for Small Molecule Drugs

Yu Shi, Jianing Li

This paper introduces a non-alchemical ABFE framework for protein-ligand binding free energy calculations, showing improved accuracy and stability over existing methods.

DOI 10.64898/2026.02.18.706686

statistical modeldrug response / drug discovery

𝕏 PostBluesky

BiochemistryJournal of Chemical Information and ModelingPeer-reviewedDec 22, 2025

Small Single-Stranded DNA Structure Prediction

Yutong Shi, Yu Shi, Jianing Li

This paper compares traditional and AlphaFold 3 methods for predicting 3D structures of small ssDNAs, finding AF3 more accurate but with limitations for complex motifs.

1 citation

DNA methylationdeep learning

𝕏 PostBluesky