Author

Zhaoyi You

Carnegie Mellon UniversityORCID 0009-0003-9281-641XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Approach:statistical model· 2 Assay:DNA methylation· 1 Organism:human· 1 Research Focus:sequence-to-function modeling· 1 Research Focus:trajectory inference· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Alex MogilneriD· 1 shared Alexander HoffmanniD· 1 shared Carl KingsfordiD· 1 shared Gün KaynariD· 1 shared Jiancheng ZhangiD· 1 shared Jiayi LiiD· 1 shared Lucas BöttcheriD· 1 shared Mingtao XiaiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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1 shared paperMolecular Biology

Alex MogilnerORCID

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2 papers

Recent·Most cited

CodonRL: Multi-Objective Codon Sequence Optimization Using Demonstration-Guided Reinforcement Learning

Shiyi Du, Gün Kaynar, Jiayi Li, Zhaoyi You, Shijie Tang, Carl Kingsford

CodonRL improves codon sequence optimization using reinforcement learning with structural feedback and expert demonstration, outperforming existing methods on multiple metrics.

bioRxiv · Feb 14, 2026 · PreprintBioinformatics

Reconstructing Noisy Gene Regulation Dynamics UsingExtrinsic-Noise-Driven Neural Stochastic Differential Equations

Jiancheng Zhang, Xiangting Li, Xiaolu Guo, Zhaoyi You, Lucas Böttcher, Alex Mogilner, Alexander Hoffmann, Tom Chou, Mingtao Xia

This paper introduces an END-nSDE framework to reconstruct noisy gene regulation dynamics from heterogeneous cell populations, outperforming RNNs and LSTMs in modeling extrinsic noise effects.

PLoS Computational Biology · Sep 17, 2025Peer-reviewedMolecular Biology