Author

Shijie Tang

Carnegie Mellon University

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

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Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Approach:deep learning· 1 Assay:DNA methylation· 1 Organism:human· 1 Approach:machine learning (classical)· 1 Research Focus:sequence-to-function modeling· 1 Research Focus:software / tool· 1 Approach:statistical model· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Carl KingsfordiD· 2 shared Jiayi LiiD· 2 shared Shiyi DuiD· 2 shared Gün KaynariD· 1 shared Hong-Sheng Lai· 1 shared Litian Liang· 1 shared Zhaoyi YouiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

7 top collaborators · 17 mutual co-author links

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2 shared papersBioinformatics

Carl KingsfordORCID

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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

ARCADE: Controllable Codon Design from Foundation Models via Activation Engineering

Jiayi Li, Hong-Sheng Lai, Litian Liang, Shiyi Du, Shijie Tang, Carl Kingsford

ARCADE enables flexible, controllable codon design using activation engineering from genomic language models to steer biological metrics like Codon Adaptation Index and GC content.

bioRxiv · Aug 19, 2025 · PreprintBioinformatics