Author

Hong-Sheng Lai

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.

Biology Disciplines

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Approach:statistical model· 3 Research Focus:benchmarking· 2 Approach:experimental assay· 2 Organism:human· 2 Research Focus:variant calling· 2 Assay:whole-genome sequencing· 2 Research Focus:database / resource· 1 Research Focus:gene regulatory network inference· 1

Frequent Co-Authors

Chia‐Lang HsuiD· 2 shared Chien‐Yu CheniD· 2 shared Hsin-Fu LiniD· 2 shared Jacob Shujui HsuiD· 2 shared Pei‐Lung CheniD· 2 shared Ting-Yu ChangiD· 2 shared Tsung-Kai HungiD· 2 shared Y LiuiD· 2 shared

Activity by Year

2024-2025 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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2 shared papersBioinformatics

Chia‐Lang HsuORCID

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4 papers

Recent·Most cited

deCYPher: Star Allele-Resolution Computational Framework of Pharmacogenes for Haplotype-Resolved Long-Read Assemblies

Ting-Yu Chang, Y Liu, Hong-Sheng Lai, Tsung-Kai Hung, Hsin-Fu Lin, Yu-Hui Lin, Chia‐Lang Hsu, Ya‐Chien Yang, Chein-Yu Chen, Pei‐Lung Chen, Jacob Shujui Hsu

deCYPher is a computational framework for pharmacogene analysis using haplotype-resolved assemblies, demonstrating high accuracy in resolving complex gene structures and identifying allele variations.

bioRxiv · Oct 13, 2025 · PreprintBioinformatics

TypeAssembly: Copy number estimation and allele typing for haplotype assemblies

Hong-Sheng Lai, Y Liu, Hsien-Chun Chiu, Ting-Yu Chang, Hsin-Fu Lin, Yi-Hsuan Tseng, Tsung-Kai Hung, Sheng-Kai Lai, Jacob Shujui Hsu, Chia‐Lang Hsu, Ya‐Chien Yang, Pei‐Lung Chen, Chien‐Yu Chen

TypeAssembly annotates complex genes in haplotype assemblies by estimating copy numbers and typing alleles, successfully applied to 41 genes, 17 KIR genes, and 15 pharmacogenes across 466 assemblies.

bioRxiv · Sep 13, 2025 · 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

Evaluating the performance of protein structure prediction in detecting structural changes of pathogenic nonsynonymous single nucleotide variants

Hong-Sheng Lai, Chien‐Yu Chen

This study evaluates how well protein structure prediction tools detect structural changes caused by pathogenic nonsynonymous single nucleotide variants.

International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC) · Jan 1, 2024Peer-reviewedBioinformatics