Author

Hongyu Duan

South China University of Technology

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 Genomics· 1 Synthetic Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 2 Research Focus:protein structure prediction· 2 Approach:contrastive learning· 1 Research Focus:differential expression· 1 Organism:fungi (other)· 1 Research Focus:gene regulatory network inference· 1 Research Focus:genome assembly· 1 Assay:Hi-C· 1

Frequent Co-Authors

Li Charlie XiaiD· 2 shared Amy Mackenzie· 1 shared Anna Sharp· 1 shared Ashley JonesiD· 1 shared Benjamin SchwessingeriD· 1 shared Bozhen Ren· 1 shared Cheng JiangiD· 1 shared Chenzhong LiiD· 1 shared

Activity by Year

2021-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersBioinformatics

Li Charlie XiaORCID

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Author profile →

4 papers

Recent·Most cited

A programmable mRNA platform for miRNA detection via miRNA-mRNA2 triplex-mediated ribosomal frameshifting

Yanyu Chen, Wanqi Zhao, Huizhen Chen, Hanting Zhou, Shijian Fan, Liping Xing, Yun Lian, Hongyu Duan, Yuze Dai, Zheng Zhao, Rongguang Lu, Chenzhong Li, Cheng Jiang, Ho Yin Edwin Chan, Gang Chen

This paper develops a programmable mRNA platform that detects specific miRNAs by converting their presence into a quantifiable protein output through miRNA-triggered ribosomal frameshifting.

ACS Synthetic Biology · Jul 17, 2026Peer-reviewedSynthetic Biology

sxLaep: a Lightweight and Accurate Enzyme Predictorfor High-throughput Mining of Metagenomic Sequences

Hongyu Duan, Xingyu Han, Yijun Mo, Bozhen Ren, Li Charlie Xia

sxLaep is a fast and accurate enzyme predictor for metagenomic sequences, achieving high accuracy and speed compared to existing tools.

bioRxiv · May 21, 2026 · PreprintBioinformatics

Predicting Enzyme Functions Using Contrastive Learning with Hierarchical Enzyme Structure Information

Hongyu Duan, Ziyan Li, Yixuan Wu, Wen Chen, Li Charlie Xia

This paper introduces EnzHier, a machine learning algorithm that improves enzyme function prediction by integrating sequence, structural information, and functional hierarchy, achieving better accuracy than existing tools.

bioRxiv · Jul 7, 2024 · PreprintBioinformatics

Identification and correction of phase switches with Hi-C data in the Nanopore and HiFi chromosome-scale assemblies of the dikaryotic leaf rust fungus Puccinia triticina

Hongyu Duan, Ashley Jones, Tim Hewitt, Amy Mackenzie, Yiheng Hu, Anna Sharp, David Lewis, Rohit Mago, Narayana M. Upadhyaya, John Paul Rathjen, Eric A. Stone, Benjamin Schwessinger, Melania Figueroa, Peter N. Dodds, Sambasivam K. Periyannan, Jana Sperschneider

The paper identifies and corrects phase switches in Hi-C data for dikaryotic fungus assemblies using Nanopore and HiFi sequencing, showing HiFi's superiority in phasing low heterozygosity genomes.

bioRxiv · Apr 28, 2021 · PreprintGenomics