Author

Zhenqiao Song

Carnegie Mellon UniversityORCID 0009-0006-6125-900XUnclaimed ORCID profile · follow to get notified of new preprints

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Zhenqiao Song1 paper

Biology Disciplines

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Bioinformatics· 2

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Research Focus:benchmarking· 1 Approach:deep learning· 1 Approach:large language model· 1 Research Focus:protein design· 1 Assay:protein sequence· 1 Assay:whole-genome sequencing· 1

Frequent Co-Authors

Danqing WangiD· 1 shared Huichong LiuiD· 1 shared Jian MaiD· 1 shared Lei LiiD· 1 shared Lei LiiD· 1 shared Muyu YangiD· 1 shared Shike Wang· 1 shared Wenduo Cheng· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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1 shared paperBioinformatics

Danqing WangORCID

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2 papers

Recent·Most cited

BioinformaticsbioRxivPreprintMar 31, 2026

Co-designing sequence and structure of functional de novo enzymes with EnzyGen2

Zhenqiao Song, Huichong Liu, Yunlong Zhao…·Lei Li

EnzyGen2 co-designs protein sequences and structures with ligand-guided functionality, outperforming existing methods in in silico benchmarks and generating active enzymes with high novelty.

1 citation

protein sequencelarge language model

𝕏 PostBluesky

BioinformaticsNature CommunicationsPeer-reviewedNov 18, 2025

DNALONGBENCH: A Benchmark Suite for Long-Range DNA Prediction Tasks

Wenduo Cheng, Zhenqiao Song, Yang Zhang…·Jian Ma

The paper introduces DNALO_SCPLOWONGC_SCPLOWBO_SCPLOWENCHC_SCPLOW, a benchmark suite for long-range DNA prediction tasks, and evaluates five methods on five genomics tasks.

12 citations

whole-genome sequencingdeep learning

𝕏 PostBluesky