Author

Lifeng Qiao

Shanghai Jiao Tong 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:deep learning· 3 Research Focus:benchmarking· 2 Assay:bulk RNA-seq· 2 Assay:protein structure· 2 Approach:benchmark study· 1 Assay:ChIP-seq· 1 Research Focus:differential expression· 1 Assay:DNA methylation· 1

Frequent Co-Authors

Hong-Liang YaniD· 2 shared Sheng Yong XuiD· 2 shared Wanli OuyangiD· 2 shared Xinzhu MaiD· 2 shared Yuchen ReniD· 2 shared Chaoqi Liang· 1 shared Dong YuaniD· 1 shared Gaoxing Guo· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

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2 shared papersBioinformatics

Hong-Liang YanORCID

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4 papers

Recent·Most cited

IntelliFold-2: Surpassing AlphaFold 3 via Architectural Refinement and Structural Consistency

Lifeng Qiao, Yan He, Gary Liu, Gaoxing Guo, Siqi Sun

IntelliFold-2 improves protein structure prediction accuracy and robustness over AlphaFold 3 using architectural refinements and structural consistency, with strong gains in antibody-antigen and protein-ligand interactions.

bioRxiv · Feb 14, 2026 · PreprintBioinformatics

FoldBench: An All-atom Benchmark for Biomolecular Structure Prediction

Sheng Yong Xu, Qiantai Feng, Lifeng Qiao, Hao Bin Wu, Tao Shen, Yu Cheng, Shuangjia Zheng, Siqi Sun

FoldBench evaluates all-atom biomolecular structure prediction models across nine tasks, revealing performance gaps and highlighting AlphaFold 3's superiority.

bioRxiv · May 22, 2025 · PreprintBioinformatics

Genomics-FM: Universal Foundation Model for Versatile andData-Efficient Functional Genomic Analysis

Peng Ye, Weiqiang Bai, Yuchen Ren, Wenran Li, Lifeng Qiao, Chaoqi Liang, Linxiao Wang, Yuchen Cai, Jianle Sun, Zejun Yang, Peng Zheng, Nanqing Dong, Tao Chen, Zhihui Wang, Xihui Liu, , Wanli Ouyang

Genomics-FM is a foundation model that reduces reliance on labeled data and outperforms existing models in genome annotation, epigenomic prediction, and variant effect assessment.

bioRxiv · Jul 16, 2024 · PreprintBioinformatics

BEACON: Benchmark for Comprehensive RNA Tasks and Language Models

Yuchen Ren, Zhiyuan Chen, Lifeng Qiao, Hongtai Jing, Y. Cai, Sheng Yong Xu, Peng Ye, Xinzhu Ma, Siqi Sun, Hong-Liang Yan, Dong Yuan, Wanli Ouyang, Xihui Liu

BEACON introduces a comprehensive RNA benchmark to evaluate deep learning models, finding that single nucleotide tokenization and ALiBi improve performance.

bioRxiv · Jun 22, 2024 · PreprintBioinformatics