Publications by authors named "Shuai Cheng Li"

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One-year restoration of vaginal health: synergistic dynamics of microbiome and metabolome following the elimination of high-grade cervical intraepithelial neoplasia.
Hui Du, Xin Jiang, Yu Liu, Jun Hou, Changzhong Li, Shuai Cheng Li

mSystems· December 2025

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Deciphering the personalized functional redundancy hierarchy in the gut microbiome.
Yiqi Jiang, Lijia Che, Shuai Cheng Li

Microbiome· December 2025

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GeneFamily: a comprehensive mammalian gene family database with extensive annotation and interactive visualization.
Yinan Wang, Yuanzheng Zhang, Xueying Wang, Yen Kaow Ng, Yi Jia, Jiahe Liu, Shuai Cheng Li

Nucleic Acids Res· November 2025

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MicrobialScope: an integrated genomic resource with rich annotations across bacteria, archaea, fungi, and viruses.
Xikang Feng, Yinhu Li, Jieyi Zheng, Xuhua Chen, Shuo Yang, Shuai Cheng Li

Nucleic Acids Res· November 2025

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Shared and distinct molecular pathways in eutopic endometrium of endometriosis and adenomyosis patients: a transcriptomic study in Chinese women.
Juncui Bao, Xin Jiang, Yu Liu, Liping Zeng, Ruinan Xu, Shuai Cheng Li, Changzhong Li

BMC Womens Health· September 2025

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Inferring causal trajectories from spatial transcriptomics using CASCAT.
Yingying Yu, Wan Nie, Qianqian Zhang, Shuai Cheng Li

Nucleic Acids Res· August 2025

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Finding spatially variable ligand-receptor interactions with functional support from downstream genes.
Shiying Li, Ruohan Wang, Sitong Liu, Shuai Cheng Li

Nat Commun· August 2025

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CeiTEA: Adaptive Hierarchy of Single Cells with Topological Entropy.
Bowen Tan, Shiying Li, Mengbo Wang, Shuai Cheng Li

Adv Sci (Weinh)· July 2025

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AffMB: affinity maturation analysis with SHM-guided B-cell lineage trees.
Jiaqi Luo, Yiping Zou, Shuai Cheng Li

Bioinformatics· July 2025

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Topology entropy: Enhancing graph partitioning for TAD identification and single-cell clustering.
Qiushi Liang, Shengjie Zhao, Lingxi Chen, Shuai Cheng Li

Comput Struct Biotechnol J· April 2025

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PlasmidScope: a comprehensive plasmid database with rich annotations and online analytical tools.
Yinhu Li, Xikang Feng, Xuhua Chen, Shuo Yang, Zicheng Zhao, Shuai Cheng Li

Nucleic Acids Res· January 2025

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GutMetaNet: an integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome.
Yiqi Jiang, Yanfei Wang, Lijia Che, Shuo Yang, Xianglilan Zhang, Yu Lin, Shuai Cheng Li

Nucleic Acids Res· January 2025

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Spatially Informed Graph Structure Learning Extracts Insights from Spatial Transcriptomics.
Wan Nie, Yingying Yu, Xueying Wang, Ruohan Wang, Shuai Cheng Li

Adv Sci (Weinh)· December 2024

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Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions.
Yiping Zou, Jiaqi Luo, Lingxi Chen, Xueying Wang, Wei Liu, Shuai Cheng Li

Mol Syst Biol· December 2024

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Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome.
Yinhu Li, Guangze Pan, Shuai Wang, Zhengtu Li, Ru Yang, Shuai Cheng Li

Brief Bioinform· November 2024

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A comprehensive benchmarking for evaluating TCR embeddings in modeling TCR-epitope interactions.
Xikang Feng, Miaozhe Huo, He Li, Yongze Yang, Yuepeng Jiang, Liang He, Shuai Cheng Li

Brief Bioinform· November 2024

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SuperTAD-Fast: Accelerating Topologically Associating Domains Detection Through Discretization.
Zhao Ling, Yu Wei Zhang, Shuai Cheng Li

J Comput Biol· September 2024

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Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.
Shuai Wang, Yiqi Jiang, Lijia Che, Ruo Han Wang, Shuai Cheng Li

Nucleic Acids Res· August 2024

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Unlocking T-cell receptor-epitope insights with structural analysis.
Miaozhe Huo, Yuepeng Jiang, Shuai Cheng Li

Nat Comput Sci· July 2024

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Corrigendum: Biomarkers and computational models for predicting efficacy to tumor ICI immunotherapy.
Yurong Qin, Miaozhe Huo, Xingwu Liu, Shuai Cheng Li

Front Immunol· June 2024

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Immune-tumor interaction dictates spatially directed evolution of esophageal squamous cell carcinoma.
Yong Zhou, Shanlan Mo, Heyang Cui, Ruifang Sun, Weimin Zhang, Hongyi Li, Meilin Liu, Huijuan Liu, Ling Zhang, ShuaiCheng Li, Zhihua Liu

Natl Sci Rev· May 2024

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A novel deep generative model for mRNA vaccine development: Designing 5' UTRs with 1-methyl-pseudouridine modification.
Xiaoshan Tang, Miaozhe Huo, Yuting Chen, Hai Huang, Shugang Qin, Yongmei Liu, Lingxi Chen, Hao Li, Shuai Cheng Li

Acta Pharm Sin B· April 2024

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Metabolic profiles outperform the microbiota in assessing the response of vaginal microenvironments to the changed state of HPV infection.
Wenkui Dai, Hui Du, Qian Zhou, Sumei Li, Yinan Wang, Changzhong Li, Shuai Cheng Li

NPJ Biofilms Microbiomes· March 2024

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Biomarkers and computational models for predicting efficacy to tumor ICI immunotherapy.
Yurong Qin, Miaozhe Huo, Xingwu Liu, Shuai Cheng Li

Front Immunol· March 2024

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Coding genomes with gapped pattern graph convolutional network.
Ruo Han Wang, Yen Kaow Ng, Xianglilan Zhang, Jianping Wang, Shuai Cheng Li

Bioinformatics· March 2024

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