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<strong><fontcolor="green">Jul 2025</font></strong>:[EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research](https://doi.org/10.1007/s11427-025-3035-0)文章在***SCIENCE CHINA Life Sciences***期刊发表,恭喜刘秉东。
<strong><fontcolor="green">Jul 2025</font></strong>:[EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research](https://www.sciengine.com/SCLS/doi/10.1007/s11427-025-3035-0)文章在***SCIENCE CHINA Life Sciences***期刊发表,恭喜刘秉东。
<strong><fontcolor="green">Jul 2025</font></strong>:2025前沿科学创新大会,文章[Thirteen years of clusterProfiler](https://doi.org/10.1016/j.xinn.2024.100722)获得Best Paper奖项,余光创获得Outstanding Contributor奖项。
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<strong><fontcolor="green">May 2025</font></strong>: [aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types](https://doi.org/10.1016/j.xinn.2025.100958) 文章在***The Innovation***期刊发表。恭喜徐双斌、王倩雯、温少迪、李俊睿和贺楠。
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<strong><fontcolor="green">May 2025</font></strong>: [aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types](https://doi.org/10.1016/j.xinn.2025.100958) 文章在***The Innovation***期刊发表,恭喜徐双斌、王倩雯、温少迪、李俊睿和贺楠。该文章入选封面导读:Complex composite graphics
<strong><fontcolor="green">Feb 2023</font></strong>: 📝🎉 专刊《Computational and systematic analysis of multi-omics data for drug discovery and development》发表[编委社论文章](https://www.frontiersin.org/articles/10.3389/fmed.2023.1146896/full),成功收关。
+ B Liu, Y Liu, S Xu, Q Wu, D Wu, Y Liao, Y Mai, M Zheng, S Wang, L Zhan, Y Chen, Z Huang, X Luo, Z Xie, X Pan, __G Yu__<sup>\*</sup>, L Xie<sup>\*</sup>. [EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research](https://doi.org/10.1007/s11427-025-3035-0). __*SCIENCE CHINA Life Sciences*__. 2025, accepted.
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+ B Liu, Y Liu, S Xu, Q Wu, D Wu, Y Liao, Y Mai, M Zheng, S Wang, L Zhan, Y Chen, Z Huang, X Luo, Z Xie, X Pan, __G Yu__<sup>\*</sup>, L Xie<sup>\*</sup>. [EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research](https://www.sciengine.com/SCLS/doi/10.1007/s11427-025-3035-0). __*SCIENCE CHINA Life Sciences*__. 2025, accepted.
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+ P Li<sup>#</sup>, L Xie<sup>#</sup>, H Zheng<sup>#</sup>, Y Feng<sup>#</sup>, F Mai, W Tang, J Wang, Z Lan, S Lv, T Jayawardana, S Koentgen, S Xu, Z Wan, Y Chen, H Xu, S Shen, F Zhang, Y Yang, G Hold, F He<sup>\*</sup>, E M. El-Omar<sup>\*</sup>, __G Yu__<sup>\*</sup>, X Chen<sup>\*</sup>. [Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome](https://onlinelibrary.wiley.com/doi/10.1002/imt2.70065). __*iMeta*__. 2025, e70065.
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+ Y Gao<sup>#</sup>, B Li<sup>#</sup>, Y Jin<sup>#</sup>, J Cheng<sup>#</sup>, W Tian, L Ying, L Hong, S Xin, B Lin, C Liu, X Sun, J Zhang, H Zhang, J Xie, X Deng, X Dai, L Liu, Y Zheng, P Zhao, __G Yu__<sup>\*</sup>, W Fang<sup>\*</sup>, X Bao<sup>\*</sup>. [Spatial multi-omics profiling of breast cancer oligo-recurrent lung metastasis](https://doi.org/10.1038/s41388-025-03388-y). __*Oncogene*__. 2025, 44(27):2268-2282.
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+ S Xu<sup>#</sup>, Q Wang<sup>#</sup>, S Wen<sup>#</sup>, J Li<sup>#</sup>, N He<sup>#</sup>, M Li, T Hackl, R Wang, D Zeng, S Wang, S Li, CH Gao, L Zhou, S Tao, Z Xie, L Deng, __G Yu__<sup>\*</sup>. [aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types](https://doi.org/10.1016/j.xinn.2025.100958). __*The Innovation*__. 2025, 6(9):100958.
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+ S Xu<sup>#</sup>, Q Wang<sup>#</sup>, S Wen<sup>#</sup>, J Li<sup>#</sup>, N He<sup>#</sup>, M Li, T Hackl, R Wang, D Zeng, S Wang, S Li, CH Gao, L Zhou, S Tao, Z Xie, L Deng, __G Yu__<sup>\*</sup>. [aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types](https://doi.org/10.1016/j.xinn.2025.100958). __*The Innovation*__. 2025, 6(9):100958. (封面导读:Complex composite graphics)
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+ Q Wang, H Zhu, L Deng, S Xu, W Xie, M Li, R Wang, L Tie, L Zhan, __G Yu__<sup>\*</sup>. [Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications](https://doi.org/10.1002/smtd.202401107). __*Small Methods*__. 2025, 9(5):2401107. [卷首插图文章Frontispiece](https://onlinelibrary.wiley.com/doi/10.1002/smtd.202570033)
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+ Y Tu<sup>#\*</sup>, S Xu<sup>#</sup>, H Shu, X Wang, W Li, __G Yu__<sup>\*</sup>, Li He<sup>\*</sup>. [16S rRNA Sequencing Reveals Dysbiosis of Skin Microbiome Associated With Disease Severity in Chronic Actinic Dermatitis](https://onlinelibrary.wiley.com/doi/full/10.1111/phpp.70022). __*Photodermatology, Photoimmunology & Photomedicine*__. 2025, 41(3):e70022.
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+ M Chen<sup>#</sup>, X Luo<sup>#</sup>, S Xu<sup>#</sup>, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen<sup>\*</sup>, TTY Lam<sup>\*</sup>, __G Yu__<sup>\*</sup>. [Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree](https://doi.org/10.1002/imt2.269). __*iMeta*__. 2025, 4(1):e269.
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+ X Zhang, B Liang, Y Huang, H Meng, Z Li, J Du, L Zhou, Y Zhong, B Wang, X Lin, __G Yu__, X Chen, W Lu, ZS Chen, X Yang, Z Huang<sup>\*</sup>. [Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics](https://doi.org/10.1002/advs.202303753). __*Advanced Science*__. 2023, 10(36):2303753. (IF = 14.3,一区)
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+ M Kang, F Lin, Z Jiang, X Tan, X Lin, Z Liang, C Xiao, Y Xia, W Guan, Z Yang, __G Yu__, M Zanin, S Tang<sup>\*</sup>, SS Wong<sup>\*</sup>. [The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults](https://onlinelibrary.wiley.com/doi/abs/10.1111/irv.13172). __*Influenza and Other Respiratory Viruses*__. 2023, 17(7):e13172. (IF = 4.3,四区)
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+ W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, __G Yu__<sup>\*</sup>. [MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm](https://dx.doi.org/10.1080/19490976.2023.2223349). __*Gut Microbes*__. 2023, 15(1):2223349. (IF = 12.2,一区)
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+ S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, __G Yu__<sup>\*</sup>. [MicrobiotaProcess: A comprehensive R package for deep mining microbiome](https://doi.org/10.1016/j.xinn.2023.100388). __*The Innovation*__. 2023, 4(2):100388. (IF = 33.2,一区)
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+ S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, __G Yu__<sup>\*</sup>. [MicrobiotaProcess: A comprehensive R package for deep mining microbiome](https://doi.org/10.1016/j.xinn.2023.100388). __*The Innovation*__. 2023, 4(2):100388. (IF = 33.2,一区) (封面导读:Microbiome Toolkit)
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+ S Guo<sup>\*</sup>, D Zhang, H Wang, Q An, __G Yu__, J Han, C Jiang, J Huang. [Computational and Systematic Analysis of Multi-omics Data for Drug Discovery and Development](https://www.frontiersin.org/articles/10.3389/fmed.2023.1146896/full). __*Frontiers in Medicine*__. 2023, 10:1146896. (IF = 3.1,三区)
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+ S Xu<sup>#</sup>, M Chen<sup>#</sup>, T Feng, L Zhan, L Zhou, __G Yu__<sup>\*</sup>. [Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers](https://www.frontiersin.org/articles/10.3389/fgene.2021.774846). __*Frontiers in Genetics*__. 2021, 12:774846. (IF=4.772,三区)
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+ CH Gao, __G Yu__, P Cai<sup>\*</sup>. [ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram](https://doi.org/10.3389/fgene.2021.706907). __*Frontiers in Genetics*__. 2021, 12:706907. <iclass="fa fa-trophy fa-2x"aria-hidden="true"style="color:#CC5500;font-size: 150%;"></i> (IF=4.772,三区)
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+ S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang<sup>\*</sup>, X Bo<sup>\*</sup>, __G Yu__<sup>\*</sup>. [ggtreeExtra: Compact visualization of richly annotated phylogenetic data](https://doi.org/10.1093/molbev/msab166). __*Molecular Biology and Evolution*__. 2021, 38(9):4039-4042. (IF=8.800,一区,Top期刊)
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+ T Wu<sup>#</sup>, E Hu<sup>#</sup>, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo<sup>\*</sup>, **G Yu**<sup>\*</sup>. [clusterProfiler 4.0: A universal enrichment tool for interpreting omics data](https://doi.org/10.1016/j.xinn.2021.100141). **_The Innovation_**. 2021, 2(3):100141.
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+ T Wu<sup>#</sup>, E Hu<sup>#</sup>, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo<sup>\*</sup>, **G Yu**<sup>\*</sup>. [clusterProfiler 4.0: A universal enrichment tool for interpreting omics data](https://doi.org/10.1016/j.xinn.2021.100141). **_The Innovation_**. 2021, 2(3):100141. (封面导读:ClusterProfiler 4: Pathway Discovery)
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+ D Zeng<sup>#</sup>, Z Ye<sup>#</sup>, R Shen, __G Yu__, J Wu, Y Xiong, R Zhou, W Qiu, N Huang, L Sun, X Li, J Bin, Y Liao, M Shi, W Liao<sup>\*</sup>. [IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures](https://doi.org/10.3389/fimmu.2021.687975). **_Frontiers in Immunology_**. 2021, 12:687975. <iclass="fa fa-trophy fa-2x"aria-hidden="true"style="color:#CC5500;font-size: 150%;"></i> (IF=8.786,二区,Top期刊)
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+ T Wu, E Hu, X Ge<sup>\*</sup>, __G Yu__<sup>\*</sup>. [nCov2019: an R package for studying the COVID-19 coronavirus pandemic](https://doi.org/10.7717/peerj.11421). __*PeerJ*__. 2021, 9:e11421. (IF=3.061,三区)
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+ R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, __G Yu__, SC Hicks, MD Robinson<sup>\*</sup>. [TreeSummarizedExperiment: a S4 class for data with hierarchical structure](https://doi.org/10.12688/f1000research.26669.2). __*F1000Research*__. 2021, 9:1246.
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