1<!doctype html><html lang=en><head><title>Publications · YuLab@SMU</title><meta charset=utf-8><meta name=viewport content="width=device-width,initial-scale=1"><meta name=color-scheme content="light dark"><meta name=author content="YuLab-SMU"><meta name=description content=" 2 3 4 5 6 7# Co-first authors 8* Co-corresponding authors 9ï¼ESI Highly Cited Paper (12X) 10ï¼ESI Hot Paper 11ååºï¼æç« å表å½å¹´çä¸ç§é¢å°ç±»ååº 12IFï¼æç« å表å½å¹´çå½±åå å 13课é¢ç»å ¬ä¼å·è§£è¯»æç« 14 15 16 17 18 19 20 21 22 2026 23 24 25 Link to heading 26 27 28 29N He, S Xu, K Mo, Y Xia, R Wang, S Tao, Q Wang, J Mo, B Pang, Y Qiu*, Q Song*, G Yu*. TCMDATA: an integrated R package for target-oriented network pharmacology analysis and AI-assisted interpretation in traditional Chinese medicine. Current Molecular Pharmacology. accepted. 30W Liu, J Ding, Y Sun, B Yan, Z Wang, C Wang, C Shu, JG Zhou, G Yu*, Y Peng*, S Wang*. Composable Visualization of HighâDimensional Biological Data with ggalign. Current Protocols. 2026, 6(9):e70453. 31S Lin, G Yu*. From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics. Advanced Genetics. 2026, 7(3):e70045. 32J Feng#, C Chen#*, Y Wu#, L Fan, Z Zhang, M Chen, H Tang, G Yu, J Ren, J Luo, Y Liao, A Luan, Z Wang, S Tang, Y Shao, Y Liang, J Wang*, J Xie*, R Xia*. How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools. Molecular Plant. 2026, 19(7):1378-1391. 33Y Feng#, L Zheng#, W Tang#, P Wang, Y Lai, J Qin, C Zhou, X Zhang, M Yang, L Jie*, G Yu*, H Ren*, Q Huang*. Gut metabolite indole-3-acetic acid aggravates neuropsychiatric lupus via the AHR/STAT3 pathway in microglia. Communications Biology. 2026, 9(1):281. 34B 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*, L Xie*. EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research. SCIENCE CHINA Life Sciences. 2026, 69(2):321-330. (å°é¢æç« , Cover Article) 35Q Wang#, L Deng#, S Xu#, P Guo, H Zhu, H Ge, Y Gong, G Du, K Huang, C Su, R Wang, Y Qiu*, G Yu*. Comparison of Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 platforms for singleâcell spatial transcriptomics of mouse brain and lung. Interdisciplinary Medicine. 2026, 4(1):e70067.
36G Yu*. Background bias in functional enrichment analysis: Insights from clusterProfiler. The Innovation Life. 2026, 4(1):100181. (å°é¢å¯¼è¯»ï¼Insights form clusterProfiler) 37 38 39 2025 40 41 42 Link to heading 43 44 45 46Y Peng, S Jiang, Y Song, P Luo, J Li, D Hu, JG Zhou, G Yu*, T Xu*, S Wang*. ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity. Advanced Science. 2025, 12(44): e07799. (IF = 14.1) 47S Wen#, X Du#, M Zhu#, C Huang, Z Lin, M Li, B Hu, X Wang, F Jiang, G Zhou, W Zhu, G Yu*, C Xu*, B Shen*. ALCAM-CD6 axis suppression: a key determinant of immune-mediated metastasis recurrence in stage III non-small cell lung cancer. Journal for ImmunoTherapy of Cancer. 2025, 13(10):e010416. (IF = 11.7) 48P Li#, L Xie#, H Zheng#, Y Feng#, 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*, E M. El-Omar*, G Yu*, X Chen*. Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome. iMeta. 2025, 4(5):e70065. (IF = 44.4) 49X Lu, K Li, Z Li, A Lin, L Zhao, R Shen, Z Xu, J Gao, D Lv, Y Zhang, T Ye, J Shen, Y Chen, H Huang, Z Hao, D Zeng, H Wang, S Guo, W Wang, Y Xiong, Y Li, H Li, J Gao, Q Liu, B Wei, J Shi, S Cheng, G Li, Y Tang, E Lin, H Xu, G Feng, Y He, Y Sun, X Liu, Y Wang, W Song, J Song, S Tian, Y Zhang, J Zhang, Z Xu, C Song, Y Zhang, H Wu, C Gao, E Hu, C Yang, J Lou, D Wang, X Wang, P Luo*, G Yu*, Y Ge*. FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency. iMetaMed. 2025, 1(1):e70005. Cover story 50S Xu#, Q Wang#, S Wen#, J Li#, N He#, M Li, T Hackl, R Wang, D Zeng, S Wang, S Li, CH Gao, L Zh
50ou, S Tao, Z Xie, L Deng, G Yu*. aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types. The Innovation. 2025, 6(9):100958. (å°é¢å¯¼è¯»ï¼Complex composite graphics) (IF = 39.5) 51Y Gao#, B Li#, Y Jin#, J Cheng#, 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*, W Fang*, X Bao*. Spatial multi-omics profiling of breast cancer oligo-recurrent lung metastasis. Oncogene. 2025, 44(27):2268-2282. (IF = 9.1) 52Q Wang, H Zhu, L Deng, S Xu, W Xie, M Li, R Wang, L Tie, L Zhan, G Yu*. Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications. Small Methods. 2025, 9(5):2401107. å·é¦æå¾æç« Frontispiece (IF = 8.7) 53Y Tu#*, S Xu#, H Shu, X Wang, W Li, G Yu*, Li He*. 16S rRNA Sequencing Reveals Dysbiosis of Skin Microbiome Associated With Disease Severity in Chronic Actinic Dermatitis. Photodermatology, Photoimmunology & Photomedicine. 2025, 41(3):e70022. 54M Chen#, X Luo#, S Xu#, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen*, TTY Lam*, G Yu*. Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree. iMeta. 2025, 4(1):e269. (IF = 44.4) 55 56 57 2024 58 59 60 Link to heading 61 62 63 64D Zeng#, Y Fang#, W Qiu; P Luo, S Wang; R Shen, W Gu, X Huang, Q Mao; G Wang, Y Lai; X Xu, M Shi, Z Wu*, G Yu*, W Liao*. Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0. Cell Reports Methods. 2024, 4(12):100910. (IF = 4.5ï¼äºåº) 65M Luo*#, W Yang#, L Bai#, L Zhang#, JW Huang#, Y Cao#, Y Xie#, L Tong, H Zhang, L Yu, LW Zhou, Y Shi, P Yu, Z Wang, Z Yuan, P Zhang, Y Zhang, F Ju, H Zhang, F Wang, Y Cui, J Zhang, G Jia, D Wan, C Ruan, Y Zeng, P Wu, Z Gao, W Zhao, Y Xu, G Yu, C Tian, LN Jin, J Dai*, B Xia*, B Sun*, F Chen*, YZ Gao*, H Wang*, B Wang*, D Zhang*, X Cao*, H Wang*, T Huang*. Artificial intelligence for life sciences: A comprehensive guide and future trends. The Innovation Life. 2024, 2(4):100105. 66Z Miao#, T Tian#, W Chen#, Q Wang#, L Ma#, D Zhang#, M Xie#, Z Yu#, X Guo, G Bai, S Zhao, X Chen, W Wang, Y Gao, S Guo*, M Luo*, L Yuan*, C Tian*, L Wu*, G Yu*, D Zhang*, S Sun*. Spatial Resolved Transcriptomics: Computational Insights into Gene Transcription Across Tissue and Organ Architecture in Diverse Applications. The Innovation Life. 2024, 2(4):100097. 67G Yu*. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722. (IF = 25.7ï¼ä¸åº) 68S Xu#, E Hu#, Y Cai#, Z Xie#, X Luo#, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, G Yu*. Using clusterProfiler to characterise Multi-Omics Data. Nature Protocols. 2024, 19(11):3292-3320. (IF = 16.0ï¼ä¸åº) 69S Wang, G Yu, L Xie*. Asymmetric Cell Division and Satellite Cell Fate Regulation in Skeletal Muscle Aging and Disease. Health and Metabol
69ism. 2024, 1(1):5. 70Y Chen#, LN He#, Y Zhang, J Gong, S Xu, Y Shu, D Zhang*, G Yu*, Z Zuo*. tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package. iMeta. 2024, 3(5):e229. (IF = 33.2ï¼ä¸åº) 71D Wang, G Chen, L Li, S Wen, Z Xie, X Luo, L Zhan, S Xu, J Li, R Wang, Q Wang*, G Yu*. Reducing language barriers, promoting information absorption, and communication using fanyi. Chinese Medical Journal. 2024, 137(16):1950-1956. (IF = 7.3ï¼äºåº) 72XK Ma#, Y Yu#, T Huang#*, D Zhang, C Tian, W Tang, M Luo, P Du*, G Yu*, L Yang*. Bioinformatics Software Development: principles and future directions. The Innovation Life. 2024, 2(3):100083. 73Y Yang#, S Xu#, Y Hong, Y Cai, W Tang, J Wang, B Shen*, H Zong*, G Yu*. Computational modeling for medical data: from data collection to knowledge discovery. The Innovation Life. 2024, 2(3):100079. 74L Zhan#, X Luo#, W Xie#, XA Zhu#, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu*, G Yu*. shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals. Journal of Genetics and Genomics. 2024, 51(7):762-768. (IF = 7.1ï¼ä¸åº) 75L Li, W Xie, L Zhan, S Wen, X Luo, S Xu, Y Cai, W Tang, Q Wang, M Li, Z Xie, L Deng, H Zhu, G Yu*. Resolving Tumor Evolution: A Phylogenetic Approach. Journal of the National Cancer Center. 2024, 4(2):97-106. (IF = 9.4ï¼ä¸åº) 76Q Wang, W Tang, L Chen, L Deng, G Yu*. Decoding the Brain: Unveiling Comprehensive Cellular Atlases through Multiomics Mega Data. The Innovation. 2024, 5(4):100637. (IF = 25.7ï¼ä¸åº) 77Y Cai#, W Hu#, Y Pei, H Zhao*, G Yu*. Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic. The Innovation. 2024, 5(3):100627. (IF = 25.7ï¼ä¸åº) 78Y Lai#, W Tang#, X Luo, H Zheng, Y Zhang*, M Wang*, G Yu*, Min Yang*. Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis. Frontiers in Immunology. 2024, 15:1369116. (IF = 5.9ï¼äºåº) 79CH Gao, C Chen, T Akyol, A Dusa, G Yu, B Cao, P Cai*. ggVennDiagram: intuitive Venn diagram software extended. iMeta. 2024, 3(1):e177. (IF = 33.2ï¼ä¸åº) 80Y Ye#, MH Shum#, JL Tsui#, G Yu#, DK Smith, H Zhu, JT Wu, Y Guan, TTY Lam*. Robust expansion of phylogeny for fast-growing genome sequence data. PLoS Computational Biology. 2024, 20(2):e1011871. (IF = 3.6ï¼äºåº) 81S Wen, S Mo, J Zhou, Y Lv, K Khazaie*, G Yu*. Single-cell and spatial-omics in delineating immune-related diseases. Frontiers in Cell and Developmental Biology. 2024, 12:1365242. (IF = 4.3ï¼äºåº) 82 83 84 2023 85 86 87 Link to heading 88 89 90 91X 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*. Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics. Advanced Science. 2023, 10(36):2303753. (IF = 14.3ï¼ä¸åº) 92M 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*, SS Wong*. The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults. Influenza and Other Respiratory Viruses. 2023, 17(7):e13172. (IF = 4.3ï¼ååº) 93W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, G Yu*. MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm. Gut Microbes. 2023, 15(1):2223349. (IF = 12.2ï¼ä¸åº) 94S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, G Yu*. MicrobiotaProcess: A comprehensive R package for deep mining microbiome. The Innovation. 2023, 4(2):100388. (IF = 33.2ï¼ä¸åº) (å°é¢å¯¼è¯»ï¼Microbiome Toolkit) 95S Guo*, 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. Frontiers in Medicine. 2023, 10:1146896. (IF = 3.1ï¼ä¸åº) 96 97 98 2022 99 100 101 Link to heading 102 103 104 105S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, G Yu*. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. iMeta, 2022, 1(4):e56. 106Q Wang#, M Li#, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, G Yu*. Exploring epigenomic datasets by ChIPseeker. Current Protocols, 2022, 2(10): e585. 107Z Dai, T Wu, S Xu, L Zhou, W Tang, E Hu, L Zhan M Chen, G Yu*. Characterization of toxin-antitoxin systems from public sequencing data: a case study in Pseudomonas aeruginosa. Frontiers in Microbiology. 2022, 13:951774. (IF = 5.2ï¼äºåºï¼Topæå) 108T Feng#, T Wu#, Y Zhang#, L Zhou#, S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang*, X Shang*, G Yu*. Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells. Frontiers in Oncology. 2022, 12:912694. (IF = 4.7ï¼ä¸åº) 109L Zhou#, T Feng#, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai*, G Yu*. ggmsa: a visual exploration tool for multiple sequence alignment and associated data. Briefings in Bioinformatics. 2022, 23(4):bbac222. (IF = 9.5ï¼ä¸åºï¼Topæå) 110N Sato, Y Tamada, G Yu, Y Okuno*. CBNplot: Bayesian network plots for enrichment analysis. Bioinformatics. 2022, 38(10):2959-2960. (IF=5.8ï¼ä¸åºï¼Topæå) 111T Wu, CL Xiao, TT Lam, G Yu*. Biomedical Data Visualization: Methods and Applications. Frontiers in Genetics. 2022, 13:890775. (IF=3.7ï¼ä¸åº) 112X Zhao#, W Tang#, H Wan#, Z Lan H Qin, Q Lin, Y Hu, G Yu*, N Jiang*, B Yu*. Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection. Frontiers in Microbiology. 2022, 13:723791. (IF = 5.2ï¼äºåºï¼Topæå) 113 114 115 2021 116 117 118 Link to heading 119 120 121 122S Xu#, M Chen#, T Feng, L Zhan, L Zhou, G Yu*. Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers. Frontiers in Genetics. 2021, 12:774846. (IF=4.772ï¼ä¸åº) 123CH Gao, G Yu, P Cai*. ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram. Frontiers in Genetics. 2021, 12:706907. (IF=4.772ï¼ä¸åº) 124S 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*, X Bo*, G Yu*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, 38(9):4039-4042. (IF=8.800ï¼ä¸åºï¼Topæå) 125T Wu#, E Hu#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo*, G Yu*. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. (å°é¢å¯¼è¯»ï¼ClusterProfiler 4: Pathway Discovery) 126D Zeng#, Z Ye#, 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*. IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures. Frontiers in Immunology. 2021, 12:687975. (IF=8.786ï¼äºåºï¼Topæå) 127T Wu, E Hu, X Ge*, G Yu*. nCov2019: an R package for studying the COVID-19 coronavirus pandemic. PeerJ. 2021, 9:e11421. (IF=3.061ï¼ä¸åº) 128R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, G Yu, SC Hicks, MD Robinson*. TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research. 2021, 9:1246. 129S Liu, G Yu*, L Liu*, X Zou, L Zhou, E Hu, Y Song. Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment. Frontiers in Genetics. 2021, 12:625236. (IF=4.772ï¼ä¸åº) 130 131 132 2020 133 134 135 Link to heading 136 137 138
139J He#, S Xu#, B Zhang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng*, G Yu*, J Chen*. Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis. Aging (Albany NY). 2020, 12(9):8583-8604. (IF=5.682ï¼äºåº) 140G Yu*. Using ggtree to Visualize Data on Tree-Like Structure. Current Protocols in Bioinformatics. 2020, 69(1):e96. (Invited paper) 141LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. (IF=16.240ï¼ä¸åºï¼Topæå) 142Z Hao, D Lv, Y Ge, J Shi, D Weijers, G Yu*, J Chen*. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Computer Science. 2020, 6:e251. (IF=1.392ï¼ä¸åº) 143 144 145 2018 146 147 148 Link to heading 149 150 151 152G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. (IF=14.797ï¼ä¸åºï¼ Topæå) 153G Yu*. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics. 2018, 34(21):3766-3767. (IF=4.531, ä¸åºï¼ Topæå) 154 155 156 Selected publications (2010-2017) 157 158 159 Link to heading 160 161 162 163G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. (IF=6.363, ä¸åºï¼Topæå) 164G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479. (IF=2.781ï¼ä¸åº) 165G Yu*, LG Wang, QY He*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization. Bioinformatics. 2015, 31(14):2382-2383. (IF=5.766, ä¸åºï¼ Topæå) 166G Yu*, LG Wang, GR Yan, QY He*. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics. 2015, 31(4):608-609. (IF=5.766, ä¸åºï¼ Topæå) 167G Yu, LG Wang, Y Han, QY He*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. (IF=2.730ï¼ ååº) 168G Yu#, F Li#, Y Qin, X Bo*, Y Wu, S Wang*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978. (IF=4.877, äºåºï¼ Topæå) 169"><meta name=keywords content="developer,bioinformatics,omics,visualization"><meta name=twitter:card content="summary"><meta name=twitter:title content="Publications"><meta name=twitter:description content="# Co-first authors * Co-corresponding authors ï¼ESI Highly Cited Paper (12X) ï¼ESI Hot Paper ååºï¼æç« å表å½å¹´çä¸ç§é¢å°ç±»ååº IFï¼æç« å表å½å¹´çå½±åå å 课é¢ç»å ¬ä¼å·è§£è¯»æç« 2026 Link to heading N He, S Xu, K Mo, Y Xia, R Wang, S Tao, Q Wang, J Mo, B Pang, Y Qiu*, Q Song*, G Yu*. TCMDATA: an integrated R package for target-oriented network pharmacology analysis and AI-assisted interpretation in traditional Chinese medicine. Current Molecular Pharmacology. accepted. W Liu, J Ding, Y Sun, B Yan, Z Wang, C Wang, C Shu, JG Zhou, G Yu*, Y Peng*, S Wang*. Composable Visualization of HighâDimensional Biological Data with ggalign. Current Protocols. 2026, 6(9):e70453. S Lin, G Yu*. From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics. Advanced Genetics. 2026, 7(3):e70045. J Feng#, C Chen#*, Y Wu#, L Fan, Z Zhang, M Chen, H Tang, G Yu, J Ren, J Luo, Y Liao, A Luan, Z Wang, S Tang, Y Shao, Y Liang, J Wang*, J Xie*, R Xia*. How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools. Molecular Plant. 2026, 19(7):1378-1391. Y Feng#, L Zheng#, W Tang#, P Wang, Y Lai, J Qin, C Zhou, X Zhang, M Yang, L Jie*, G Yu*, H Ren*, Q Huang*. Gut metabolite indole-3-acetic acid aggravates neuropsychiatric lupus via the AHR/STAT3 pathway in microglia. Communications Biology. 2026, 9(1):281. 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*, L Xie*. EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research. SCIENCE CHINA Life Sciences. 2026, 69(2):321-330. (å°é¢æç« , Cover Article) Q Wang#, L Deng#, S Xu#, P Guo, H Zhu, H Ge, Y Gong, G Du, K Huang, C Su, R Wang, Y Qiu*, G Yu*. Comparison of Illumina NovaSeq 6000 and GeneMind
169SURFSeq 5000 platforms for singleâcell spatial transcriptomics of mouse brain and lung. Interdisciplinary Medicine. 2026, 4(1):e70067. G Yu*. Background bias in functional enrichment analysis: Insights from clusterProfiler. The Innovation Life. 2026, 4(1):100181. (å°é¢å¯¼è¯»ï¼Insights form clusterProfiler) 2025 Link to heading Y Peng, S Jiang, Y Song, P Luo, J Li, D Hu, JG Zhou, G Yu*, T Xu*, S Wang*. ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity. Advanced Science. 2025, 12(44): e07799. (IF = 14.1) S Wen#, X Du#, M Zhu#, C Huang, Z Lin, M Li, B Hu, X Wang, F Jiang, G Zhou, W Zhu, G Yu*, C Xu*, B Shen*. ALCAM-CD6 axis suppression: a key determinant of immune-mediated metastasis recurrence in stage III non-small cell lung cancer. Journal for ImmunoTherapy of Cancer. 2025, 13(10):e010416. (IF = 11.7) P Li#, L Xie#, H Zheng#, Y Feng#, 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*, E M. El-Omar*, G Yu*, X Chen*. Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome. iMeta. 2025, 4(5):e70065. (IF = 44.4) X Lu, K Li, Z Li, A Lin, L Zhao, R Shen, Z Xu, J Gao, D Lv, Y Zhang, T Ye, J Shen, Y Chen, H Huang, Z Hao, D Zeng, H Wang, S Guo, W Wang, Y Xiong, Y Li, H Li, J Gao, Q Liu, B Wei, J Shi, S Cheng, G Li, Y Tang, E Lin, H Xu, G Feng, Y He, Y Sun, X Liu, Y Wang, W Song, J Song, S Tian, Y Zhang, J Zhang, Z Xu, C Song, Y Zhang, H Wu, C Gao, E Hu, C Yang, J Lou, D Wang, X Wang, P Luo*, G Yu*, Y Ge*. FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency. iMetaMed. 2025, 1(1):e70005. Cover story S Xu#, Q Wang#, S Wen#, J Li#, N He#, M Li, T Hackl, R Wang, D Zeng, S Wang, S Li, CH Gao, L Zh
169ou, S Tao, Z Xie, L Deng, G Yu*. aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types. The Innovation. 2025, 6(9):100958. (å°é¢å¯¼è¯»ï¼Complex composite graphics) (IF = 39.5) Y Gao#, B Li#, Y Jin#, J Cheng#, 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*, W Fang*, X Bao*. Spatial multi-omics profiling of breast cancer oligo-recurrent lung metastasis. Oncogene. 2025, 44(27):2268-2282. (IF = 9.1) Q Wang, H Zhu, L Deng, S Xu, W Xie, M Li, R Wang, L Tie, L Zhan, G Yu*. Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications. Small Methods. 2025, 9(5):2401107. å·é¦æå¾æç« Frontispiece (IF = 8.7) Y Tu#*, S Xu#, H Shu, X Wang, W Li, G Yu*, Li He*. 16S rRNA Sequencing Reveals Dysbiosis of Skin Microbiome Associated With Disease Severity in Chronic Actinic Dermatitis. Photodermatology, Photoimmunology & Photomedicine. 2025, 41(3):e70022. M Chen#, X Luo#, S Xu#, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen*, TTY Lam*, G Yu*. Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree. iMeta. 2025, 4(1):e269. (IF = 44.4) 2024 Link to heading D Zeng#, Y Fang#, W Qiu; P Luo, S Wang; R Shen, W Gu, X Huang, Q Mao; G Wang, Y Lai; X Xu, M Shi, Z Wu*, G Yu*, W Liao*. Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0. Cell Reports Methods. 2024, 4(12):100910. (IF = 4.5ï¼äºåº) M Luo*#, W Yang#, L Bai#, L Zhang#, JW Huang#, Y Cao#, Y Xie#, L Tong, H Zhang, L Yu, LW Zhou, Y Shi, P Yu, Z Wang, Z Yuan, P Zhang, Y Zhang, F Ju, H Zhang, F Wang, Y Cui, J Zhang, G Jia, D Wan, C Ruan, Y Zeng, P Wu, Z Gao, W Zhao, Y Xu, G Yu, C Tian, LN Jin, J Dai*, B Xia*, B Sun*, F Chen*, YZ Gao*, H Wang*, B Wang*, D Zhang*, X Cao*, H Wang*, T Huang*. Artificial intelligence for life sciences: A comprehensive guide and future trends. The Innovation Life. 2024, 2(4):100105. Z Miao#, T Tian#, W Chen#, Q Wang#, L Ma#, D Zhang#, M Xie#, Z Yu#, X Guo, G Bai, S Zhao, X Chen, W Wang, Y Gao, S Guo*, M Luo*, L Yuan*, C Tian*, L Wu*, G Yu*, D Zhang*, S Sun*. Spatial Resolved Transcriptomics: Computational Insights into Gene Transcription Across Tissue and Organ Architecture in Diverse Applications. The Innovation Life. 2024, 2(4):100097. G Yu*. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722. (IF = 25.7ï¼ä¸åº) S Xu#, E Hu#, Y Cai#, Z Xie#, X Luo#, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, G Yu*. Using clusterProfiler to characterise Multi-Omics Data. Nature Protocols. 2024, 19(11):3292-3320. (IF = 16.0ï¼ä¸åº) S Wang, G Yu, L Xie*. Asymmetric Cell Division and Satellite Cell Fate Regulation in Skeletal Muscle Aging and Disease. Health and Metabol
169ism. 2024, 1(1):5. Y Chen#, LN He#, Y Zhang, J Gong, S Xu, Y Shu, D Zhang*, G Yu*, Z Zuo*. tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package. iMeta. 2024, 3(5):e229. (IF = 33.2ï¼ä¸åº) D Wang, G Chen, L Li, S Wen, Z Xie, X Luo, L Zhan, S Xu, J Li, R Wang, Q Wang*, G Yu*. Reducing language barriers, promoting information absorption, and communication using fanyi. Chinese Medical Journal. 2024, 137(16):1950-1956. (IF = 7.3ï¼äºåº) XK Ma#, Y Yu#, T Huang#*, D Zhang, C Tian, W Tang, M Luo, P Du*, G Yu*, L Yang*. Bioinformatics Software Development: principles and future directions. The Innovation Life. 2024, 2(3):100083. Y Yang#, S Xu#, Y Hong, Y Cai, W Tang, J Wang, B Shen*, H Zong*, G Yu*. Computational modeling for medical data: from data collection to knowledge discovery. The Innovation Life. 2024, 2(3):100079. L Zhan#, X Luo#, W Xie#, XA Zhu#, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu*, G Yu*. shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals. Journal of Genetics and Genomics. 2024, 51(7):762-768. (IF = 7.1ï¼ä¸åº) L Li, W Xie, L Zhan, S Wen, X Luo, S Xu, Y Cai, W Tang, Q Wang, M Li, Z Xie, L Deng, H Zhu, G Yu*. Resolving Tumor Evolution: A Phylogenetic Approach. Journal of the National Cancer Center. 2024, 4(2):97-106. (IF = 9.4ï¼ä¸åº) Q Wang, W Tang, L Chen, L Deng, G Yu*. Decoding the Brain: Unveiling Comprehensive Cellular Atlases through Multiomics Mega Data. The Innovation. 2024, 5(4):100637. (IF = 25.7ï¼ä¸åº) Y Cai#, W Hu#, Y Pei, H Zhao*, G Yu*. Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic. The Innovation. 2024, 5(3):100627. (IF = 25.7ï¼ä¸åº) Y Lai#, W Tang#, X Luo, H Zheng, Y Zhang*, M Wang*, G Yu*, Min Yang*. Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis. Frontiers in Immunology. 2024, 15:1369116. (IF = 5.9ï¼äºåº) CH Gao, C Chen, T Akyol, A Dusa, G Yu, B Cao, P Cai*. ggVennDiagram: intuitive Venn diagram software extended. iMeta. 2024, 3(1):e177. (IF = 33.2ï¼ä¸åº) Y Ye#, MH Shum#, JL Tsui#, G Yu#, DK Smith, H Zhu, JT Wu, Y Guan, TTY Lam*. Robust expansion of phylogeny for fast-growing genome sequence data. PLoS Computational Biology. 2024, 20(2):e1011871. (IF = 3.6ï¼äºåº) S Wen, S Mo, J Zhou, Y Lv, K Khazaie*, G Yu*. Single-cell and spatial-omics in delineating immune-related diseases. Frontiers in Cell and Developmental Biology. 2024, 12:1365242. (IF = 4.3ï¼äºåº) 2023 Link to heading 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*. Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics. Advanced Science. 2023, 10(36):2303753. (IF = 14.3ï¼ä¸åº) 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*, SS Wong*. The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults. Influenza and Other Respiratory Viruses. 2023, 17(7):e13172. (IF = 4.3ï¼ååº) W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, G Yu*. MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm. Gut Microbes. 2023, 15(1):2223349. (IF = 12.2ï¼ä¸åº) S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, G Yu*. MicrobiotaProcess: A comprehensive R package for deep mining microbiome. The Innovation. 2023, 4(2):100388. (IF = 33.2ï¼ä¸åº) (å°é¢å¯¼è¯»ï¼Microbiome Toolkit) S Guo*, 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. Frontiers in Medicine. 2023, 10:1146896. (IF = 3.1ï¼ä¸åº) 2022 Link to heading S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, G Yu*. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. iMeta, 2022, 1(4):e56. Q Wang#, M Li#, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, G Yu*. Exploring epigenomic datasets by ChIPseeker. Current Protocols, 2022, 2(10): e585. Z Dai, T Wu, S Xu, L Zhou, W Tang, E Hu, L Zhan M Chen, G Yu*. Characterization of toxin-antitoxin systems from public sequencing data: a case study in Pseudomonas aeruginosa. Frontiers in Microbiology. 2022, 13:951774. (IF = 5.2ï¼äºåºï¼Topæå) T Feng#, T Wu#, Y Zhang#, L Zhou#, S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang*, X Shang*, G Yu*. Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells. Frontiers in Oncology. 2022, 12:912694. (IF = 4.7ï¼ä¸åº) L Zhou#, T Feng#, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai*, G Yu*. ggmsa: a visual exploration tool for multiple sequence alignment and associated data. Briefings in Bioinformatics. 2022, 23(4):bbac222. (IF = 9.5ï¼ä¸åºï¼Topæå) N Sato, Y Tamada, G Yu, Y Okuno*. CBNplot: Bayesian network plots for enrichment analysis. Bioinformatics. 2022, 38(10):2959-2960. (IF=5.8ï¼ä¸åºï¼Topæå) T Wu, CL Xiao, TT Lam, G Yu*. Biomedical Data Visualization: Methods and Applications. Frontiers in Genetics. 2022, 13:890775. (IF=3.7ï¼ä¸åº) X Zhao#, W Tang#, H Wan#, Z Lan H Qin, Q Lin, Y Hu, G Yu*, N Jiang*, B Yu*. Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection. Frontiers in Microbiology. 2022, 13:723791. (IF = 5.2ï¼äºåºï¼Topæå) 2021 Link to heading S Xu#, M Chen#, T Feng, L Zhan, L Zhou, G Yu*. Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers. Frontiers in Genetics. 2021, 12:774846. (IF=4.772ï¼ä¸åº) CH Gao, G Yu, P Cai*. ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram. Frontiers in Genetics. 2021, 12:706907. (IF=4.772ï¼ä¸åº) 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*, X Bo*, G Yu*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, 38(9):4039-4042. (IF=8.800ï¼ä¸åºï¼Topæå) T Wu#, E Hu#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo*, G Yu*. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. (å°é¢å¯¼è¯»ï¼ClusterProfiler 4: Pathway Discovery) D Zeng#, Z Ye#, 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*. IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures. Frontiers in Immunology. 2021, 12:687975. (IF=8.786ï¼äºåºï¼Topæå) T Wu, E Hu, X Ge*, G Yu*. nCov2019: an R package for studying the COVID-19 coronavirus pandemic. PeerJ. 2021, 9:e11421. (IF=3.061ï¼ä¸åº) R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, G Yu, SC Hicks, MD Robinson*. TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research. 2021, 9:1246. S Liu, G Yu*, L Liu*, X Zou, L Zhou, E Hu, Y Song. Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment. Frontiers in Genetics. 2021, 12:625236. (IF=4.772ï¼ä¸åº) 2020 Link to heading J He#, S Xu#, B Zh
169ang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng*, G Yu*, J Chen*. Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis. Aging (Albany NY). 2020, 12(9):8583-8604. (IF=5.682ï¼äºåº) G Yu*. Using ggtree to Visualize Data on Tree-Like Structure. Current Protocols in Bioinformatics. 2020, 69(1):e96. (Invited paper) LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. (IF=16.240ï¼ä¸åºï¼Topæå) Z Hao, D Lv, Y Ge, J Shi, D Weijers, G Yu*, J Chen*. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Computer Science. 2020, 6:e251. (IF=1.392ï¼ä¸åº) 2018 Link to heading G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. (IF=14.797ï¼ä¸åºï¼ Topæå) G Yu*. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics. 2018, 34(21):3766-3767. (IF=4.531, ä¸åºï¼ Topæå) Selected publications (2010-2017) Link to heading G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. (IF=6.363, ä¸åºï¼Topæå) G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479. (IF=2.781ï¼ä¸åº) G Yu*, LG Wang, QY He*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization. Bioinformatics. 2015, 31(14):2382-2383. (IF=5.766, ä¸åºï¼ Topæå) G Yu*, LG Wang, GR Yan, QY He*. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics. 2015, 31(4):608-609. (IF=5.766, ä¸åºï¼ Topæå) G Yu, LG Wang, Y Han, QY He*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. (IF=2.730ï¼ ååº) G Yu#, F Li#, Y Qin, X Bo*, Y Wu, S Wang*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978. (IF=4.877, äºåºï¼ Topæå)"><meta property="og:url" content="http://yulab-smu.top/publications/"><meta property="og:site_name" content="YuLab@SMU"><meta property="og:title" content="Publications"><meta property="og:description" content="# Co-first authors * Co-corresponding authors ï¼ESI Highly Cited Paper (12X) ï¼ESI Hot Paper ååºï¼æç« å表å½å¹´çä¸ç§é¢å°ç±»ååº IFï¼æç« å表å½å¹´çå½±åå å 课é¢ç»å
¬ä¼å·è§£è¯»æç« 2026 Link to heading N He, S Xu, K Mo, Y Xia, R Wang, S Tao, Q Wang, J Mo, B Pang, Y Qiu*, Q Song*, G Yu*. TCMDATA: an integrated R package for target-oriented network pharmacology analysis and AI-assisted interpretation in traditional Chinese medicine. Current Molecular Pharmacology. accepted. W Liu, J Ding, Y Sun, B Yan, Z Wang, C Wang, C Shu, JG Zhou, G Yu*, Y Peng*, S Wang*. Composable Visualization of HighâDimensional Biological Data with ggalign. Current Protocols. 2026, 6(9):e70453. S Lin, G Yu*. From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics. Advanced Genetics. 2026, 7(3):e70045. J Feng#, C Chen#*, Y Wu#, L Fan, Z Zhang, M Chen, H Tang, G Yu, J Ren, J Luo, Y Liao, A Luan, Z Wang, S Tang, Y Shao, Y Liang, J Wang*, J Xie*, R Xia*. How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools. Molecular Plant. 2026, 19(7):1378-1391. Y Feng#, L Zheng#, W Tang#, P Wang, Y Lai, J Qin, C Zhou, X Zhang, M Yang, L Jie*, G Yu*, H Ren*, Q Huang*. Gut metabolite indole-3-acetic acid aggravates neuropsychiatric lupus via the AHR/STAT3 pathway in microglia. Communications Biology. 2026, 9(1):281. 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*, L Xie*. EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research. SCIENCE CHINA Life Sciences. 2026, 69(2):321-330. (å°é¢æç« , Cover Article) Q Wang#, L Deng#, S Xu#, P Guo, H Zhu, H Ge, Y Gong, G Du, K Huang, C Su, R Wang, Y Qiu*, G Yu*. Comparison of Illumina NovaSeq 6000 and GeneMind
169SURFSeq 5000 platforms for singleâcell spatial transcriptomics of mouse brain and lung. Interdisciplinary Medicine. 2026, 4(1):e70067. G Yu*. Background bias in functional enrichment analysis: Insights from clusterProfiler. The Innovation Life. 2026, 4(1):100181. (å°é¢å¯¼è¯»ï¼Insights form clusterProfiler) 2025 Link to heading Y Peng, S Jiang, Y Song, P Luo, J Li, D Hu, JG Zhou, G Yu*, T Xu*, S Wang*. ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity. Advanced Science. 2025, 12(44): e07799. (IF = 14.1) S Wen#, X Du#, M Zhu#, C Huang, Z Lin, M Li, B Hu, X Wang, F Jiang, G Zhou, W Zhu, G Yu*, C Xu*, B Shen*. ALCAM-CD6 axis suppression: a key determinant of immune-mediated metastasis recurrence in stage III non-small cell lung cancer. Journal for ImmunoTherapy of Cancer. 2025, 13(10):e010416. (IF = 11.7) P Li#, L Xie#, H Zheng#, Y Feng#, 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*, E M. El-Omar*, G Yu*, X Chen*. Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome. iMeta. 2025, 4(5):e70065. (IF = 44.4) X Lu, K Li, Z Li, A Lin, L Zhao, R Shen, Z Xu, J Gao, D Lv, Y Zhang, T Ye, J Shen, Y Chen, H Huang, Z Hao, D Zeng, H Wang, S Guo, W Wang, Y Xiong, Y Li, H Li, J Gao, Q Liu, B Wei, J Shi, S Cheng, G Li, Y Tang, E Lin, H Xu, G Feng, Y He, Y Sun, X Liu, Y Wang, W Song, J Song, S Tian, Y Zhang, J Zhang, Z Xu, C Song, Y Zhang, H Wu, C Gao, E Hu, C Yang, J Lou, D Wang, X Wang, P Luo*, G Yu*, Y Ge*. FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency. iMetaMed. 2025, 1(1):e70005. Cover story S Xu#, Q Wang#, S Wen#, J Li#, N He#, M Li, T Hackl, R Wang, D Zeng, S Wang, S Li, CH Gao, L Zh
169ou, S Tao, Z Xie, L Deng, G Yu*. aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types. The Innovation. 2025, 6(9):100958. (å°é¢å¯¼è¯»ï¼Complex composite graphics) (IF = 39.5) Y Gao#, B Li#, Y Jin#, J Cheng#, 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*, W Fang*, X Bao*. Spatial multi-omics profiling of breast cancer oligo-recurrent lung metastasis. Oncogene. 2025, 44(27):2268-2282. (IF = 9.1) Q Wang, H Zhu, L Deng, S Xu, W Xie, M Li, R Wang, L Tie, L Zhan, G Yu*. Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications. Small Methods. 2025, 9(5):2401107. å·é¦æå¾æç« Frontispiece (IF = 8.7) Y Tu#*, S Xu#, H Shu, X Wang, W Li, G Yu*, Li He*. 16S rRNA Sequencing Reveals Dysbiosis of Skin Microbiome Associated With Disease Severity in Chronic Actinic Dermatitis. Photodermatology, Photoimmunology & Photomedicine. 2025, 41(3):e70022. M Chen#, X Luo#, S Xu#, L Li, J Li, Z Xie, Q Wang, Y Liao, B Liu, W Liang, K Mo, Q Song, X Chen*, TTY Lam*, G Yu*. Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree. iMeta. 2025, 4(1):e269. (IF = 44.4) 2024 Link to heading D Zeng#, Y Fang#, W Qiu; P Luo, S Wang; R Shen, W Gu, X Huang, Q Mao; G Wang, Y Lai; X Xu, M Shi, Z Wu*, G Yu*, W Liao*. Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0. Cell Reports Methods. 2024, 4(12):100910. (IF = 4.5ï¼äºåº) M Luo*#, W Yang#, L Bai#, L Zhang#, JW Huang#, Y Cao#, Y Xie#, L Tong, H Zhang, L Yu, LW Zhou, Y Shi, P Yu, Z Wang, Z Yuan, P Zhang, Y Zhang, F Ju, H Zhang, F Wang, Y Cui, J Zhang, G Jia, D Wan, C Ruan, Y Zeng, P Wu, Z Gao, W Zhao, Y Xu, G Yu, C Tian, LN Jin, J Dai*, B Xia*, B Sun*, F Chen*, YZ Gao*, H Wang*, B Wang*, D Zhang*, X Cao*, H Wang*, T Huang*. Artificial intelligence for life sciences: A comprehensive guide and future trends. The Innovation Life. 2024, 2(4):100105. Z Miao#, T Tian#, W Chen#, Q Wang#, L Ma#, D Zhang#, M Xie#, Z Yu#, X Guo, G Bai, S Zhao, X Chen, W Wang, Y Gao, S Guo*, M Luo*, L Yuan*, C Tian*, L Wu*, G Yu*, D Zhang*, S Sun*. Spatial Resolved Transcriptomics: Computational Insights into Gene Transcription Across Tissue and Organ Architecture in Diverse Applications. The Innovation Life. 2024, 2(4):100097. G Yu*. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722. (IF = 25.7ï¼ä¸åº) S Xu#, E Hu#, Y Cai#, Z Xie#, X Luo#, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, G Yu*. Using clusterProfiler to characterise Multi-Omics Data. Nature Protocols. 2024, 19(11):3292-3320. (IF = 16.0ï¼ä¸åº) S Wang, G Yu, L Xie*. Asymmetric Cell Division and Satellite Cell Fate Regulation in Skeletal Muscle Aging and Disease. Health and Metabol
169ism. 2024, 1(1):5. Y Chen#, LN He#, Y Zhang, J Gong, S Xu, Y Shu, D Zhang*, G Yu*, Z Zuo*. tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package. iMeta. 2024, 3(5):e229. (IF = 33.2ï¼ä¸åº) D Wang, G Chen, L Li, S Wen, Z Xie, X Luo, L Zhan, S Xu, J Li, R Wang, Q Wang*, G Yu*. Reducing language barriers, promoting information absorption, and communication using fanyi. Chinese Medical Journal. 2024, 137(16):1950-1956. (IF = 7.3ï¼äºåº) XK Ma#, Y Yu#, T Huang#*, D Zhang, C Tian, W Tang, M Luo, P Du*, G Yu*, L Yang*. Bioinformatics Software Development: principles and future directions. The Innovation Life. 2024, 2(3):100083. Y Yang#, S Xu#, Y Hong, Y Cai, W Tang, J Wang, B Shen*, H Zong*, G Yu*. Computational modeling for medical data: from data collection to knowledge discovery. The Innovation Life. 2024, 2(3):100079. L Zhan#, X Luo#, W Xie#, XA Zhu#, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu*, G Yu*. shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals. Journal of Genetics and Genomics. 2024, 51(7):762-768. (IF = 7.1ï¼ä¸åº) L Li, W Xie, L Zhan, S Wen, X Luo, S Xu, Y Cai, W Tang, Q Wang, M Li, Z Xie, L Deng, H Zhu, G Yu*. Resolving Tumor Evolution: A Phylogenetic Approach. Journal of the National Cancer Center. 2024, 4(2):97-106. (IF = 9.4ï¼ä¸åº) Q Wang, W Tang, L Chen, L Deng, G Yu*. Decoding the Brain: Unveiling Comprehensive Cellular Atlases through Multiomics Mega Data. The Innovation. 2024, 5(4):100637. (IF = 25.7ï¼ä¸åº) Y Cai#, W Hu#, Y Pei, H Zhao*, G Yu*. Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic. The Innovation. 2024, 5(3):100627. (IF = 25.7ï¼ä¸åº) Y Lai#, W Tang#, X Luo, H Zheng, Y Zhang*, M Wang*, G Yu*, Min Yang*. Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis. Frontiers in Immunology. 2024, 15:1369116. (IF = 5.9ï¼äºåº) CH Gao, C Chen, T Akyol, A Dusa, G Yu, B Cao, P Cai*. ggVennDiagram: intuitive Venn diagram software extended. iMeta. 2024, 3(1):e177. (IF = 33.2ï¼ä¸åº) Y Ye#, MH Shum#, JL Tsui#, G Yu#, DK Smith, H Zhu, JT Wu, Y Guan, TTY Lam*. Robust expansion of phylogeny for fast-growing genome sequence data. PLoS Computational Biology. 2024, 20(2):e1011871. (IF = 3.6ï¼äºåº) S Wen, S Mo, J Zhou, Y Lv, K Khazaie*, G Yu*. Single-cell and spatial-omics in delineating immune-related diseases. Frontiers in Cell and Developmental Biology. 2024, 12:1365242. (IF = 4.3ï¼äºåº) 2023 Link to heading 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*. Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics. Advanced Science. 2023, 10(36):2303753. (IF = 14.3ï¼ä¸åº) 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*, SS Wong*. The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults. Influenza and Other Respiratory Viruses. 2023, 17(7):e13172. (IF = 4.3ï¼ååº) W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, G Yu*. MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm. Gut Microbes. 2023, 15(1):2223349. (IF = 12.2ï¼ä¸åº) S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, G Yu*. MicrobiotaProcess: A comprehensive R package for deep mining microbiome. The Innovation. 2023, 4(2):100388. (IF = 33.2ï¼ä¸åº) (å°é¢å¯¼è¯»ï¼Microbiome Toolkit) S Guo*, 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. Frontiers in Medicine. 2023, 10:1146896. (IF = 3.1ï¼ä¸åº) 2022 Link to heading S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, G Yu*. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. iMeta, 2022, 1(4):e56. Q Wang#, M Li#, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, G Yu*. Exploring epigenomic datasets by ChIPseeker. Current Protocols, 2022, 2(10): e585. Z Dai, T Wu, S Xu, L Zhou, W Tang, E Hu, L Zhan M Chen, G Yu*. Characterization of toxin-antitoxin systems from public sequencing data: a case study in Pseudomonas aeruginosa. Frontiers in Microbiology. 2022, 13:951774. (IF = 5.2ï¼äºåºï¼Topæå) T Feng#, T Wu#, Y Zhang#, L Zhou#, S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang*, X Shang*, G Yu*. Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells. Frontiers in Oncology. 2022, 12:912694. (IF = 4.7ï¼ä¸åº) L Zhou#, T Feng#, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai*, G Yu*. ggmsa: a visual exploration tool for multiple sequence alignment and associated data. Briefings in Bioinformatics. 2022, 23(4):bbac222. (IF = 9.5ï¼ä¸åºï¼Topæå) N Sato, Y Tamada, G Yu, Y Okuno*. CBNplot: Bayesian network plots for enrichment analysis. Bioinformatics. 2022, 38(10):2959-2960. (IF=5.8ï¼ä¸åºï¼Topæå) T Wu, CL Xiao, TT Lam, G Yu*. Biomedical Data Visualization: Methods and Applications. Frontiers in Genetics. 2022, 13:890775. (IF=3.7ï¼ä¸åº) X Zhao#, W Tang#, H Wan#, Z Lan H Qin, Q Lin, Y Hu, G Yu*, N Jiang*, B Yu*. Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection. Frontiers in Microbiology. 2022, 13:723791. (IF = 5.2ï¼äºåºï¼Topæå) 2021 Link to heading S Xu#, M Chen#, T Feng, L Zhan, L Zhou, G Yu*. Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers. Frontiers in Genetics. 2021, 12:774846. (IF=4.772ï¼ä¸åº) CH Gao, G Yu, P Cai*. ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram. Frontiers in Genetics. 2021, 12:706907. (IF=4.772ï¼ä¸åº) 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*, X Bo*, G Yu*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, 38(9):4039-4042. (IF=8.800ï¼ä¸åºï¼Topæå) T Wu#, E Hu#, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo*, G Yu*. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. The Innovation. 2021, 2(3):100141. (å°é¢å¯¼è¯»ï¼ClusterProfiler 4: Pathway Discovery) D Zeng#, Z Ye#, 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*. IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures. Frontiers in Immunology. 2021, 12:687975. (IF=8.786ï¼äºåºï¼Topæå) T Wu, E Hu, X Ge*, G Yu*. nCov2019: an R package for studying the COVID-19 coronavirus pandemic. PeerJ. 2021, 9:e11421. (IF=3.061ï¼ä¸åº) R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, G Yu, SC Hicks, MD Robinson*. TreeSummarizedExperiment: a S4 class for data with hierarchical structure. F1000Research. 2021, 9:1246. S Liu, G Yu*, L Liu*, X Zou, L Zhou, E Hu, Y Song. Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment. Frontiers in Genetics. 2021, 12:625236. (IF=4.772ï¼ä¸åº) 2020 Link to heading J He#, S Xu#, B Zh
169ang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng*, G Yu*, J Chen*. Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis. Aging (Albany NY). 2020, 12(9):8583-8604. (IF=5.682ï¼äºåº) G Yu*. Using ggtree to Visualize Data on Tree-Like Structure. Current Protocols in Bioinformatics. 2020, 69(1):e96. (Invited paper) LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu*. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution. 2020, 37(2):599-603. (IF=16.240ï¼ä¸åºï¼Topæå) Z Hao, D Lv, Y Ge, J Shi, D Weijers, G Yu*, J Chen*. RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. PeerJ Computer Science. 2020, 6:e251. (IF=1.392ï¼ä¸åº) 2018 Link to heading G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. (IF=14.797ï¼ä¸åºï¼ Topæå) G Yu*. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics. 2018, 34(21):3766-3767. (IF=4.531, ä¸åºï¼ Topæå) Selected publications (2010-2017) Link to heading G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. (IF=6.363, ä¸åºï¼Topæå) G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479. (IF=2.781ï¼ä¸åº) G Yu*, LG Wang, QY He*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization. Bioinformatics. 2015, 31(14):2382-2383. (IF=5.766, ä¸åºï¼ Topæå) G Yu*, LG Wang, GR Yan, QY He*. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics. 2015, 31(4):608-609. (IF=5.766, ä¸åºï¼ Topæå) G Yu, LG Wang, Y Han, QY He*. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287. (IF=2.730ï¼ ååº) G Yu#, F Li#, Y Qin, X Bo*, Y Wu, S Wang*. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010, 26(7):976-978. (IF=4.877, äºåºï¼ Topæå)"><meta property="og:locale" content="en"><meta property="og:type" content="article"><link rel=canonical href=http://yulab-smu.top/publications/><link rel=preload href=/fonts/fa-brands-400.woff2 as=font type=font/woff2 crossorigin><link rel=preload href=/fonts/fa-regular-400.woff2 as=font type=font/woff2 crossorigin><link rel=preload href=/fonts/fa-solid-900.woff2 as=font type=font/woff2 crossorigin><link rel=stylesheet href=/css/coder.min.38c4552ac40f9ae3408bad40358f654ebd8804412fe74ed56f2d6c8a7af82dd3.css integrity="sha256-OMRVKsQPmuNAi61ANY9lTr2IBEEv507Vby1sinr4LdM=" crossorigin=anonymous media=screen><link rel=icon type=image/svg+xml href=/images/favicon.svg sizes=any><link rel=icon type=image/png href=/images/favicon-32x32.png sizes=32x32><link rel=icon type=image/png href=/images/favicon-16x16.png sizes=16x16><link rel=apple-touch-icon href=/images/apple-touch-icon.png><link rel=apple-touch-icon sizes=180x180 href=/images/apple-touch-icon.png><link rel=manifest href=/site.webmanifest><link rel=mask-icon href=/images/safari-pinned-tab.svg color=#5bbad5></head><body class="preload-transitions colorscheme-light"><div class=float-container><a id=dark-mode-toggle class=colorscheme-toggle><i class="fa-solid fa-adjust fa-fw" aria-hidden=true></i></a></div><main class=wrapper><nav class=navigation><section class=container><a class=navigation-title href=http://yulab-smu.top/>YuLab@SMU 170</a><input type=checkbox id=menu-toggle> 171<label class="menu-button float-right" for=menu-toggle><i class="fa-solid fa-bars fa-fw" aria-hidden=true></i></label><ul class=navigation-list><li class=navigation-item><a class=navigation-link href=/about/>About</a></li><li class=navigation-item><a class=navigation-link href=/publications/>Publications</a></li><li class=navigation-item><a class=navigation-link href=/books/>Books</a></li><li class=navigation-item><a class=navigation-link href=/contributions/>Contributions</a></li><li class=navigation-item><a class=navigation-link href=/members/>Members</a></li><li class=navigation-item><a class=navigation-link href=/news/>News</a></li><li class=navigation-item><a class=navigation-link href=/contact/>Contact</a></li></ul></section></nav><div class=content><section class="container page"><article><header><h1 class=title><a class=title-link href=http://yulab-smu.top/publications/>Publications</a></h1></header><style>@media only screen and (max-width:768px){td{display:block}}</style>
171<script async src=https://badge.dimensions.ai/badge.js></script>
171<table style=border:none;font-size:90%;width:100%><tr style=border:none><td style=border:none><ul><li><sup>#</sup> Co-first authors</li><li><sup>*</sup> Co-corresponding authors</li><li><i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i>ï¼ESI Highly Cited Paper (12X)</li><li><i class="fa fa-fire fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i>ï¼ESI Hot Paper</li><li>ååºï¼æç« å表å½å¹´çä¸ç§é¢å°ç±»ååº</li><li>IFï¼æç« å表å½å¹´çå½±åå å</li><li><a href="https://mp.weixin.qq.com/mp/appmsgalbum?__biz=MzI5NjUyNzkxMg==&action=getalbum&album_id=1300603819033788419&scene=173&subscene=91&sessionid=1745919684&enterid=1745919688&from_msgid=2247497064&from_itemidx=1&count=3&nolastread=1#wechat_redirect" class=external-link target=_blank rel=noopener>课é¢ç»å ¬ä¼å·è§£è¯»æç« </a></li></ul></td><td style=border:none><a href="https://scholar.google.com/citations?user=DO5oG40AAAAJ"><img src=/images/citation.png height=200px></a></td></tr></table><h2 id=year-2026><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2026 172<a class=heading-link href=#year-2026><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 173<span class=sr-only>Link to heading</span></a></h2><ul><li>N He, S Xu, K Mo, Y Xia, R Wang, S Tao, Q Wang, J Mo, B Pang, Y Qiu<sup>*</sup>, Q Song<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.sciencedirect.com/science/article/pii/S1874467226000231 class=external-link target=_blank rel=noopener>TCMDATA: an integrated R package for target-oriented network pharmacology analysis and AI-assisted interpretation in traditional Chinese medicine</a>. <strong><em>Current Molecular Pharmacology</em></strong>. accepted.</li><li>W Liu, J Ding, Y Sun, B Yan, Z Wang, C Wang, C Shu, JG Zhou, G Yu<sup>*</sup>, Y Peng<sup>*</sup>, S Wang<sup>*</sup>. <a href=https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpz1.70453 class=external-link target=_blank rel=noopener>Composable Visualization of HighâDimensional Biological Data with ggalign</a>. <strong><em>Current Protocols</em></strong>. 2026, 6(9):e70453.</li><li>S Lin, <strong>G Yu</strong><sup>*</sup>. <a href=https://advanced.onlinelibrary.wiley.com/doi/10.1002/ggn2.70045 class=external-link target=_blank rel=noopener>From Cluster to Claim: Calibrating Interpretation in Single-Cell Transcriptomics</a>. <strong><em>Advanced Genetics</em></strong>. 2026, 7(3):e70045.</li><li>J Feng<sup>#</sup>, C Chen<sup>#*</sup>, Y Wu<sup>#</sup>, L Fan, Z Zhang, M Chen, H Tang, <strong>G Yu</strong>, J Ren, J Luo, Y Liao, A Luan, Z Wang, S Tang, Y Shao, Y Liang, J Wang<sup>*</sup>, J Xie<sup>*</sup>, R Xia<sup>*</sup>. <a href="https://www.sciencedirect.com/science/article/pii/S1674205226001589?sessionid=" class=external-link target=_blank rel=noopener>How to make big data accessible to plant biologists and beyond: Ten years of lessons from TBtools</a>. <strong><em>Molecular Plant</em></strong>. 2026, 19(7):1378-1391.</li><li>Y Feng<sup>#</sup>, L Zheng<sup>#</sup>, W Tang<sup>#</sup>, P Wang, Y Lai, J Qin, C Zhou, X Zhang, M Yang, L Jie<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, H Ren<sup>*</sup>, Q Huang<sup>*</sup>. <a href=https://www.nature.com/articles/s42003-026-09561-7 class=external-link target=_blank rel=noopener>Gut metabolite indole-3-acetic acid aggravates neuropsychiatric lupus via the AHR/STAT3 pathway in microglia</a>. <strong><em>Communications Biology</em></strong>. 2026, 9(1):281.</li><li>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, <strong>G Yu</strong><sup>*</sup>, L Xie<sup>*</sup>. <a href=https://doi.org/10.1007/s11427-025-3035-0 class=external-link target=_blank rel=noopener>EasyMultiProfiler: An Efficient Multi-Omics Data Integration and Analysis Workflow for Microbiome Research</a>. <strong><em>SCIENCE CHINA Life Sciences</em></strong>. 2026, 69(2):321-330. (å°é¢æç« , Cover Article)</li><li>Q Wang<sup>#</sup>, L Deng<sup>#</sup>, S Xu<sup>#</sup>, P Guo, H Zhu, H Ge, Y Gong, G Du, K Huang, C Su, R Wang, Y Qiu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1002/inmd.70067 class=external-link target=_blank rel=noopener>
173Comparison of Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 platforms for singleâcell spatial transcriptomics of mouse brain and lung</a>. <strong><em>Interdisciplinary Medicine</em></strong>. 2026, 4(1):e70067.</li><li><strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.59717/j.xinn-life.2025.100181 class=external-link target=_blank rel=noopener>Background bias in functional enrichment analysis: Insights from clusterProfiler</a>. <strong><em>The Innovation Life</em></strong>. 2026, 4(1):100181. (å°é¢å¯¼è¯»ï¼Insights form clusterProfiler)</li></ul><h2 id=year-2025><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2025 174<a class=heading-link href=#year-2025><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 175<span class=sr-only>Link to heading</span></a></h2><ul><li>Y Peng, S Jiang, Y Song, P Luo, J Li, D Hu, JG Zhou, <strong>G Yu</strong><sup>*</sup>, T Xu<sup>*</sup>, S Wang<sup>*</sup>. <a href=https://advanced.onlinelibrary.wiley.com/doi/10.1002/advs.202507799 class=external-link target=_blank rel=noopener>ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity</a>. <strong><em>Advanced Science</em></strong>. 2025, 12(44): e07799. (IF = 14.1)</li><li>S Wen<sup>#</sup>, X Du<sup>#</sup>, M Zhu<sup>#</sup>, C Huang, Z Lin, M Li, B Hu, X Wang, F Jiang, G Zhou, W Zhu, <strong>G Yu</strong><sup>*</sup>, C Xu<sup>*</sup>, B Shen<sup>*</sup>. <a href=https://jitc.bmj.com/content/13/10/e010416 class=external-link target=_blank rel=noopener>ALCAM-CD6 axis suppression: a key determinant of immune-mediated metastasis recurrence in stage III non-small cell lung cancer</a>. <strong><em>Journal for ImmunoTherapy of Cancer</em></strong>. 2025, 13(10):e010416. (IF = 11.7)</li><li>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>, <strong>G Yu</strong><sup>*</sup>, X Chen<sup>*</sup>. <a href=https://onlinelibrary.wiley.com/doi/10.1002/imt2.70065 class=external-link target=_blank rel=noopener>Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome</a>. <strong><em>iMeta</em></strong>. 2025, 4(5):e70065. (IF = 44.4)</li><li>X Lu, K Li, Z Li, A Lin, L Zhao, R Shen, Z Xu, J Gao, D Lv, Y Zhang, T Ye, J Shen, Y Chen, H Huang, Z Hao, D Zeng, H Wang, S Guo, W Wang, Y Xiong, Y Li, H Li, J Gao, Q Liu, B Wei, J Shi, S Cheng, G Li, Y Tang, E Lin, H Xu, G Feng, Y He, Y Sun, X Liu, Y Wang, W Song, J Song, S Tian, Y Zhang, J Zhang, Z Xu, C Song, Y Zhang, H Wu, C Gao, E Hu, C Yang, J Lou, D Wang, X Wang, P Luo<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, Y Ge<sup>*</sup>. <a href=https://doi.org/10.1002/imm3.70005 class=external-link target=_blank rel=noopener>FigureYa: A Standardized Visualization Framework for Enhancing Biomedical Data Interpretation and Research Efficiency</a>. <strong><em>iMetaMed</em></strong>. 2025, 1(1):e70005. <a href=https://onlinelibrary.wiley.com/cms/asset/242e8b33-73e2-448a-bacc-e68837e3437b/default_cover.jpg class=external-link target=_blank rel=noopener>Cover story</a></li><li>S Xu<sup>#</sup>, Q Wang<sup>#</sup>, S Wen<sup>#</sup>, J Li<sup>#</sup>, N He<sup>#</sup>
175, M Li, T Hackl, R Wang, D Zeng, S Wang, S Li, CH Gao, L Zhou, S Tao, Z Xie, L Deng, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1016/j.xinn.2025.100958 class=external-link target=_blank rel=noopener>aplot: Simplifying the creation of complex graphs to visualize associations across diverse data types</a>. <strong><em>The Innovation</em></strong>. 2025, 6(9):100958. (å°é¢å¯¼è¯»ï¼Complex composite graphics) (IF = 39.5)</li><li>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, <strong>G Yu</strong><sup>*</sup>, W Fang<sup>*</sup>, X Bao<sup>*</sup>. <a href=https://doi.org/10.1038/s41388-025-03388-y class=external-link target=_blank rel=noopener>Spatial multi-omics profiling of breast cancer oligo-recurrent lung metastasis</a>. <strong><em>Oncogene</em></strong>. 2025, 44(27):2268-2282. (IF = 9.1)</li><li>Q Wang, H Zhu, L Deng, S Xu, W Xie, M Li, R Wang, L Tie, L Zhan, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1002/smtd.202401107 class=external-link target=_blank rel=noopener>Spatial Transcriptomics: Biotechnologies, Computational Tools, and Neuroscience Applications</a>. <strong><em>Small Methods</em></strong>. 2025, 9(5):2401107. <a href=https://onlinelibrary.wiley.com/doi/10.1002/smtd.202570033 class=external-link target=_blank rel=noopener>å·é¦æå¾æç« Frontispiece</a> (IF = 8.7)</li><li>Y Tu<sup>#*</sup>, S Xu<sup>#</sup>, H Shu, X Wang, W Li, <strong>G Yu</strong><sup>*</sup>, Li He<sup>*</sup>. <a href=https://onlinelibrary.wiley.com/doi/full/10.1111/phpp.70022 class=external-link target=_blank rel=noopener>16S rRNA Sequencing Reveals Dysbiosis of Skin Microbiome Associated With Disease Severity in Chronic Actinic Dermatitis</a>. <strong><em>Photodermatology, Photoimmunology & Photomedicine</em></strong>. 2025, 41(3):e70022.</li><li>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>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1002/imt2.269 class=external-link target=_blank rel=noopener>Scalable method for exploring phylogenetic placement uncertainty with custom visualizations using treeio and ggtree</a>. <strong><em>iMeta</em></strong>. 2025, 4(1):e269. (IF = 44.4)</li></ul><h2 id=year-2024><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2024 176<a class=heading-link href=#year-2024><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 177<span class=sr-only>Link to heading</span></a></h2><ul><li>D Zeng<sup>#</sup>, Y Fang<sup>#</sup>, W Qiu; P Luo, S Wang; R Shen, W Gu, X Huang, Q Mao; G Wang, Y Lai; X Xu, M Shi, Z Wu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, W Liao<sup>*</sup>. <a href=https://doi.org/10.1016/j.crmeth.2024.100910 class=external-link target=_blank rel=noopener>Enhancing Immuno-Oncology Investigations Through Multidimensional Decoding of Tumour Microenvironment with IOBR 2.0</a>. <strong><em>Cell Reports Methods</em></strong>. 2024, 4(12):100910. (IF = 4.5ï¼äºåº)</li><li>M Luo<sup>*#</sup>, W Yang<sup>#</sup>, L Bai<sup>#</sup>, L Zhang<sup>#</sup>, JW Huang<sup>#</sup>, Y Cao<sup>#</sup>, Y Xie<sup>#</sup>, L Tong, H Zhang, L Yu, LW Zhou, Y Shi, P Yu, Z Wang, Z Yuan, P Zhang, Y Zhang, F Ju, H Zhang, F Wang, Y Cui, J Zhang, G Jia, D Wan, C Ruan, Y Zeng, P Wu, Z Gao, W Zhao, Y Xu, <strong>G Yu</strong>, C Tian, LN Jin, J Dai<sup>*</sup>, B Xia<sup>*</sup>, B Sun<sup>*</sup>, F Chen<sup>*</sup>, YZ Gao<sup>*</sup>, H Wang<sup>*</sup>, B Wang<sup>*</sup>, D Zhang<sup>*</sup>, X Cao<sup>*</sup>, H Wang<sup>*</sup>, T Huang<sup>*</sup>. <a href=https://doi.org/10.59717/j.xinn-life.2024.100105 class=external-link target=_blank rel=noopener>Artificial intelligence for life sciences: A comprehensive guide and future trends</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(4):100105.</li><li>Z Miao<sup>#</sup>, T Tian<sup>#</sup>, W Chen<sup>#</sup>, Q Wang<sup>#</sup>, L Ma<sup>#</sup>, D Zhang<sup>#</sup>, M Xie<sup>#</sup>, Z Yu<sup>#</sup>, X Guo, G Bai, S Zhao, X Chen, W Wang, Y Gao, S Guo<sup>*</sup>, M Luo<sup>*</sup>, L Yuan<sup>*</sup>, C Tian<sup>*</sup>, L Wu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, D Zhang<sup>*</sup>, S Sun<sup>*</sup>. <a href=https://www.the-innovation.org/article/doi/10.59717/j.xinn-life.2024.100097 class=external-link target=_blank rel=noopener>Spatial Resolved Transcriptomics: Computational Insights into Gene Transcription Across Tissue and Organ Architecture in Diverse Applications</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(4):100097.</li><li><strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1016/j.xinn.2024.100722 class=external-link target=_blank rel=noopener>Thirteen years of clusterProfiler</a>. <strong><em>The Innovation</em></strong>. 2024, 5(6):100722. (IF = 25.7ï¼ä¸åº)</li><li>S Xu<sup>#</sup>, E Hu<sup>#</sup>, Y Cai<sup>#</sup>, Z Xie<sup>#</sup>, X Luo<sup>#</sup>
177, L Zhan, W Tang, Q Wang, B Liu, R Wang, W Xie, T Wu, L Xie, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.nature.com/articles/s41596-024-01020-z class=external-link target=_blank rel=noopener>Using clusterProfiler to characterise Multi-Omics Data</a>. <strong><em>Nature Protocols</em></strong>. 2024, 19(11):3292-3320. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> <i class="fa fa-fire fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF = 16.0ï¼ä¸åº) <span class=__dimensions_badge_embed__ data-doi=10.1038/s41596-024-01020-z data-style=small_rectangle></span></li><li>S Wang, <strong>G Yu</strong>, L Xie<sup>*</sup>. <a href=https://www.sciltp.com/journals/hm/article/view/433 class=external-link target=_blank rel=noopener>Asymmetric Cell Division and Satellite Cell Fate Regulation in Skeletal Muscle Aging and Disease</a>. <strong><em>Health and Metabolism</em></strong>. 2024, 1(1):5.</li><li>Y Chen<sup>#</sup>, LN He<sup>#</sup>, Y Zhang, J Gong, S Xu, Y Shu, D Zhang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, Z Zuo<sup>*</sup>. <a href=http://doi.org/10.1002/imt2.229 class=external-link target=_blank rel=noopener>tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package</a>. <strong><em>iMeta</em></strong>. 2024, 3(5):e229. (IF = 33.2ï¼ä¸åº)</li><li>D Wang, G Chen, L Li, S Wen, Z Xie, X Luo, L Zhan, S Xu, J Li, R Wang, Q Wang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://journals.lww.com/cmj/fulltext/2024/08200/reducing_language_barriers,_promoting_information.7.aspx class=external-link target=_blank rel=noopener>Reducing language barriers, promoting information absorption, and communication using <em>fanyi</em></a>. <strong><em>Chinese Medical Journal</em></strong>. 2024, 137(16):1950-1956. (IF = 7.3ï¼äºåº)</li><li>XK Ma<sup>#</sup>, Y Yu<sup>#</sup>, T Huang<sup>#</sup><sup>*</sup>, D Zhang, C Tian, W Tang, M Luo, P Du<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, L Yang<sup>*</sup>. <a href=https://www.the-innovation.org/article/doi/10.59717/j.xinn-life.2024.100083 class=external-link target=_blank rel=noopener>Bioinformatics Software Development: principles and future directions</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(3):100083.</li><li>Y Yang<sup>#</sup>, S Xu<sup>#</sup>, Y Hong, Y Cai, W Tang, J Wang, B Shen<sup>*</sup>, H Zong<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.59717/j.xinn-life.2024.100079 class=external-link target=_blank rel=noopener>Computational modeling for medical data: from data collection to knowledge discovery</a>. <strong><em>The Innovation Life</em></strong>. 2024, 2(3):100079.</li><li>L Zhan<sup>#</sup>, X Luo<sup>#</sup>, W Xie<sup>#</sup>, XA Zhu<sup>#</sup>, Z Xie, J Lin, L Li, W Tang, R Wang, L Deng, Y Liao, B Liu, Y Cai, Q Wang, S Xu<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.sciencedirect.com/science/article/pii/S167385272400033X class=external-link target=_blank rel=noopener>shinyTempSignal: an R shiny application for exploring temporal and other phylogenetic signals</a>. <strong><em>Journal of Genetics and Genomics</em></strong>. 2024, 51(7):762-768. (IF = 7.1ï¼ä¸åº)</li><li>L Li, W Xie, L Zhan, S Wen, X Luo, S Xu, Y Cai, W Tang, Q Wang, M Li, Z Xie, L Deng, H Zhu, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.sciencedirect.com/science/article/pii/S2667005424000206 class=external-link target=_blank rel=noopener>Resolving Tumor Evolution: A Phylogenetic Approach</a>. <strong><em>Journal of the National Cancer Center</em></strong>. 2024, 4(2):97-106. (IF = 9.4ï¼ä¸åº)</li><li>Q Wang, W Tang, L Chen, L Deng, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1016/j.xinn.2024.100637 class=external-link target=_blank rel=noopener>Decoding the Brain: Unveiling Comprehensive Cellular Atlases through Multiomics Mega Data</a>. <strong><em>The Innovation</em></strong>. 2024, 5(4):100637. (IF = 25.7ï¼ä¸åº)</li><li>Y Cai<sup>#</sup>, W Hu<sup>#</sup>, Y Pei, H Zhao<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1016/j.xinn.2024.100627 class=external-link target=_blank rel=noopener>Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic</a>. <strong><em>The Innovation</em></strong>. 2024, 5(3):100627. (IF = 25.7ï¼ä¸åº)</li><li>Y Lai<sup>#</sup>, W Tang<sup>#</sup>, X Luo, H Zheng, Y Zhang<sup>*</sup>, M Wang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, Min Yang<sup>*</sup>. <a href=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2024.1369116 class=external-link target=_blank rel=noopener>Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis</a>. <strong><em>Frontiers in Immunology</em></strong>. 2024, 15:1369116. (IF = 5.9ï¼äºåº)</li><li>CH Gao, C Chen, T Akyol, A Dusa, <strong>G Yu</strong>, B Cao, P Cai<sup>*</sup>
177. <a href=https://onlinelibrary.wiley.com/doi/10.1002/imt2.177 class=external-link target=_blank rel=noopener>ggVennDiagram: intuitive Venn diagram software extended</a>. <strong><em>iMeta</em></strong>. 2024, 3(1):e177. (IF = 33.2ï¼ä¸åº)</li><li>Y Ye<sup>#</sup>, MH Shum<sup>#</sup>, JL Tsui<sup>#</sup>, <strong>G Yu</strong><sup>#</sup>, DK Smith, H Zhu, JT Wu, Y Guan, TTY Lam<sup>*</sup>. <a href=https://doi.org/10.1371/journal.pcbi.1011871 class=external-link target=_blank rel=noopener>Robust expansion of phylogeny for fast-growing genome sequence data</a>. <strong><em>PLoS Computational Biology</em></strong>. 2024, 20(2):e1011871. (IF = 3.6ï¼äºåº)</li><li>S Wen, S Mo, J Zhou, Y Lv, K Khazaie<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.frontiersin.org/articles/10.3389/fcell.2024.1365242/full class=external-link target=_blank rel=noopener>Single-cell and spatial-omics in delineating immune-related diseases</a>. <strong><em>Frontiers in Cell and Developmental Biology</em></strong>. 2024, 12:1365242. (IF = 4.3ï¼äºåº)</li></ul><h2 id=year-2023><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2023 178<a class=heading-link href=#year-2023><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 179<span class=sr-only>Link to heading</span></a></h2><ul><li>X Zhang, B Liang, Y Huang, H Meng, Z Li, J Du, L Zhou, Y Zhong, B Wang, X Lin, <strong>G Yu</strong>, X Chen, W Lu, ZS Chen, X Yang, Z Huang<sup>*</sup>. <a href=https://doi.org/10.1002/advs.202303753 class=external-link target=_blank rel=noopener>Behind the Indolent Facade: Uncovering the Molecular Features and Malignancy Potential in Lung Minimally Invasive Adenocarcinoma by Single-Cell Transcriptomics</a>. <strong><em>Advanced Science</em></strong>. 2023, 10(36):2303753. (IF = 14.3ï¼ä¸åº)</li><li>M Kang, F Lin, Z Jiang, X Tan, X Lin, Z Liang, C Xiao, Y Xia, W Guan, Z Yang, <strong>G Yu</strong>, M Zanin, S Tang<sup>*</sup>, SS Wong<sup>*</sup>. <a href=https://onlinelibrary.wiley.com/doi/abs/10.1111/irv.13172 class=external-link target=_blank rel=noopener>The impact of pre-existing influenza antibodies and inflammatory status on the influenza vaccine responses in older adults</a>. <strong><em>Influenza and Other Respiratory Viruses</em></strong>. 2023, 17(7):e13172. (IF = 4.3ï¼ååº)</li><li>W Tang, H Zheng, S Xu, P Li, L Zhan, X Luo, Z Dai, Q Wang, <strong>G Yu</strong><sup>*</sup>. <a href=https://dx.doi.org/10.1080/19490976.2023.2223349 class=external-link target=_blank rel=noopener>MMINP: A computational framework of microbe-Metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm</a>. <strong><em>Gut Microbes</em></strong>. 2023, 15(1):2223349. (IF = 12.2ï¼ä¸åº)</li><li>S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng, M Chen, T Wu, E Hu, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1016/j.xinn.2023.100388 class=external-link target=_blank rel=noopener>MicrobiotaProcess: A comprehensive R package for deep mining microbiome</a>. <strong><em>The Innovation</em></strong>. 2023, 4(2):100388. (IF = 33.2ï¼ä¸åº) (å°é¢å¯¼è¯»ï¼Microbiome Toolkit)</li><li>S Guo<sup>*</sup>, D Zhang, H Wang, Q An, <strong>G Yu</strong>, J Han, C Jiang, J Huang. <a href=https://www.frontiersin.org/articles/10.3389/fmed.2023.1146896/full class=external-link target=_blank rel=noopener>Computational and Systematic Analysis of Multi-omics Data for Drug Discovery and Development</a>. <strong><em>Frontiers in Medicine</em></strong>. 2023, 10:1146896. (IF = 3.1ï¼ä¸åº)</li></ul><h2 id=year-2022><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2022 180<a class=heading-link href=#year-2022><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 181<span class=sr-only>Link to heading</span></a></h2><ul><li>S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, <strong>G Yu</strong><sup>*</sup>. <a href=https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56 class=external-link target=_blank rel=noopener>Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data</a>. <strong><em>iMeta</em></strong>, 2022, 1(4):e56. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i></li><li>Q Wang<sup>#</sup>, M Li<sup>#</sup>, T Wu, L Zhan, L Li, M Chen, W Xie, Z Xie, E Hu, S Xu, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1002/cpz1.585 class=external-link target=_blank rel=noopener>Exploring epigenomic datasets by ChIPseeker</a>. <strong><em>Current Protocols</em></strong>, 2022, 2(10): e585. <a href="https://onlinelibrary.wiley.com/share/author/GYJGUBYCTRMYJFN2JFZZ?target=10.1002/cpz1.585" class=external-link target=_blank rel=noopener><i class="fa fa-file-pdf-o fa-2x" aria-hidden=true style=color:#000;font-size:150%></i></a></li><li>Z Dai, T Wu, S Xu, L Zhou, W Tang, E Hu, L Zhan M Chen, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.frontiersin.org/articles/10.3389/fmicb.2022.951774 class=external-link target=_blank rel=noopener>Characterization of toxin-antitoxin systems from public sequencing data: a case study in <em>Pseudomonas aeruginosa</em></a>. <strong><em>Frontiers in Microbiology</em></strong>. 2022, 13:951774. (IF = 5.2ï¼äºåºï¼Topæå)</li><li>T Feng<sup>#</sup>, T Wu<sup>#</sup>, Y Zhang<sup>#</sup>, L Zhou<sup>#</sup>, S Liu, L Li, M Li, E Hu, Q Wang, X Fu, L Zhan, Z Xie, W Xie, X Huang<sup>*</sup>, X Shang<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.frontiersin.org/articles/10.3389/fonc.2022.912694/ class=external-link target=_blank rel=noopener>Stemness Analysis Uncovers That The Peroxisome Proliferator-Activated Receptor Signaling Pathway Can Mediate Fatty Acid Homeostasis In Sorafenib-Resistant Hepatocellular Carcinoma Cells</a>. <strong><em>Frontiers in Oncology</em></strong>. 2022, 12:912694. (IF = 4.7ï¼ä¸åº)</li><li>L Zhou<sup>#</sup>, T Feng<sup>#</sup>, S Xu, F Gao, TT Lam, Q Wang, T Wu, H Huang, L Zhan, L Li, Y Guan, Z Dai<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1093/bib/bbac222 class=external-link target=_blank rel=noopener>ggmsa: a visual exploration tool for multiple sequence alignment and associated data</a>. <strong><em>Briefings in Bioinformatics</em></strong>. 2022, 23(4):bbac222. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF = 9.5ï¼ä¸åºï¼Topæå)</li><li>N Sato, Y Tamada, <strong>G Yu</strong>, Y Okuno<sup>*</sup>. <a href=https://doi.org/10.1093/bioinformatics/btac175 class=external-link target=_blank rel=noopener>CBNplot: Bayesian network plots for enrichment analysis</a>. <strong><em>Bioinformatics</em></strong>. 2022, 38(10):2959-2960. (IF=5.8ï¼ä¸åºï¼Topæå)</li><li>T Wu, CL Xiao, TT Lam, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.frontiersin.org/articles/10.3389/fgene.2022.890775/full class=external-link target=_blank rel=noopener>Biomedical Data Visualization: Methods and Applications</a>. <strong><em>Frontiers in Genetics</em></strong>. 2022, 13:890775. (IF=3.7ï¼ä¸åº)</li><li>X Zhao<sup>#</sup>, W Tang<sup>#</sup>, H Wan<sup>#</sup>, Z Lan H Qin, Q Lin, Y Hu, <strong>G Yu</strong><sup>*</sup>, N Jiang<sup>*</sup>, B Yu<sup>*</sup>. <a href=https://www.frontiersin.org/articles/10.3389/fmicb.2022.723791/full class=external-link target=_blank rel=noopener>Altered gut microbiota as an auxiliary diagnostic indicator for patients with fracture-related infection</a>. <strong><em>Frontiers in Microbiology</em></strong>. 2022, 13:723791. (IF = 5.2ï¼äºåºï¼Topæå)</li></ul><h2 id=year-2021><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2021 182<a class=heading-link href=#year-2021><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 183<span class=sr-only>Link to heading</span></a></h2><ul><li>S Xu<sup>#</sup>, M Chen<sup>#</sup>, T Feng, L Zhan, L Zhou, <strong>G Yu</strong><sup>*</sup>. <a href=https://www.frontiersin.org/articles/10.3389/fgene.2021.774846 class=external-link target=_blank rel=noopener>Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:774846. (IF=4.772ï¼ä¸åº)</li><li>CH Gao, <strong>G Yu</strong>, P Cai<sup>*</sup>. <a href=https://doi.org/10.3389/fgene.2021.706907 class=external-link target=_blank rel=noopener>ggVennDiagram: An intuitive, easy-to-use, and highly customizable R package to generate Venn diagram</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:706907. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF=4.772ï¼ä¸åº)</li><li>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>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1093/molbev/msab166 class=external-link target=_blank rel=noopener>ggtreeExtra: Compact visualization of richly annotated phylogenetic data</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2021, 38(9):4039-4042. (IF=8.800ï¼ä¸åºï¼Topæå)</li><li>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>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1016/j.xinn.2021.100141 class=external-link target=_blank rel=noopener>clusterProfiler 4.0: A universal enrichment tool for interpreting omics data</a>. <strong><em>The Innovation</em></strong>. 2021, 2(3):100141. (å°é¢å¯¼è¯»ï¼ClusterProfiler 4: Pathway Discovery)</li><li>D Zeng<sup>#</sup>, Z Ye<sup>#</sup>, R Shen, <strong>G Yu</strong>, J Wu, Y Xiong, R Zhou, W Qiu, N Huang, L Sun, X Li, J Bin, Y Liao, M Shi, W Liao<sup>*</sup>. <a href=https://doi.org/10.3389/fimmu.2021.687975 class=external-link target=_blank rel=noopener>IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures</a>. <strong><em>Frontiers in Immunology</em></strong>. 2021, 12:687975. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF=8.786ï¼äºåºï¼Topæå) <span class=__dimensions_badge_embed__ data-doi=10.3389/fimmu.2021.687975 data-style=small_rectangle></span></li><li>T Wu, E Hu, X Ge<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.7717/peerj.11421 class=external-link target=_blank rel=noopener>nCov2019: an R package for studying the COVID-19 coronavirus pandemic</a>. <strong><em>PeerJ</em></strong>. 2021, 9:e11421. (IF=3.061ï¼ä¸åº)</li><li>R Huang, C Soneson, FGM Ernst, KC Rue-Albrecht, <strong>G Yu</strong>, SC Hicks, MD Robinson<sup>*</sup>. <a href=https://doi.org/10.12688/f1000research.26669.2 class=external-link target=_blank rel=noopener>TreeSummarizedExperiment: a S4 class for data with hierarchical structure</a>. <strong><em>F1000Research</em></strong>. 2021, 9:1246.</li><li>S Liu, <strong>G Yu</strong><sup>*</sup>, L Liu<sup>*</sup>, X Zou, L Zhou, E Hu, Y Song. <a href=https://www.frontiersin.org/articles/10.3389/fgene.2021.625236 class=external-link target=_blank rel=noopener>Identification of prognostic Stromal-Immune Score-Based Genes in Hepatocellular Carcinoma microenvironment</a>. <strong><em>Frontiers in Genetics</em></strong>. 2021, 12:625236. (IF=4.772ï¼ä¸åº)</li></ul><h2 id=year-2020><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2020 184<a class=heading-link href=#year-2020><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 185<span class=sr-only>Link to heading</span></a></h2><ul><li>J He<sup>#</sup>, S Xu<sup>#</sup>, B Zhang, C Xiao, Z Chen, F Si, J Fu, X Lin, G Zheng<sup>*</sup>, <strong>G Yu</strong><sup>*</sup>, J Chen<sup>*</sup>. <a href=https://doi.org/10.18632/aging.103168 class=external-link target=_blank rel=noopener>Gut microbiota and metabolite alterations associated with reduced bone mineral density or bone metabolic indexes in postmenopausal osteoporosis</a>. <strong><em>Aging (Albany NY)</em></strong>
185. 2020, 12(9):8583-8604. (IF=5.682ï¼äºåº)</li><li><strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1002/cpbi.96 class=external-link target=_blank rel=noopener>Using ggtree to Visualize Data on Tree-Like Structure</a>. <strong><em>Current Protocols in Bioinformatics</em></strong>. 2020, 69(1):e96. (<em><strong>Invited paper</strong></em>) <a href="https://onlinelibrary.wiley.com/share/author/WQ5Z45WFKYDM43DXQGAI?target=10.1002/cpbi.96" class=external-link target=_blank rel=noopener><i class="fa fa-file-pdf-o fa-2x" aria-hidden=true style=color:#000;font-size:150%></i></a> <span class=__dimensions_badge_embed__ data-doi=10.1002/cpbi.96 data-style=small_rectangle></span></li><li>LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, <strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1093/molbev/msz240 class=external-link target=_blank rel=noopener>treeio: an R package for phylogenetic tree input and output with richly annotated and associated data</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2020, 37(2):599-603. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (<strong>IF=16.240</strong>ï¼ä¸åºï¼Topæå) <span class=__dimensions_badge_embed__ data-doi=10.1093/molbev/msz240 data-style=small_rectangle></span></li><li>Z Hao, D Lv, Y Ge, J Shi, D Weijers, <strong>G Yu</strong><sup>*</sup>, J Chen<sup>*</sup>. <a href=https://peerj.com/articles/cs-251/ class=external-link target=_blank rel=noopener>RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms</a>. <strong><em>PeerJ Computer Science</em></strong>. 2020, 6:e251. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF=1.392ï¼ä¸åº)</li></ul><h2 id=year-2018><i class="fa fa-calendar fa-1x" aria-hidden=true></i> 2018 186<a class=heading-link href=#year-2018><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 187<span class=sr-only>Link to heading</span></a></h2><ul><li><strong>G Yu</strong><sup>*</sup>, TTY Lam, H Zhu, Y Guan<sup>*</sup>. <a href=https://academic.oup.com/mbe/article-abstract/35/12/3041/5142656 class=external-link target=_blank rel=noopener>Two methods for mapping and visualizing associated data on phylogeny using ggtree</a>. <strong><em>Molecular Biology and Evolution</em></strong>. 2018, 35(12):3041-3043. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (<strong>IF=14.797</strong>ï¼ä¸åºï¼ Topæå) <span class=__dimensions_badge_embed__ data-doi=10.1093/molbev/msy194 data-style=small_rectangle></span></li><li><strong>G Yu</strong><sup>*</sup>. <a href=https://doi.org/10.1093/bioinformatics/bty410 class=external-link target=_blank rel=noopener>Using meshes for MeSH term enrichment and semantic analyses</a>. <strong><em>Bioinformatics</em></strong>. 2018, 34(21):3766-3767. (IF=4.531, ä¸åºï¼ Topæå)</li></ul><h2 id=year-2010-2017><i class="fa fa-bar-chart fa-1x" aria-hidden=true></i> Selected publications (2010-2017) 188<a class=heading-link href=#year-2010-2017><i class="fa-solid fa-link" aria-hidden=true title="Link to heading"></i> 189<span class=sr-only>Link to heading</span></a></h2><ul><li><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. <a href=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract class=external-link target=_blank rel=noopener>ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a>. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF=6.363, ä¸åºï¼Topæå) <span class=__dimensions_badge_embed__ data-doi=10.1111/2041-210X.12628 data-style=small_rectangle></span></li><li><strong>G Yu</strong>, QY He<sup>*</sup>. <a href=http://pubs.rsc.org/en/Content/ArticleLanding/2016/MB/C5MB00663E class=external-link target=_blank rel=noopener>ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization</a>. <strong><em>Molecular BioSystems</em></strong>. 2016, 12(2):477-479. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF=2.781ï¼ä¸åº) <span class=__dimensions_badge_embed__ data-doi=10.1039/C5MB00663
189E data-style=small_rectangle></span></li><li><strong>G Yu</strong><sup>*</sup>, LG Wang, QY He<sup>*</sup>. <a href=http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btv145 class=external-link target=_blank rel=noopener>ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization</a>. <strong><em>Bioinformatics</em></strong>. 2015, 31(14):2382-2383. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF=5.766, ä¸åºï¼ Topæå) <span class=__dimensions_badge_embed__ data-doi=10.1093/bioinformatics/btv145 data-style=small_rectangle></span></li><li><strong>G Yu</strong><sup>*</sup>, LG Wang, GR Yan, QY He<sup>*</sup>. <a href=http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btu684 class=external-link target=_blank rel=noopener>DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis</a>. <strong><em>Bioinformatics</em></strong>. 2015, 31(4):608-609. <i class="fa fa-trophy fa-2x" aria-hidden=true style=color:#c50;font-size:150%></i> (IF=5.766, ä¸åºï¼ Topæå) <span class=__dimensions_badge_embed__ data-doi=10.1093/bioinformatics/btu684 data-style=small_rectangle></span></li><li><strong>G Yu</strong>, LG Wang, Y Han, QY He<sup>*</sup>. <a href=http://online.liebertpub.com/doi/abs/10.1089/omi.2011.0118 class=external-link target=_blank rel=noopener>clusterProfiler: an R package for comparing biological themes among gene clusters</a>. <strong><em>OMICS: A Journal of Integrative Biology</em></strong>. 2012, 16(5):284-287. (IF=2.730ï¼ ååº) <span class=__dimensions_badge_embed__ data-doi=10.1089/omi.2011.0118 data-style=small_rectangle></span></li><li><strong>G Yu</strong><sup>#</sup>, F Li<sup>#</sup>, Y Qin, X Bo<sup>*</sup>, Y Wu, S Wang<sup>*</sup>. <a href=http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/7/976 class=external-link target=_blank rel=noopener>GOSemSim: an R package for measuring semantic similarity among GO terms and gene products</a>. <strong><em>Bioinformatics</em></strong>. 2010, 26(7):976-978. (IF=4.877, äºåºï¼ Topæå) <span class=__dimensions_badge_embed__ data-doi=10.1093/bioinformatics/btq064 data-style=small_rectangle></span></li></ul></article></section></div><footer class=footer><section class=container>© 1902018 - 1912026 192YuLab-SMU 193· 194Powered by <a href=https://gohugo.io/ target=_blank rel=noopener>Hugo</a> & <a href=https://github.com/luizdepra/hugo-coder/ target=_blank rel=noopener>Coder</a>.</section></footer></main>
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