Publications

^# Co-first authors
^* Co-corresponding authors
：ESI Highly Cited Paper (9X)
分区：文章发表当年的中科院小类分区
IF：文章发表当年的影响因子
课题组学术榜

2025 Link to heading

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. accepted.
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. accepted.

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.
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.
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.
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.
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.
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.
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.
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.
Y Cai^#, W Hu^#, Y Pei, Hao Zhao^*, G Yu^*. Encoding biological metaverse: Advancements and challenges in neural fields from macroscopic to microscopic. The Innovation. 2024, 5(3):100627.
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.
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.
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.
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.

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 = 14.3，一区)
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 = 4.3，四区)
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 = 12.2，一区)
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 = 33.2，一区)
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 = 3.1，三区)

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 = 5.2，二区，Top期刊)
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 = 4.7，三区)
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 = 9.5，一区，Top期刊)
N Sato, Y Tamada, G Yu, Y Okuno^*. CBNplot: Bayesian network plots for enrichment analysis. Bioinformatics. 2022, 38(10):2959-2960. (IF=5.8，一区，Top期刊)
T Wu, CL Xiao, TT Lam, G Yu^*. Biomedical Data Visualization: Methods and Applications. Frontiers in Genetics. 2022, 13:890775. (IF=3.7，三区)
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 = 5.2，二区，Top期刊)

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=4.772，三区)
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=4.772，三区)
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=8.800，一区，Top期刊)
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.
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=8.786，二区，Top期刊)
T Wu, E Hu, X Ge^*, G Yu^*. nCov2019: an R package for studying the COVID-19 coronavirus pandemic. PeerJ. 2021, 9:e11421. (IF=3.061，三区)
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=4.772，三区)

2020 Link to heading

J 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=5.682，二区)
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=16.240，一区，Top期刊)
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=1.392，三区)

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=14.797，一区， Top期刊)
G Yu^*. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics. 2018, 34(21):3766-3767. (IF=4.531, 一区， Top期刊)

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, 一区，Top期刊)
G Yu, QY He^*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479. (IF=2.781，三区)
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, 一区， Top期刊)
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, 一区， Top期刊)
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=2.730，四区)
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, 二区， Top期刊)

Books Link to heading

沈百荣，杨恩策. 基于理工信的医学数据采集与分析（基础医学“101计划”核心教材）. 北京大学医学出版社, 2024. ISBN: 9787565931987
余光创（著）, 李林, 罗晓（译）. R实战：系统发育树的数据集成操作及可视化. 电子工业出版社, 2023. ISBN: 9787121451829
G Yu. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). Chapman and Hall/CRC, 2023. doi: 10.1201/9781003279242, ISBN: 9781032233574
Yu G. Gene Ontology Semantic Similarity Analysis Using GOSemSim. In: Kidder B. (eds) Stem Cell Transcriptional Networks. Methods in Molecular Biology, 2020, 2117:207-215. Humana, New York, NY. ISBN: 9781071603000