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# Co-first authors; * Co-corresponding authors
- 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.
- 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.
- 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. (Feature article 1)
- 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.
- T Wu, E Hu, X Ge*, G Yu*. nCov2019: an R package for studying the COVID-19 coronavirus pandemic. PeerJ. 2021, 9:e11421.
- 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.
- 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.
- 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.
- 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. Highly Cited Paper
- 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.
- G Yu. Using meshes for MeSH term enrichment and semantic analyses. Bioinformatics. 2018, 34(21):3766-3767.
Selected publications (2010-2017)
- 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. (Feature article 2) Highly Cited Paper
- G Yu, QY He*. ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization. Molecular BioSystems. 2016, 12(2):477-479. Highly Cited Paper
- G Yu*, LG Wang, QY He*. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparision and visualization. Bioinformatics. 2015, 31(14):2382-2383. Highly Cited Paper
- 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. Highly Cited Paper
- 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. Highly Cited Paper
- 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. Highly Cited Paper