Publications

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^# Co-first authors; ^* Co-corresponding authors

2021

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.

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.

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 ¹) 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

The ggtree (Yu et al. 2017) paper was selected as a feature article to celebrate the 10^th anniversary of the launch of Methods in Ecology and Evolution. ↩︎