Towards a Comprehensive HBV-Human Interaction Map. - Fei Li 004; Yuxing Peng 001; Wenjian Xu; Guangchuang Yu; Peng Li; Xiaochen Bo; Shengqi Wang (IJCBS, 2009)

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. - Guangchuang Yu; Fei Li 004; Yide Qin; Xiaochen Bo; Yibo Wu; Shengqi Wang (Bioinform., 2010)

Functional similarity analysis of human virus-encoded miRNAs. - Guangchuang Yu; Qing-Yu He (J. Clin. Bioinform., 2011)

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. - Guangchuang Yu; Li-Gen Wang; Qing-Yu He (Bioinform., 2015)

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis. - Guangchuang Yu; Li-Gen Wang; Guang-Rong Yan; Qing-Yu He (Bioinform., 2015)

Using meshes for MeSH term enrichment and semantic analyses. - Guangchuang Yu (Bioinform., 2018)

RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms. - Zhaodong Hao; Dekang Lv; Ying Ge; Jisen Shi; Dolf Weijers; Guangchuang Yu; Jinhui Chen (PeerJ Prepr., 2019)

TreeSummarizedExperiment: a S4 class for data with hierarchical structure. - Ruizhu Huang; Charlotte Soneson; Felix G. M. Ernst; Kevin C. Rue-Albrecht; Guangchuang Yu; Stephanie C. Hicks; Mark D. Robinson (F1000Research, 2020)

ggmsa: a visual exploration tool for multiple sequence alignment and associated data. - Lang Zhou; Tingze Feng; Shuangbin Xu; Fangluan Gao; Tommy T. Lam; Qianwen Wang; Tianzhi Wu; Huina Huang; Li Zhan; Lin Li; Yi Guan; Zehan Dai; et al. (Briefings Bioinform., 2022)

CBNplot: Bayesian network plots for enrichment analysis. - Noriaki Sato; Yoshinori Tamada; Guangchuang Yu; Yasushi Okuno (Bioinform., 2022)

Robust expansion of phylogeny for fast-growing genome sequence data. - Yongtao Ye; Marcus H. Shum; Joseph L. Tsui; Guangchuang Yu; David K. Smith; Huachen Zhu; Joseph T. Wu; Yi Guan; Tommy Tsan-Yuk Lam (PLoS Comput. Biol., 2024)