Adaptive Evolution of cry Genes in Bacillus thuringiensis: Implications for Their Specificity Determination. - Jinyu Wu; Fangqing Zhao; Jie Bai; Gang Deng; Song Qin; Qiyu Bao (Genom. Proteom. Bioinform., 2007)

PlasmoGF: an integrated system for comparative genomics and phylogenetic analysis of Plasmodium gene families. - Xiang Xu; Jinyu Wu; Jian Xiao 007; Yi Tan; Qiyu Bao; Fangqing Zhao; Xiaokun Li (Bioinform., 2008)

FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families. - Jinyu Wu; Xiang Xu; Jian Xiao 007; Long Xu; Huiguang Yi; Shengjie Gao; Jing Liu; Qiyu Bao; Fangqing Zhao; Xiaokun Li (BMC Bioinform., 2009)

inGAP: an integrated next-generation genome analysis pipeline. - Ji Qi; Fangqing Zhao; Anne Buboltz; Stephan C. Schuster (Bioinform., 2010)

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation. - Huabin Hou; Fangqing Zhao; LingLin Zhou; Erle Zhu; Huajing Teng; Xiaokun Li; Qiyu Bao; Jinyu Wu; Zhongsheng Sun (Nucleic Acids Res., 2010)

mirTools: microRNA profiling and discovery based on high-throughput sequencing. - Erle Zhu; Fangqing Zhao; Gang Xu; Huabin Hou; LingLin Zhou; Xiaokun Li; Zhongsheng Sun; Jinyu Wu (Nucleic Acids Res., 2010)

inGAP-sv: a novel scheme to identify and visualize structural variation from paired end mapping data. - Ji Qi; Fangqing Zhao (Nucleic Acids Res., 2011)

HTQC: a fast quality control toolkit for Illumina sequencing data. - Xi Yang; Di Liu 016; Fei Liu 035; Jun Wu; Jing Zou; Xue Xiao; Fangqing Zhao; Baoli Zhu (BMC Bioinform., 2013)

The Value and Significance of Metagenomics of Marine Environments. - Fangqing Zhao; Vladimir B. Bajic (Genom. Proteom. Bioinform., 2015)

Precision Medicine: What Challenges Are We Facing? - Yu Xue 001; Eric-Wubbo Lameijer; Kai Ye 001; Kunlin Zhang; Suhua Chang; Xiaoyue Wang; Jianmin Wu; Ge Gao; Fangqing Zhao; Jian Li; Chunsheng Han; Shuhua Xu; et al. (Genom. Proteom. Bioinform., 2016)

Circular RNA identification based on multiple seed matching. - Yuan Gao; Jinyang Zhang; Fangqing Zhao (Briefings Bioinform., 2018)

Bioinformatics Commons: The Cornerstone of Life and Health Sciences. - Zhang Zhang 002; Yu Xue 001; Fangqing Zhao (Genom. Proteom. Bioinform., 2018)

gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data. - Wenyu Shi; Heyuan Qi; Qinglan Sun; Guomei Fan; Shuangjiang Liu; Jun Wang 074; Baoli Zhu; Hongwei Liu; Fangqing Zhao; Xiaochen Wang; Xiaoxuan Hu; Wei Li 261; et al. (Nucleic Acids Res., 2019)

Visualization of circular RNAs and their internal splicing events from transcriptomic data. - Yi Zheng; Fangqing Zhao (Bioinform., 2020)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Shuhui Song; Lina Ma; et al. (Nucleic Acids Res., 2021)

First Glimpse of Gut Microbiota of Quarantine Insects in China. - Yanxue Yu; Qi Wang; Ping Zhou; Na Lv; Wei Li 261; Fangqing Zhao; Shuifang Zhu; Di Liu 016 (Genom. Proteom. Bioinform., 2022)

Variation of the Vaginal Microbiome During and After Pregnancy in Chinese Women. - Xiaoai Zhang; Qingzhi Zhai; Jinfeng Wang; Xiuling Ma; Bo Xing; Hang Fan; Zhiying Gao; Fangqing Zhao; Wei Liu (Genom. Proteom. Bioinform., 2022)

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. - Yongbiao Xue; Yiming Bao; Zhang Zhang 002; Wenming Zhao; Jing-Fa Xiao; Shunmin He; Guoqing Zhang 006; Yixue Li; Guoping Zhao; Runsheng Chen; Jingyao Zeng; Yadong Zhang; et al. (Nucleic Acids Res., 2022)

Large-scale microbiome data integration enables robust biomarker identification. - Liwen Xiao; Fengyi Zhang; Fangqing Zhao (Nat. Comput. Sci., 2022)

STEEL enables high-resolution delineation of spatiotemporal transcriptomic data. - Yamao Chen; Shengyu Zhou; Ming Li; Fangqing Zhao; Ji Qi (Briefings Bioinform., 2023)

Screening Linear and Circular RNA Transcripts from Stress Granules. - Shuai Chen; Jinyang Zhang; Fangqing Zhao (Genom. Proteom. Bioinform., 2023)

Microbiome in Female Reproductive Health: Implications for Fertility and Assisted Reproductive Technologies. - Liwen Xiao; Zhenqiang Zuo; Fangqing Zhao (Genom. Proteom. Bioinform., 2024)

Decoding Spatial Complexity of Diverse RNA Species in Archival Tissues. - Junjie Zhu; Fangqing Zhao (Genom. Proteom. Bioinform., 2025)