一、基本信息
暴云娟，博士，教授，硕士生导师，湖北省省级人才入选者
电子邮件：yjbao@hubu.edu.cn
研究领域：生物信息学，计算生物学，数据挖掘，机器学习
研究方向：
1. 运用生物信息学、生物统计学、多模态组学、机器学习等方法，对生物组学大数据进行深度挖掘，发现与生物性状或疾病表型相关的生物标志物（肿瘤与传染病方向），解析生物标志物参与的代谢、调控、信号转导等生物学过程；
2. 运用群体遗传学、代谢网络等方法研究微生物群体的遗传进化规律，发现生命活动过程中的重要遗传事件和效应分子，揭示效应分子引起的代谢、调控网络的变化；
3. 生物信息分析工具开发与组学数据库构建。
二、教育背景
2005-2008 香港大学，理论物理学，博士
2003-2005 香港大学，理论物理学，硕士
1999-2003 山西大学，物理学国家基地，学士
三、工作经历
2019至今 湖北大学，生命科学学院，教授
2015-2018 美国圣母大学, 转基因研究中心，研究助理教授
2012-2014 中国科学院天津工业生物技术研究所, 副研究员
2008-2012 香港大学，李嘉诚医学院，博士后研究员
四、研究项目
1. 非靶向代谢组差异代谢物鉴定与分析，横向项目，项目负责人
2. 生物大样本量非靶向代谢组数据并行分析方法开发，横向项目，项目负责人
3. 天津市应用基础及前沿技术研究计划（13JCYBJC39500），极端微生物酶基因簇的预测及其形成机理的研究，2013-2016，项目负责人
4. 美国圣母大学研究启动基金（FY18FRSPL），Toward discovery of early diagnostic biomarkers for skin and nasal diseases caused by Streptococcus pyogenes，2018-2019，项目负责人
五．发表论文或著作 (#共同第一作者，*通讯作者)
1. Zhou Q, Ye W, Yu X, Bao YJ*. A pathway-based computational framework for identification of a new modal of multi-omics biomarkers and its application in esophageal cancer. Computer Methods & Programs in Biomedicine 2024, 247:108077.
2. Jiang W., Wang PY., Zhou Q. Lin QT, Yao Y, Tan X, Yang S, Ye W, Yang Y*, Bao YJ*. Tri©DB: an integrated platform of knowledgebase and reporting system for cancer precision medicine. Journal of Translational Medicine 2023, 21:885.
3. Bao YJ*, Zhou Q, Yu X, Yu X*, and FJ Castellino*, Analysis and Characterization of Glutathione Peroxidases in an Environmental Microbiome and Isolated Bacterial Microorganisms. Journal of Microbiol. & Biotech. 2023, 33(3):1-11.
4. Wang PY, Yang SH, Bao YJ*. An integrative analysis framework for identifying the prognostic markers from multidimensional RNA data of clear cell renal cell carcinoma. The American Journal of Pathology 2022, 192(4):671-686.
5. Qiu JH, Zhou Q, Ye W, Chen Q, Bao YJ*. SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes. BMC Bioinformatics 2022, 23:19. DOI: 10.1186/s12859-021-04533-6.
6. Fatima M, Luo Y, Zhang L, Wang PY, Song H, Fu Y, Li Y, Sun Y, Bao YJ*, Qiu HJ*. Genotyping and Molecular Characterization of Classical Swine Fever Virus Isolated in China during 2016–2018. Viruses 2021, 13:664.
7. Bao YJ*, Qiu J, Luo Y, Rodríguez F, Qiu HJ*. The genetic variation landscape of African swine fever virus reveals frequent positive selection and adaptive flexibility. Transb. and Emerging Diseases 2021, 68(5):2703-2721. DOI: 10.1111/tbed.14018.
8. Wei Lu, Jinhui Feng, Xi Chen, Bao YJ, Yu Wang, Qiaqing Wu, Yanhe Ma, Dunming Zhu. Distinct Regioselectivity of Fungal P450 Enzymes for Steroidal Hydroxylation. Applied and Environ. Microbiol. 2019, 85(18):e01182.
9. Zhang N#, Bao YJ#, Tong HY#, Zuyderduyn S#, Bader G, Peiris JS, Lok S, Lee MY. Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection. BMC Medical Genomics 2018, 11:20.
10. Bao YJ*, Li Y, Liang Z, Agrahari G, Lee S, Ploplis V, and Castellino F. Comparative pathogenomic characterization of a non-invasive serotype M71 strain Streptococcus pyogenes NS53 reveals incongruent phenotypic implications from distinct genotypic markers. FEMS Pathogens & Disease 2017, 75(5):ftx056.
11. Bao YJ, Shapiro J, Lee SW, Ploplis V, and Castellino F. Phenotypic differentiation of Streptococcus pyogenes populations is induced by recombination-driven gene-specific sweeps. Scientific Reports 2016, 6:36644.
12. Bao YJ*, Xu Z, Li Y, Yao Z, Sun J, and Song H. High-throughput metagenomic analysis of petroleum-contaminated soil microbiome reveals the versatility in xenobiotic aromatics metabolism. Journal of Environmental Sciences 2016, 56:25-35.
13. Bao YJ, Liang Z, Mayfield J, McShan W, Lee S, Ploplis V, and Castellino F. Novel genomic rearrangements mediated by multiple genetic elements in Streptococcus pyogenes M23ND confer potentials for evolutionary persistence. Microbiology 2016, 162(8):1346-1359.
14. Zhu Y, Chen P, Bao YJ, Men Y, Zeng Y, Yang J, Sun J, and Sun Y. Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation. Scientific Reports 2016, 6:38248.
15. Bao YJ, Liang Z, Mayfield J, Donahue D, Carothers Katelyn E., Lee Shaun W, Ploplis V, and Castellino F. Genomic Characterization of a Pattern D Streptococcus pyogenes emm53 Isolate Reveals a Genetic Rationale for Invasive Skin Tropicity. Journal of Bacteriology 2016, 198(12):1712-1724.
16. Bao YJ, Liang Z, Mayfield J, Lee S, Ploplis V, and Castellino F. CovRS regulated transcriptome analysis of a hypervirulent M23 strain of Group A Streptococcus pyogenes provides new insights on virulence determinants. Journal of Bacteriology 2015, 197(19): 3191-3205.
17. Gui H, Bao YJ, Tang CS, SO MT, Ngo DN, Tran AQ, Bui DH, Pham DH, Nguyen TL, Tong AH, Lok S, Sham PC, Tam PK, Cherny SS, and Garcia-Barcelo MM. Targeted next-generation sequencing on Hirschsprung disease: a pilot study exploits DNA pooling. Annals of Human Genetics 2014, 78(5): 381-387.
18. Bao YJ#, Liang Z#, Booyjzsen C#, Mayfield J, Li Y, Lee S, Ploplis V, Song H, and Castellino F. Unique genomic arrangements in an invasive serotype M23 strain of Streptococcus pyogenes that induce hypervirulence. Journal of Bacteriology 2014, 196(23): 4089-4102.
19. Tong M, Chan KW, Bao YJ, Wong KY, Chen JN, Kwan PS, Tang KH, Fu L, Qin YR, Lok R, Guan XY, and Ma S. Rab25 is a tumor suppressor gene with anti-angiogenic and anti-invasive activities in esophageal squamous cell carcinoma. Cancer Research 2012, 72(22):6204-6035.
20. Tse H, Bao YJ, Davies MR, Maamary P, Tsoi HW, Tong AH, Ho TC, Lin CH, Gillen CM, Barnett TC, Chen JH, Lee M, Yam WC, Wong CK, Ong CL, Chan YW, Wu CW, Ng T, Lim WW, Tsang TH, Tse CW, Dougan G, Walker MJ, Lok S, and Yuen KY. Molecular characterization of the 2011 Hong Kong scarlet fever outbreak. The Journal of Infectious Disease 2012, 206(3):341-51.
21. Ma S, Bao YJ, Kwan PS, Chan YP, Tong CM, Fu L, Zhang N, Tong AHY, Qin YR, Tsao SW, Chan KW, Lok S, and Guan XY. Identification of PTK6, via RNA sequencing analysis, as a suppressor of esophageal squamous cell carcinoma. Gastroenterology 2012, 143(3):675-86.
六． 开源工具开发
1. 软件著作权：组织取样肿瘤体细胞靶点信息自动化分析流程系统SweepSomMut v1.0 (登记号2021SR1761483).
2. SweepCluster: https://github.com/BaoCodeLab/SweepCluster
3. CompGWAS: https://github.com/BaoCodeLab/CompGWAS
4. VarAnnoFastJ: https://github.com/BaoCodeLab/VarAnnoFastJ
