• 国家自然科学基金地区项目，61963001，泛癌关联的ncRNA协同调控网络与模块识别的生物信息学方法研究，2020/01-2023/12，36万元，在研，主持。
• 国家自然科学基金青年项目，61702069，癌症miRNA海绵因果网络与模块识别及其功能特性研究，2018/1-2020/12，25万元，在研，主持。
• 云南省应用基础研究计划面上项目，2017FB099，复杂疾病关联的miRNA海绵及其互作网络识别的生物信息学融合方法研究，2017/6-2020/5，10万元，在研，主持。
• 云南省应用基础研究计划青年项目，2013FD038，基于异构数据的microRNA和TF因果调控网络识别，2013/10-2016/9，6万元，已结题，主持。
• 大理大学青年教师科研基金项目，KYQN201203，基于LDA主题模型的功能性miRNA-mRNA调控模块识别，2013/1-2014/12，0.5万元，已结题，主持。
• 昆明理工大学开放课题，201600001，《云南省面向东南亚、南亚国家农业农村适用技术转移服务平台建设》项目开放子课题：数据采集与分析，2015/12-2016/11，2万元，已结题，主持。
• 云南省教育厅科学研究基金项目，2011J079，基于概率话题模型的功能性TF-miRNA-mRNA调控模块挖掘，2011/10-2013/9，0.5万元，已结题，主持。

 

发表论文以及专利（*为共同第一作者，#为通讯作者）：

1. Junpeng Zhang, Taosheng Xu, Lin Liu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le. LMSM: a modular approach for identifying lncRNA related miRNA sponge modules in breast cancer. bioRxiv, 2019, DOI: 10.1101/841502.
2. Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li. Inferring and analyzing module-specific lncRNA-mRNA causal regulatory networks in human cancer. Briefings in Bioinformatics, 2019, 20(4): 1403-1419.
3. Junpeng Zhang#, Vu Viet Hoang Pham#, Lin Liu, Taosheng Xu, Buu Truong, Jiuyong Li, Nini Rao, Thuc Duy Le. Identifying miRNA synergism using multiple-intervention causal inference. BMC Bioinformatics, 2019, 20(Suppl 23):.
4. Junpeng Zhang, Lin Liu, Taosheng Xu, Yong Xie, Chunwen Zhao, Jiuyong Li, Thuc Duy Le. miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules. BMC Bioinformatics, 2019, 20:235.
5. Vu Viet Hoang Pham#, Junpeng Zhang#, Lin Liu, Buu Truong, Taosheng Xu, Trung Tin Nguyen, Jiuyong Li, Thuc Duy Le. Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction. BMC Bioinformatics, 2019, 20:143.
6. Weili Jiang, Zhenhua Chen, Yan Xiang, Dangguo Shao, Lei Ma*, Junpeng Zhang*. SSEM: a novel self-adaptive stacking ensemble model for classification. IEEE Access, 2019, 7(1): 120337-120349.
7. Peter Brown, RELISH Consortium (One of co-authors), Yaoqi Zhou. Large expert-curated database for benchmarking document similarity detection in biomedical literature search. Database, 2019, 2019: baz085, DOI:10.1093/database/baz085.
8. Sarvenaz Choobdar, Mehmet E. Ahsen, Jake Crawford, Mattia Tomasoni, Tao Fang, David Lamparter, Junyuan Lin, Benjamin Hescott, Xiaozhe Hu, Johnathan Mercer, Ted Natoli, Rajiv Narayan, The DREAM Moduledentification Challenge Consortium (One of co-authors), Aravind Subramanian, Jitao D. Zhang, Gustavo Stolovitzky, Zoltán Kutalik, Kasper Lage, Donna K. Slonim, Julio Saez-Rodriguez, Lenore J. Cowen, Sven Bergmann, Daniel Marbach. Assessment of network module identification across complex diseases. Nature Methods, 2019, 16: 843–852.
9. Guodong Du, Lei Ma, Jin-Shan Hu, Junpeng Zhang, Yan Xiang, Dangguo Shao, and Hongbin Wang. Prediction of 30-Day Readmission: An Improved Gradient Boosting Decision Tree Approach. Journal of Medical Imaging and Health Informatics, 2019, 9(3): 620–627.
10. Junpeng Zhang, Lin Liu, Jiuyong Li, Thuc Duy Le. LncmiRSRN: identification and analysis of long non-coding RNA related miRNA sponge regulatory network in human cancer. Bioinformatics, 2018, 34(24): 4232-4240.
11. Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Weijia Zhang, Jie Gui, Kui Yu, Jiuyong Li, Thuc Duy Le. miRBaseConverter: An R/Bioconductor Package for Converting and Retrieving miRNA Name, Accession, Sequence and Family Information in Different Versions of miRBase. BMC Bioinformatics, 2018, 19 (Suppl 19) :514.
12. Thuc Duy Le#, Junpeng Zhang#, Lin Liu, Buu Minh Thanh Truong, Shu Hu, Taosheng Xu, Jiuyong Li. Identifying microRNA targets in epithelial-mesenchymal transition using joint-intervention causal inference. In Proceedings of the 8th International Conference on Computational Systems-Biology and Bioinformatics (CSBio '17). ACM, New York, NY, USA, 2017, 34-41. DOI: 10.1145/3156346.3156353.
13. Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li. Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. BMC Bioinformatics, 2017, 18:243.
14. Junpeng Zhang, Thuc Duy Le, Lin Liu, Jiuyong Li. Identifying miRNA sponge modules using biclustering and regulatory scores. BMC Bioinformatics, 2017, 18(Suppl 3):44.
15. Thuc Duy Le#, Junpeng Zhang#, Lin Liu, Jiuyong Li. Computational methods for identifying miRNA sponge interactions. Briefings in Bioinformatics, 2017, 18 (4): 577-90.
16. Junpeng Zhang, Thuc Duy Le, Lin Liu, Jianfeng He, Jiuyong Li. A novel framework for inferring condition-specific TF and miRNA co-regulation of protein-protein interactions. Gene, 2016, 577(1):55-64.
17. Junpeng Zhang, Thuc Duy Le, Lin Liu, Jianfeng He, Jiuyong Li. Identifying miRNA synergistic regulatory network in heterogeneous human data via network motifs. Molecular Biosystems, 2016, 12(2):454-63.
18. Thuc Duy Le, Lin Liu, Junpeng Zhang, Bing Liu, Jiuyong Li. From miRNA regulation to miRNA-TF co-regulation: computational approaches and challenges. Briefings in Bioinformatics, 2015, 16(3):475-96.
19. Thuc Duy Le, Junpeng Zhang, Lin Liu, Bing Liu, Jiuyong Li. miRLAB: an R based dry lab for exploring miRNA-mRNA regulatory relationships. PLoS ONE, 2015, 10(12): e0145386.
20. Thuc Duy Le, Junpeng Zhang, Lin Liu, Jiuyong Li. Ensemble methods for miRNA target prediction from expression data. PLoS ONE, 2015, 10(6): e0131627.
21. Junpeng Zhang, Thuc Duy Le, Lin Liu, Bing Liu, Jianfeng He, Gregory J Goodall, Jiuyong Li. Inferring condition-specific miRNA activity from matched miRNA and mRNA expression data. Bioinformatics, 2014, 30(21):3070-7.
22. Junpeng Zhang, Thuc Duy Le, Lin Liu, Bing Liu, Jianfeng He, Gregory J Goodall, Jiuyong Li. Identifying direct miRNA-mRNA causal regulatory relationships in heterogeneous data. Journal of Biomedical Informatics, 2014, 52:438- 47.
23. Junpeng Zhang, Bing Liu, Jianfeng He, Lei Ma and Jiuyong Li.  Inferring functional miRNA-mRNA regulatory modules in epithelial–mesenchymal transition with a probabilistic topic model. Computers in Biology and Medicine, 2012, 42(4):428-37.

 

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