1.基本信息
张俊鹏，男，1987年04月，中共党员，博士，副教授，硕士生导师，云南省医学会医学工程学分会第七届委员会委员，大理大学第九批中青年学术带头人，提出了一系列新模型新方法来研究人类复杂疾病关联的ncRNA调控模式、竞争模式和协同模式。系列研究成果分别发表在《Wiley Interdisciplinary Reviews: RNA》、《Briefings in Bioinformatics》、《PLOS Computational Biology》、《Bioinformatics》等国际期刊上。主持国家自然科学基金项目2项，云南省自然科学基金项目3项。 公开发表学术论文50余篇（SCI学术论文30余篇），授权国家发明专利7项，软件著作权2件，开发R软件包3套。担任《Nucleic Acids Research》, 《Bioinformatics》,《Briefings in Bioinformatics》,《PLOS Computational Biology》,等国际SCI期刊审稿人。受邀担任《Frontiers in Genetics》审稿编辑和《Frontiers in Molecular Biosciences》客座副编辑，打造了计算生物信息学微信公众号BMELab。
Email: 595289825@qq.com
2. 研究方向：
[1] 生物信息学与计算生物学
[2] 临床医疗数据挖掘
3.主持科研课题
[1] 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。
[2] 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，已结题，主持。
[3] 云南省应用基础研究计划面上项目，202001AT070024，融合单细胞转录组数据的miRNA调控网络与功能模块识别研究，2020/6-2023/5，10万元，在研，主持。
[4] 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，已结题，主持。
[5] 大理大学第九批中青年学术带头人后备人才项目，2018/1-2021/12，3万元，已结题，主持。
[6] 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。
[7] 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。
[8] 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。
[9] 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。
4.主要成果
[1] Junpeng Zhang, Lin Liu, Wu Zhang, Xiaomei Li, Chunwen Zhao, Sijing Li, Jiuyong Li, Thuc Duy Le. miRspongeR 2.0: an enhanced R package for exploring miRNA sponge regulation. Bioinformatics Advances. 2022, 2(1): vbac063.
[2] Junpeng Zhang, Yun Zheng, Juan Xu. Editorial: computational identification of ceRNA regulation. Frontiers in Molecular Biosciences. 2022, 9: 937505.
[3] Junpeng Zhang, Lin Liu, Taosheng Xu, Wu Zhang, Jiuyong Li, Nini Rao, Thuc Duy Le. Time to infer miRNA sponge modules. Wiley Interdisciplinary Reviews: RNA. 2022, 13(2): e1686.
[4] Junpeng Zhang, Lin Liu, Taosheng Xu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le. miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data. RNA Biology, 2021, 18(12):2308-2320.
[5] Junpeng Zhang, Lin Liu, Taosheng Xu, Wu Zhang, Chunwen Zhao, Sijing Li, Jiuyong Li, Nini Rao, Thuc Duy Le. Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data. BMC Bioinformatics, 2021, 22:578.
[6] Junpeng Zhang, Thin Nguyen, Buu Truong, Lin Liu, Jiuyong Li, Thuc Duy Le. Computational methods for predicting autism spectrum disorder from gene expression data. In International Conference on Advanced Data Mining and Applications (ADMA 2020), Lecture Notes in Computer Science, vol 12447. Springer, Cham. 2020. DOI: 10.1007/978-3-030-65390-3_31.
[7] Weili Jiang, Kangneng Zhou, Chenchen Xiong, Guodong Du, Chubin Ou*, Junpeng Zhang*. KSCB: a novel unsupervised method for text sentiment analysis. Applied Intelligence. 2023, 53: 301–311.
[8] Chenchen Xiong, Shaoping Sun, Weili Jiang, Lei Ma*, Junpeng Zhang*. ASDmiR: a stepwise method to uncover miRNA regulation related to autism spectrum disorder. Frontiers in Genetics, 2020, 11:562971.
[9] 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. PLoS Computational Biology, 2020, 16(4):e1007851.
[10] 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.
[11] 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):613.
[12] 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.
[13] 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.
[14] 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.
[15] 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.
[16] 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.
[17] 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.
[18] 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.
[19] 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.
[20] Thuc Duy Le#, Junpeng Zhang#, Lin Liu, Jiuyong Li. Computational methods for identifying miRNA sponge interactions. Briefings in Bioinformatics, 2017, 18 (4): 577-90.
[21] 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.
[22] 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.
[23] 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.
[24] 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.
[25] Thuc Duy Le, Junpeng Zhang, Lin Liu, Jiuyong Li. Ensemble methods for miRNA target prediction from expression data. PLoS ONE, 2015, 10(6): e0131627.
[26] 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.
[27] 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.
[28] Junpeng Zhang, Bing Liu, Jianfeng He, Lei Ma, 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.
[29] 张俊鹏, 饶妮妮, 王光斌. ceRNA竞争模块识别方法、装置、电子设备及存储介质: 中国, 专利: ZL202010158035.3, 2021年06月08日.
[30] 张俊鹏, 饶妮妮, 王光斌. miRNA因果调控网络识别方法、装置、电子设备及存储介质: 中国, 专利: ZL202010146037.0, 2021年04年09日.
[31] 张俊鹏, 饶妮妮, 王光斌. 一种ncRNA协同竞争网络识别方法和装置: 中国, 专利: ZL201911229601.9, 2021年04月06日.
[32] 张俊鹏, 饶妮妮, 王光斌. 一种miRNA海绵互作对的识别方法: 中国, 专利: ZL201911064153.1, 2021年05月14日.
[33] 张俊鹏, 饶妮妮, 王光斌. 单细胞miRNA调控网络的识别方法、装置、设备及存储介质: 中国, 专利: ZL201910751340.0, 2021年06年04日.
[34] 张俊鹏, 饶妮妮. miRNA海绵模块的识别方法和装置: 中国, 专利: ZL201910684738.7, 2021年06月08日.
[35] 张俊鹏, 赵春文, 李司婧, 杨燕婷. 基因模块群的相似性度量方法、装置、电子设备及存储介质: 中国, 专利: ZL202111214178.2, 2022年08月23日.