蔡云鹏（Cai Yunpeng），中心执行主任，博士，研究员，博士生导师。 中国科学院深圳先进技术研究院 生物医学信息技术研究中心执行主任、 广东省健康大数据分析技术工程中心主任、深圳市健康大数据分析技术工程实验室主任。
主要研究方向为生物信息学、健康信息学、医学健康大数据挖掘及医疗人工智能。 2001年毕业于清华大学工程物理系，2007年于清华大学计算机科学与技术系获得博士学位，2007年至2011年在美国佛罗里达大学生物技术多学科研究中心从事博士后研究，2011年6月起加入中国科学院深圳先进技术研究院。现任中国科学院深圳先进技术研究院生物医学信息技术研究中心执行主任、健康大数据智能分析技术国家地方联合工程实验室副主任、广东省健康大数据分析技术工程中心主任、深圳市健康大数据分析技术工程实验室主任。已发表学术论文八十余篇，包括作为主要作者在Nucleic Acids Research, Briefings in Bioinformatics, PLOS Computational Biology 、IEEE Trans NNLS、IEEE TOC等生物信息和机器学习顶级期刊上的多篇论文，引用近2000次，已获得授权发明专利22项，软件著作权6项。主持广东省应用型科技研发专项、国家科技支撑计划（子课题）等项目，曾担任国家863计划课题副组长。作为参与人获广东省科学技术奖二等奖、深圳市技术发明一等奖、中华医学会卫生管理奖各一项。
联系方式：yp.cai@siat.ac.cn
代表性学术论文：
1. Graph Polish: a novel graph generation paradigm for molecular optimization. Ji C, Zheng Y, Wang R, Cai Y, Wu H. IEEE Transactions on Neural Networks and Learning Systems. 2021.
2. Smoothness Sensor: Adaptive Smoothness-Transition Graph Convolutions for Attributed Graph Clustering. Ji C, Chen H, Wang R, Cai Y, Wu H. IEEE Transactions on Cybernetics. 2021.
3. Risk Prediction of Renal Failure for Chronic Disease Population Based on Electronic Health Record Big Data. Yang Y, Li Y, Chen R, Zheng J, Cai Y, Fortino G. Big Data Research. 2021 Jul 15;25:100234.
4. Risk stratification of cutaneous melanoma reveals carcinogen metabolism enrichment and immune inhibition in high-risk patients，X Li, Y Cai, Aging 12 (16), 16457, 2020
5. Heterogeneous graph convolutional networks and matrix completion for miRNA-disease association prediction, R Zhu, C Ji, Y Wang, Y Cai, H Wu, Frontiers in Bioengineering and Biotechnology 8, 901,2020
6. Accurate Prediction of Coronary Heart Disease for Patients With Hypertension From Electronic Health Records With Big Data and Machine-Learning Methods: Model Development and Performance Evaluation, Z Du, Y Yang, J Zheng, Q Li, D Lin, Y Li, J Fan, W Cheng, XH Chen, Y Cai, JMIR medical informatics 8 (7), e17257, 2020
7. Better prognostic determination and feature characterization of cutaneous melanoma through integrative genomic analysis. X Li, Y Cai, Aging 11, 6, 2019
8. A Systems Analysis of the Relationships Between Anemia and Ischemic Stroke Rehabilitation Based on RNA-Seq Data, Y Wang, X Huang, J Liu, X Zhao, H Yu, Y Cai, Frontiers in Genetics 10, 456, 2, 2019
9. A novel hybrid network of fusing rhythmic and morphological features for atrial fibrillation detection on mobile ECG signals, X Fan, Z Hu, R Wang, L Yin, Y Li, Y Cai, Neural Computing and Applications, 1-13,1,2019
10. Methylation-Based Classification of Cervical Squamous Cell Carcinoma into Two New Subclasses Differing in Immune-Related Gene Expression, X Li, Y Cai, International journal of molecular sciences 19 (11), 3607,3, 2018
11. A survey on database resources for microRNA–disease relationships, Y Wang, Y Cai, Briefings in functional genomics 16 (3), 146-151,2017
12. ESPRIT-Forest: Parallel clustering of massive amplicon sequence data in subquadratic time, Yunpeng Cai*，Wei Zheng, Jin Yao, Yujie Yang, Volker Mai, Qi Mao, Yijun Sun, PLOS Computational Biology 13 (4), e1005518, 2017
13. A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis. Sun*, Yijun and Cai, Yunpengand Huse, Susan M and Knight, Rob and Farmerie, William G and Wang, Xiaoyu and Mai, Volker. Briefings in bioinformatics: 2012 ,13(1) ,107--121
14. ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time. Cai, Yunpeng and Sun, Yijun*. Nucleic acids research: 2011 ,39(14) ,e95--e95 (155引用)
15. Advanced computational algorithms for microbial community analysis using massive 16S rRNA sequence data. Sun, Yijun and Cai, Yunpeng(共一作)and Mai, Volker and Farmerie, William and Yu, Fahong and Li, Jian and Goodison, Steve. Nucleic acids research: 2010 ,38(22) ,e205--e205 (172引用)
16. ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Sun, Yijun* and Cai, Yunpeng （共一作）and Liu, Li and Yu, Fahong and Farrell, Michael L and McKendree, William and Farmerie, William. Nucleic acids research: 2009 ,37(10) ,e76--e76 (312引用)
17. Parallel Hierarchical Clustering in Linearithmic Time for Large-Scale Sequence Analysis. Mao, Qi and Zheng, Wei and Wang, Li and Cai, Yunpeng and Mai, Volker and Sun, Yijun. Data Mining (ICDM), 2015 IEEE International Conference on: 2015 ,310--319 （CCF B类会议）
18. Learning Sparse Gaussian Bayesian Network Structure by Variable Grouping. Yang, Jie and Leung, Henry and Yiu, SM and Cai, Yunpeng and Chin, Francis YL. Data Mining (ICDM), 2014 IEEE International Conference on: 2014 ,1073--1078 （CCF B类会议）
19. The hindgut lumen prokaryotic microbiota of the termite Reticulitermes flavipes and its responses to dietary lignocellulose composition. Boucias, Drion G and Cai, Yunpeng and Sun, Yijun and Lietze, Verena-Ulrike and Sen, Ruchira and Raychoudhury, Rhitoban and Scharf, Michael E. Molecular ecology: 2013 (117引用)
20. IgM repertoire biodiversity is reduced in HIV-1 infection and systemic lupus erythematosus. Yin, Li and Hou, Wei and Liu, Li and Cai, Yunpeng and Wallet, Mark Andrew and Gardner, Brent Paul and Chang, Kaifen and Lowe, Amanda Catherine and Rodriguez, Carina Adriana and Sriaroon, Panida and others. Frontiers in immunology: 2013 ,4
21. Differential impacts of juvenile hormone, soldier head extract and alternate caste phenotypes on host and symbiont transcriptome composition in the gut of the termite Reticulitermes flavipes. Sen, Ruchira and Raychoudhury, Rhitoban and Cai, Yunpeng and Sun, Yijun and Lietze, Verena-Ulrike and Boucias, Drion G and Scharf, Michael E. BMC genomics: 2013 ,14(1) ,491
22. Comparative metatranscriptomic signatures of wood and paper feeding in the gut of the termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). Raychoudhury, Rhitoban and Sen, Ruchira and Cai, Yunpeng and Sun, Yijun and Lietze, Verena-Ulrike and Boucias, Drion G and Scharf, Michael E. Insect Molecular Biology: 2013
23. A Candidate Molecular Biomarker Panel for the Detection of Bladder Cancer. Urquidi, Virginia and Goodison, Steve and Cai, Yunpeng and Sun, Yijun and Rosser, Charles J. Cancer Epidemiology Biomarkers & Prevention: 2012 ,21(12) ,2149--2158
24. Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences. Wang, Xiaoyu and Cai, Yunpeng and Sun, Yijun and Knight, Rob and Mai, Volker. The ISME Journal: 2011
主持的代表性项目列表：
项目来源 | 经费(万元) | 项目名称 | 起止时间 |
中国科学院先导计划（课题负责人） | 300 | 新型生物医学研究支撑系统的数据与知识整合研究服务体系 | 2020-2025 |
国家科技支撑计划（单位负责人） | 125 | 缺血性脑血管病和脑肿瘤防治关键技术研究 | 2015-2017 |
国家自然科学基金 | 70 | 面向进化基因组学的高通量测序数据流形建模 | 2015-2018 |
国家自然科学基金 | 20 | 基于伪度量空间分割树的超高深度测序比对处理与定量基因组学分析 | 2013-2015 |
广东省应用型科技研发专项 | 500 | 穿戴式睡眠监测与夜间心脑血管事件预警系统 | 2016-2018 |
中国科学院科技服务网络（子课题负责人） | 98 | 运动促进健康技术服务网络与典型行业应用示范 | 2016-2018 |
深圳市发改委 | 500 | 健康大数据分析技术工程实验室 | 2016-2018 |
深圳市海外高层次人才创新创业计划 | 100 | 脑卒中基因表达谱的系统生物学研究及应用 | 2014-2015 |
深圳市科创委深港创新圈 | 300 | 基于多源数据的精准健康管理方法与系统 | 2021-2013 |
深圳市科创委技术攻关(单位负责人) | 125 | 面向代谢疾病的肠道菌群分析关键技术研发 | 2017-2019 |
