教育经历

(1) 2016-1至2016-4, 斯坦福大学, 统计, 访问学生, 导师: Wing Hung Wong
(2) 2012-9至2017-7, 清华大学, 自动化, 博士, 导师: 李衍达
(3) 2008-9至2012-7, 西安交通大学, 自动化, 学士

工作经历

(1) 2020-12至现在, 上海交通大学, 自动化系, 副教授
(2) 2017-7至2017-9, 百度在线网络技术（北京）有限公司, 大数据实验室, 高级研发工程师

(3) 2017-10至2020-12, 卡内基梅隆大学计算机学院机器学习系, 博士后, 导师: Ziv Bar-Joseph

代表性工作

1. Cell clustering for spatial transcriptomics data with graph neural networks; Nature Computational Science; Jiachen Li; Siheng Chen; Xiaoyong Pan; Ye Yuan*; Hong-Bin Shen*, 2022 [Nature子刊]
2.  Deep learning for inferring gene relationships from single-cell expression data; Proceedings of the National Academy of Sciences of the United States of America (PNAS); 116 (52); 27151-27158; Ye Yuan; Ziv Bar-Joseph*,2019 [美国国家科学院院刊]
3. Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit; Proceedings of the National Academy of Sciences of the United States of America (PNAS); 112 (10); 3158-3163; Ye Yuan#; Bing Liu#; Peng Xie; Michael Q. Zhang; Yanda Li; Zhen Xie*; Xiaowo Wang*, 2015 [美国国家科学院院刊]
4. GCNG: graph convolutional networks for inferring gene interaction from spatial transcriptomics data; Genome Biology; 21 (1); 1-16; Ye Yuan; Ziv Bar-Joseph*, 2020 [5年影响因子19]
5. Deep learning of gene relationships from single cell time-course expression data; Briefings in            Bioinformatics, Ye Yuan, Ziv Bar-Joseph*, 2021
6. Regulation by competition: a hidden layer of gene regulatory network; Quantitative Biology; 7 (2); 110-121; Lei Wei#; Ye Yuan#; Tao Hu; Shuailin Li; Tianrun Cheng; Jinzhi Lei; Zhen Xie; Michael Q. Zhang; Xiaowo Wang*, 2019
7. A quantitative understanding of microRNA- mediated competing endogenous RNA regulation; Quantitative Biology; 4 (1); 47-57; Ye Yuan#; Xinying Ren#; Zhen Xie; Xiaowo Wang*, 2016
8. Challenges in large-scale synthetic gene circuits design; Sheng wu gong cheng xue bao = Chinese journal of biotechnology; 33 (3); 372-385; Lei Wei; Ye Yuan; Xiaowo Wang*, 2017
9. Reconstructing SARS-CoV-2 response signaling and regulatory networks; bioRxiv; Jun Ding#, Jose Lugo-Martinez#, Ye Yuan#, Darrell N. Kotton, Ziv Bar-Joseph*, 2021
10. Causal inference using deep neural networks; arXiv; Ye Yuan#, Xueying Ding#, Ziv Bar-Joseph*, 2021
11. Cell Type Assignments for Spatial Transcriptomics Data; bioRxiv, Haotian Teng, Ye Yuan, Ziv Bar-Joseph*, 2021
12. CINS: Cell Interaction Network inference from Single cell expression data; bioRxiv; Ye Yuan, Carlos Cosme Jr., Taylor Sterling Adams, Jonas Schupp, Koji Sakamoto, Nikos Xylourgidis, Matthew Ruffalo, Naftali Kaminski, Ziv Bar-Joseph*, 2021

担任 Nature Machine Intelligence、Cell Systems、 Briefings in Bioinformatics、 Bioinformatics、 PLOS Computational Biology、 ISMB 等多个知名生物信息学期刊、会议审稿人

招生、招聘信息

• 博士生、硕士生：欢迎计划明年入学同学提前联系。
• 本科生：长期接收未来准备出国、希望本科阶段发表论文的同学加入课题组进行研究、做毕业设计。