曾坚阳

曾坚阳
曾坚阳 研究员

清华大学生命科学学院

个人简历:  

 

2012年至今,清华大学,交叉信息研究院,Tenure-Track助理教授

2016年至今,清华大学,生命科学学院,兼职Tenure-Track助理教授

2011年-2012年,美国杜克大学(Duke University),计算机科学系和杜克医学院,博士后

2006年-2011年,美国杜克大学(Duke University),计算机科学系,博士

1999年-2002年,浙江大学,硕士

1995年-1999年,浙江大学,学士位

 

主要科研领域及方向:         

 

主要研究方向包括计算生物学、机器学习和大规模数据分析,目前侧重在:

1. 多组学分析、基因组的三维结构和基因调控;

2.基于人工智能的药物发现;

3. 冷冻电镜技术计算方法的开发;

4.人工智能、机器学习。

代表论文:     

1. Zhenhai Du, Hui Zheng, Bo Huang, Rui Ma, Jingyi Wu, Xianglin Zhang, Jing He, Yunlong Xiang, Qiujun Wang, Yuanyuan Li, Jing Ma, Xu Zhang, Ke Zhang, Yang Wang, Michael Q. Zhang, Juntao Gao, Jesse R. Dixon, Xiaowo Wang, Jianyang Zeng and Wei Xie*. Allelic reprogramming of 3D chromatin architecture during early mammalian development. Nature. 2017.

2. Yunan Luo#, Xinbin Zhao#, Jingtian Zhou#, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng*, Ligong Chen* and Jianyang Zeng*. A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. Nature Communications. 2017. Accepted.

3. Shuya Li#, Fanghong Dong#, Yuexin Wu#, Sai Zhang, Chen Zhang, Xiao Liu, Tao Jiang, Jianyang Zeng*. A deep boosting based approach for capturing the sequence binding preferences of RNA-binding proteins from high-throughput CLIP-seq data. Nucleic Acids Research. 2017.

4. Sai Zhang#, Hailin Hu#, Jingtian Zhou#, Xuan He, Tao Jiang, Jianyang Zeng*. Analysis of ribosome stalling and translation elongation dynamics by deep learning. Cell Systems. 2017. In press.

5. Dapeng Xiong, Jianyang Zeng*, Haipeng Gong*. A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy. Bioinformatics. 2017.

6. Sai Zhang, Hailin Hu, Tao Jiang, Lei Zhang* and Jianyang Zeng*. Predicting translation initiation sites by deep learning. ISMB/ECCB. Bioinformatics. 2017.

7. Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng*, Ligong Chen*, Jianyang Zeng*. A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. RECOMB. 2017.

8. Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang and Jianyang Zeng*. ROSE: a deep learning based framework for predicting ribosome stalling. RECOMB. 2017.

9. Sai Zhang, Muxuan Liang, Zhongjun Zhou, Chen Zhang, Ning Chen, Ting Chen and Jianyang Zeng*. Elastic Restricted Boltzmann Machines for Cancer Data Analysis. Quantitative biology. 2017. Cover Article.

10. Feng Wang, Huichao Gong, Gaochao Liu, Meijing Lia, Chuangye Yana, Tian Xia*, Xueming Li*, Jianyang Zeng*. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM . Journal of Structural Biology. Volume 195, Issue 3. 2016.

11. Yuchao Pan, Yuxi Dong, Jingtian Zhou, Mark Hallen, Bruce R. Donald*, Jianyang Zeng* and Wei Xu*. cOSPREY: A Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design. Journal of Computational Biology. 2016. Code.

12. Yunan Luo, Jianyang Zeng, Bonnie Berger* and Jian Peng*. Low-density localitysensitive hashing boosts metagenomic binning. International Conference on Research in Computational Molecular Biology (RECOMB). 2016.

13. Sai Zhang, Jingtian Zhou, Hailin Hu, Haipeng Gong, Ligong Chen, Chao Cheng*, Jianyang Zeng*. A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Research. 2015. (Impact Factor: 10.162).

14. Yichao Zhou, Bruce R. Donald, Jianyang Zeng*. Parallel computational protein design. Methods in Molecular Biology. 2015.

15. Dapeng Xiong, Jianyang Zeng and Haipeng Gong*. RBRIdent: an algorithm for improved identification of RNA-binding residues in proteins from primary sequences. Proteins: Structure, Function, and Bioinformatics. 2015.

16. Siyu Wang, Jinbo Xu and Jianyang Zeng*. Inferential modeling of 3D chromatin structure. Nucleic Acids Research. 2015. (Impact Factor: 10.162).

17. Huichao Gong, Sai Zhang, Jiangdian Wang, Haipeng Gong and Jianyang Zeng*. Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data. International Conference on Research in Computational Molecular Biology (RECOMB 2015). Also in the Journal of Computational Biology. 2015.

18. Yichao Zhou, Yuexin Wu and Jianyang Zeng*. Computational Protein Design Using AND/OR Branch-and-Bound Search. International Conference on Research in Computational Molecular Biology (RECOMB 2015). Also in the Journal of Computational Biology. 2015.

19. Muxuan Liang, Zhizhong Li, Ting Chen and Jianyang Zeng*. Integrative Data Analysis of Multi-platform Cancer Data with a Multimodal Deep Learning Approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2015. Code.

20. Yichao Zhou and Jianyang Zeng*. Massively Parallel A* Search on a GPU. Proceeding of the Twenty-Ninth AAAI Conference on Artificial Intelligence (AAAI 2015). 2015. Oral Paper. PDF, Appendix. Code. [Acceptance Rate (Oral): 11.95%]

21. Yufeng Liu, Jianyang Zeng and Haipeng Gong*. Improving the orientation-dependent statistical potential using a reference state. Proteins: Structure, Function, and Bioinformatics. 82(10):2383-93. 2014. PDF.

22. Yichao Zhou, Wei Xu, Bruce R. Donald, Jianyang Zeng*. An Efficient Parallel Algorithm for Accelerating Computational Protein Design. ISMB. July 2014. Bioinformatics. PDF, Software.

23. Fan Yang, Jinbo Xu and Jianyang Zeng*. Drug-Target Interaction Prediction by Integrating Chemical, Genomic, Functional and Pharmacological Data. Pacific Symposium on Biocomputing (PSB). 2014. PDF, Supplementary Material.

24. Yuhao Wang, Jianyang Zeng*. Predicting Drug-Target Interactions Using Restricted Boltzmann Machines. Proceedings of 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB)/12th European Conference on Computational Biology (ECCB). July 2013. Bioinformatics. 2013 July 1; 29(13): i126-i134. PDF, Supplementary Material.

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