86-13269920987; 550238460@qq.com

Work Experiences

Jul 2020-Present Assistant professor, Institute of Molecular Medicine, Shanghai Jiao Tong University, Shanghai, China.

Jul 2018-Jun 2020 Postdoctoral fellow, Institute of Molecular Medicine, Shanghai Jiao Tong University, Shanghai, China.

Education

Sep 2013-Jun 2018 Ph.D. in Bioinformatics, College of Life Science, Beijing Normal University, Beijing, China
Sep 2009-Jun 2013 B.S. of Mathematics and applied mathematics, Lanzhou University, Lanzhou, China

Honors and Awards

2019  Postdoctoral Incentive Program of Shanghai Jiao Tong University School of Medicine
2013  Outstanding graduate of Lanzhou University
2010  Meritorious Winner of Mathematical Contest in Modeling
2010  National Scholarship

Publications 

1. Jia Song#, Yao Liu#, Xuebing Zhang, Qiuyue Wu, Juan Gao, Wei Wang, Jin Li*, Yanling Song*, Chaoyong Yang*. Entropy Subspace Separation-based Clustering for Noise Reduction (ENCORE) of scRNA-seq Data. Nucleic Acids Res., 2021, 49, e18.

2. Jia Song, Yuan Zheng, Mengjiao Huang, Lingling Wu, Wei Wang, Zhi Zhu, Yanling Song*, Chaoyong Yang. A sequential multi-dimensional analysis algorithm for aptamer identification based on structure analysis and machine learning. Anal. Chem., 2020, 92, 3307-3314.

3. Jia Song, Sisi Zheng, Nhung Nguyen, Youjun Wang, Yubin Zhou, Kui Lin*. Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family. BMC Bioinform., 2017, 18, 439-446.

4. Liyuan Lin#, Jia Song#, Jian Li#, Xiaolei Zuo, Hong Wei*, Chaoyong Yang*, Wei Wang*. Imaging the in vivo Growth Patterns of Bacteria in Human Gut Microbiota. Gut Microbes, 2021, 13, 1.

5. Fengsheng Li#, Jia Song#, Yingkun Zhang#, Shuaikang Wang, Li Lin, Chaoyong Yang*, Peng Li*, He Huang*. LINT-web: a web-based intra-omic data mining toolbox for lipidomic dataset. Small Methods, 2021, 2100206.

6. Ru Chen#, Jia Song#, Liyuan Lin, Jie Liu*, Chaoyong Yang*, Wei Wang*. Visualizing the Growth and Division of Rat Gut Bacteria by D-Amino Acid-based in vivo Labeling and FISH Staining. Front. Mol. Biosci., 2021. DOI: 10.3389/fmolb.2021.681938

7. Xing Xu#, Qianqian Zhang#, Jia Song#, Qingyu Ruan#, Weidong Ruan, Yujie Chen, Jian Yang, Xuebing Zhang, Yanling Song, Zhi Zhu, Chaoyong Yang*. A Highly Sensitive, Accurate, and Automated Single-Cell RNA Sequencing Platform with Digital Microfluidics. Anal. Chem., 2020, 92, 8599-8606.

8. Li Lin, Yufeng Zhang, Weizhou Qian, Yao Liu, Yingkun Zhang, Fanghe Lin, Cenxi Liu, Guangxing Lu, Di Sun, Xiaoxu Guo, YanLing Song, Jia Song*, Chaoyong Yang*, Jin Li*. LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis. Proceedings of the National Academy of Sciences of the United States of America, 2022, 119, e2119767119.

9. Kun Yin, Meijuan Zhao, Li Lin, Yinwen Chen, Shanqing Huang, Chun Zhu, Xuan Liang, Fanghe Lin, Haiping Wei, Huimin Zeng, Zhi Zhu, Jia Song*, Chaoyong Yang*. Well-Paired-Seq: A Size-Exclusion and Locally Quasi-Static Hydrodynamic Microwell Chip for Single-Cell RNA-Seq. Small Methods, 2022, 2200341. 

10. Ziyang Lu, Fanghe Lin, Tao Li, Jinhui Wang, Cenxi Liu, Guangxing Lu, Bin Li, MingPei Pan, Shaohua Fan, Junqiu Yue, He Huang, Jia Song*, Chao Gu*; Jin Li*. Identification of Clinical and Molecular Features of Recurrent Serous Borderline Ovarian Tumour. eClinicalMedicine, 2022, 46, 101377.

11. Qianqian Zhang#, Xing Xu#, Li Lin#, Jian Yang, Xing Na, Xin Chen, Lingling Wu, Jia Song*, Chaoyong Yang*. Cilo-seq: highly sensitive cell-in-library-out single-cell transcriptome sequencing with digital microfluidics. Lab Chip, 2022, 22, 1971-1979.

12. Yingwen Chen, Jia Song*, Qingyu Ruan, Xi Zeng, Lingling Wu, Linfeng Cai, Xuanqun Wang, Chaoyong Yang*. Single-cell sequencing methodologies: from transcriptome to multi-dimensional measurement. Small Methods, 2021, 5, 2100111.

13. Yingwen Chen, Weizhou Qian, Li Lin, Linfeng Cai, Kun Yin, Shaowei Jiang, Jia Song*, Ray P.S. Han*, and Chaoyong Yang*; Mapping gene expression in the spatial dimension. Small Methods, 2021, 5, 2100722. 

14. Jia Song, Xia Han, Kui Lin*. Evolutionary patterns of 64 vertebrate genomes (species) revealed by phylogenomics analysis of protein-coding gene families. BioRxiv. DOI: 10.1101/2020.03.31.017467

15. Liyuan Lin, Yahui Du, Jia Song, Wei Wang*, Chaoyong Yang*. Imaging Commensal Microbiota and Pathogenic Bacteria in the Gut. Acc. Chem. Res., 2021, 54, 9, 2076.

16. Liyuan Lin, Jia Song, Yahui Du, Qiuyue Wu, Juan Gao, Yanling Song, Chaoyong Yang*, Wei Wang*. Quantification of Bacterial Metabolic Activities in the Gut by D- Amino Acid-based in vivo Labeling, Angew. Chem. Int. Ed., 2020, 59, 11923-11926.