Tel: 0086-21-31242090

Email: chenli_imib@fudan.edu.cn

Office Adrress: Room C7015, Interdisciplinary Building No.2, Fudan University 

Personal Profile

Dr. Li Chen obtained his B.S. in Chemistry from Peking University in 2013, and Ph.D. in Chemistry at Princeton University in 2019. After graduation, he became a postdoctoral fellow at Lewis-Sigler Institute at Princeton University. In late 2020, he started his lab at Institute of Metabolism and Integrative Biology (IMIB) at Fudan University. 

Dr. Li Chen has studied metabolomics and metabolic flux for over 7 years. His main publications include (1) developed NetID algorithm that annotates untargeted LC-MS metabolomics data by combining known biochemical and metabolomics principles with a global network optimization strategy (Nature Methods, 2021); (2) discovered a novel regulatory mechanism for folic acid and NADPH metabolic pathways using metabolomics and isotope tracing techniques (Nature Metabolism, 2019); (3) revealed NADP(H) is the actual target of Nocturnin, an enzyme regulated by circadian rhythms, while Nocturnin was considered a deadenylase that hydrolyzes mRNA for more than a decade (Nature Communication, 2019).

Research Interests

Our lab focus on developing novel metabolomics and metabolic flux analysis methods, integrating with bioinformatics, molecular biology, and multi-omics approaches, to gain a holistic understanding of cellular metabolism and metabolic diseases. Specifically, we are working on:

1. integrating bioinformatics and machine-learning approaches with metabolomics big data to better perform metabolic pathway analysis;

2. developing novel stable isotope tracer techniques to monitor the metabolic pathway activites;

3. studying how small molecule cofactors (such as NAD, folic acid, thiamine, etc.) impact metabolic pathways, and exploring their physiological and pathological role in human health and disease.

Selected Publications

1. Li Chen, Wenyun Lu, Lin Wang, Xi Xing, Ziyang Chen, Xin Teng, Xianfeng Zeng, Antonio D. Muscarella, Yihui Shen, Alexis Cowan, Melanie R. McReynolds, Brandon J. Kennedy, Ashley M. Lato, Shawn R. Campagna, Mona Singh, Joshua D. Rabinowitz. Metabolite discovery through global annotation of untargeted metabolomics data. Nat Methods. 2021, 18(11):1377–85.

2. Li Chen, Zhaoyue Zhang, Atsushi Hoshino, Henry D. Zheng, Michael Morley, Zoltan Arany, Joshua D. Rabinowitz. NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism. Nature Metabolism. 2019, 1(3):404–15.

3. Zhikun Jia, Qiongju Qiu, Ruiping He, Tianyu Zhou, Li Chen. Identification of Metabolite Interference Is Necessary for Accurate LC-MS Targeted Metabolomics Analysis. Anal Chem. 2023, 95(20):7985–92.

4. Michael A. Estrella#, Jin Du#, Li Chen#, Sneha Rath, Eliza Prangley, Alisha Chitrakar, Tsutomu Aoki, Paul Schedl, Joshua Rabinowitz*, Alexei Korennykh*. The metabolites NADP+ and NADPH are the targets of the circadian protein Nocturnin (Curled). Nature Communications. 2019, 10(1):2367.

5. Zhaoyue Zhang#, Li Chen#, Ling Liu, Xiaoyang Su*, Joshua D. Rabinowitz*. Chemical basis for deuterium labeling of fat and NADPH. J Am Chem Soc. 2017, 139(41):14368−14371.

6. Cholsoon Jang, Li Chen, Joshua D. Rabinowitz. Metabolomics and Isotope Tracing. Cell. 2018, 173(4):822–37. 

7. Chen L, Lu W, Wang L, Xing X, Chen Z, Teng X, Zeng X, Muscarella A D, Shen Y, Cowan A, McReynolds M R, Kennedy B J, Lato A M, Campagna S R, Singh M, Rabinowitz J D. Metabolite Discovery through Global Annotation of Untargeted Metabolomics Data. Nat Methods 2021, 18 (11), 1377–1385. https://doi.org/10.1038/s41592-021-01303-3.

8. Chen L, Zhang Z, Hoshino A, Zheng H,D, Morley M, Arany Z, and Rabinowitz J D. NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism. Nature Metabolism, 2019, 1: 404-415.  https://doi.org/10.1038/s42255-019-0043-x.

9. Estrella M* ,Du J*, Chen L*, Rath S, Prangley E, Chitrakar A, Aoki T, Schedl P, Rabinowitz J, and Korennykh A. The Metabolites NADP+ and NADPH are the Targets of Circadian Protein Nocturnin (Curled). Nature Communication, 2019, 10, 2367. https://doi.org/10.1038/s41467-019-10125-z. (*Co-first author)

10. Jang C, Chen L, Rabinowitz J D. Metabolomics and isotope tracing. Cell, 2018, 173, 822-837. https://doi.org/10.1016/j.cell.2018.03.055.

11.  Zhang Z*, Chen L*, Liu L, Su X, Rabinowitz J D. Chemical Basis for Deuterium Labeling of Fat and NADPH. J Am Chem Soc, 2017, 139, 14368-14371. https://doi.org/10.1021/jacs.7b08012.  (*Co-first author)

12. Chen L, Ducker G S, Lu W, Teng X, Rabinowitz J D. An LC-MS chemical derivatization method for the measurement of five different one-carbon states of cellular tetrahydrofolate. Anal Bioanal Chem, 2017, 409, 5955-5964. https://doi.org/10.1007/s00216-017-0514-4.