Lab of Imaging and Systems Metabolism
Systems Biology
Metabolic pathway preference for energy production
Shen Y, Dinh HV, Cruz E, Chen Z, Bartman CR, Xiao T, Call CM, Ryseck RP, Pratas J, Weilandt D, Baron H, Subramanian A, Fatma Z, Wu ZY, Dwaraknath S, Hendry JI, Tran V, Yang L, Yoshikuni Y, Zhao H, Maranas CD, Wühr MH†, Rabinowitz JD †. Mitochondrial ATP generation is more proteome efficient than glycolysis. Nat. Chem. Biol. 2023 https://doi.org/10.1038/s41589-024-01571-y (†co-corresponding)
Bartman CR, Weilandt DR, Shen Y, Lee WD, Han Y, TeSlaa T, Jankowski CSR, Samarah L, Park NR, da Silva-Diz V, Aleksandrova M, Gultekin Y, Marishta A, Wang L, Yang L, Roichman A, Bhatt V, Lan T, Hu Z, Xing X, Lu W, Davidson S, Wühr M, Vander Heiden MG, Herranz D, Guo JY, Kang Y, Rabinowitz JD. Slow TCA flux and ATP production in primary solid tumours but not metastases. Nature. 2023 Feb;614(7947):349-357. PubMed Central PMCID: PMC10288502.
Xiao T, Khan A, Shen Y, Chen L, Rabinowitz JD. Glucose feeds the tricarboxylic acid cycle via excreted ethanol in fermenting yeast. Nat Chem Biol. 2022 Dec;18(12):1380-1387. PubMed PMID: 35970997.
Systems biology of yeast metabolism
Hu M, Dinh HV, Shen Y, Suthers PF, Foster CJ, Call CM, Ye X, Pratas J, Fatma Z, Zhao H, Rabinowitz JD, Maranas CD. Comparative study of two Saccharomyces cerevisiae strains with kinetic models at genome-scale. Metab Eng. 2023 Mar;76:1-17. PubMed PMID: 36603705.
Suthers PF, Dinh HV, Fatma Z, Shen Y, Chan SHJ, Rabinowitz JD, Zhao H, Maranas CD. Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. Metab Eng Commun. 2020 Dec;11:e00148. PubMed Central PMCID: PMC7586132.
Dinh HV, Suthers PF, Chan SHJ, Shen Y, Xiao T, Deewan A, Jagtap SS, Zhao H, Rao CV, Rabinowitz JD, Maranas CD. A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. Metab Eng Commun. 2019 Dec;9:e00101. PubMed Central PMCID: PMC6838544.
Optical Imaging
Imaging metabolic activity
Shen Y, Wei L, Min W. Raman Imaging Reveals Insights into Membrane Phase Biophysics in Cells. J Phys Chem B. 2023 Jul 20;127(28):6233-6240. PubMed PMID: 37431772.
Zhang L*, Shi L*, Shen Y*, Miao Y, Wei M, Qian N, Liu Y, Min W. Spectral tracing of deuterium for imaging glucose metabolism. Nat Biomed Eng. 2019 May;3(5):402-413. PubMed Central PMCID: PMC6599680.
Zhu XG, Puthenveedu SN, Shen Y, La K, Ozlu C, Wang T, Klompstra D, Gultekin Y, Chi J, Fidelin J, Peng T, Molina H, Hang HC, Min W, Birsoy K. CHP1 Regulates Compartmentalized Glycerolipid Synthesis by Activating GPAT4. Mol Cell. 2019 Apr 4;74(1):45-58.e7. PubMed Central PMCID: PMC6450717.
Shi L, Zheng C, Shen Y, Chen Z, Silveira ES, Zhang L, Wei M, Liu C, de Sena-Tomas C, Targoff K, Min W. Optical imaging of metabolic dynamics in animals. Nat Commun. 2018 Aug 6;9(1):2995. PubMed Central PMCID: PMC6079036.
Shen Y, Zhao Z, Zhang L, Shi L, Shahriar S, Chan RB, Di Paolo G, Min W. Metabolic activity induces membrane phase separation in endoplasmic reticulum. Proc Natl Acad Sci U S A. 2017 Dec 19;114(51):13394-13399. PubMed Central PMCID: PMC5754785.
Shen Y, Xu F, Wei L, Hu F, Min W. Live-cell quantitative imaging of proteome degradation by stimulated Raman scattering. Angew Chem Int Ed Engl. 2014 May 26;53(22):5596-9. PubMed Central PMCID: PMC4231775.
Wei L, Yu Y, Shen Y, Wang MC, Min W. Vibrational imaging of newly synthesized proteins in live cells by stimulated Raman scattering microscopy. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11226-31. PubMed Central PMCID: PMC3710790.
Imaging small molecules
Shen Y, Hu F, Min W. Raman Imaging of Small Biomolecules. Annu Rev Biophys. 2019 May 6;48:347-369. PubMed PMID: 30892920.
Garcia-Bermudez J, Baudrier L, Bayraktar EC, Shen Y, La K, Guarecuco R, Yucel B, Fiore D, Tavora B, Freinkman E, Chan SH, Lewis C, Min W, Inghirami G, Sabatini DM, Birsoy K. Squalene accumulation in cholesterol auxotrophic lymphomas prevents oxidative cell death. Nature. 2019 Mar;567(7746):118-122. PubMed Central PMCID: PMC6405297.
Wei L, Hu F, Shen Y, Chen Z, Yu Y, Lin CC, Wang MC, Min W. Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering. Nat Methods. 2014 Apr;11(4):410-2. PubMed Central PMCID: PMC4040164.
