Our lab has worked with different research groups and companies to explore microbial metabolisms.

Recent Papers 2015~2017 (You can find a complete publication list in my Google Scholar)

27. Abernathy MH, Yu J, Ma F, Liberton M, Ungerer J, Hollinshead WD, Gopalakrishnan S, He L, Maranas CD, Pakrasi HB, Allen DK, Tang YJ. Deciphering cyanobacterial phenotypes for fast photoautotrophic growth via isotopically nonstationary metabolic flux analysis. Biotechnology for Biofuel. 2017. 

26. Wan N, Sathish A, You L, Tang YJ, Wen Z. Deciphering Clostridium metabolism and its responses to bioreactor mass transfer during syngas fermentation. Scientific Reports. 2017.

25. Abernathy M, He L, Tang YJ. Channeling in native microbial pathways: Implications and challenges for metabolic engineering. Biotechnology Advances. 2017.

24. Shopera T; He L; Oyetunde T; Tang Y; Moon TS. Decoupling resource-coupled gene expression in living cells. ACS Synthetic Biology. 2017.  

23. Manjrekar O; Sun Y; He L; Tang YJ; Dudukovic MP. Hydrodynamics and Mass Transfer Coefficients in a Bubble Column Photo-bioreactor. Chemical Engineering Science. 2017.

22. Wan N, Delorenzo D, He L, You L, Wang G, Baidoo EK, Immethun C, Hollinshead W, Keasling JD, Moon TS, Tang YJ. Cyanobacterial carbon metabolism: fluxome plasticity and oxygen dependence. Biotechnology and Bioengineering. 2017.

21. He L, Xiu Y, Jones A, Baidoo EE, Keasling JD, Tang YJ, Koffas MAG. Deciphering flux adjustments of engineered E. coli cells during fermentation with changing growth conditions. Metabolic Engineering. 2017.

20. Liu Z, Oyetunde T, Hollinshead WD, Hermanns A. Tang YJ, Liao W, Liu Y, Exploring Fungal Formate Metabolisms to enhance Microbial Growth and Lipid Accumulation. Biotechnology for Biofuel. 2017.

19. Li Z, Li Y, Chen W, Cao Q, Guo Y, Wan N, Jiang X, Tang YJ, Wang Q, Shui W. Integrating MS1 and MS2 scans in high-resolution parallel reaction monitoring assays for targeted metabolite quantification and dynamic 13C-metabolism analysis. Analytical Chemistry. 2017.

18. Oyetunde T, Zhang M, Chen Y, Tang YJ, and Lo C. BoostGAPFILL: Improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods. Bioinformatics. 2017. 

17. Varman AM, He L, Follenfant R, Wemmer S, Wrobel SA, Tang YJ and Singh S. Decoding how a soil bacterium extracts building blocks and metabolic energy from ligninolysis provides road map for lignin valorization. PNAS. 2017. 

16. Liu D, Ni W, Zhang F, Tang YJ, Wu SG. Enhancing fatty acid production in Escherichia coli by Vitreoscilla Hemoglobin overexpression. Biotechnology and Bioengineering. 2017. 

15. He L, Wu SG, Zhang M, Chen Y, and Tang YJ, WUFlux: an open-source platform for ¹³C metabolic flux analysis of bacterial metabolism. BMC Bioinformatics. 2016.

14. Hollinshead WD, Rodriguez S, Martin HG, Wang G, Baidoo EK, Sale KL, Keasling JD, Mukhopadhyay A, Tang YJ. Examining Escherichia coli glycolytic pathways, catabolite repression, and metabolite channeling using Δpfk mutants. Biotechnology for Biofuel. 2016. 

13. Wu SG, Qiang Yan, Tang YJ, Fong SS, Koffas M. Metabolic burden: cornerstones in synthetic biology and metabolic engineering applications. Trends in Biotechnology. 2016. 

12. Wu SG, Wang Y, Jiang W, Oyetunde T, Yao R, Zhang X, Shimizu K, Tang YJ, Bao FS. Rapid prediction of bacterial fluxomics using machine learning and constraint programming. Plos Computational Biology. 2016.

11. Wu SG, Shimizu K, Tang JKH, Tang YJ. Facilitate collaborations among synthetic biology, metabolic engineering and machine learning. ChemBioEng Reviews. 2016.   

10. Hollinshead WD, Henson WR, Abernathy M, Moon TS, Tang YJ. Metabolic Analysis of Rhodococcus opacus PD630 via rapid parallel 13C Metabolite Fingerprinting. Biotechnology and Bioengineering. 2016.


9. He L, Wu G, Wan N, Reding AC, Tang YJ. Simulating cyanobacterial phenotypes in photobioreactors by coupling flux balance analysis, kinetics and hydrodynamics. Microbial Cell Factories. 2015.


8. He L, Wang Y, You L, Yang Y, Khin Y, Zhuang W, Tang JK, Tang YJ. Glycine Cleavage System Promotes Photoheterotrophic Growth of Chloroflexus aurantiacus. Frontier in Microbiology. 2015.


7. Wan N, Abernathy M, Tang JKH, Tang YJ, You L. Cyanobacterial photo-driven mixotrophic metabolism and its advantages for biosynthesis. Frontiers of Chemical Science and Engineering. 2015.


6. Kim M, Le H, Xie X, Feng X, Tang YJ, Mouttaki H, McInerney M, and Buckel W. Two pathways for glutamate biosynthesis in the syntrophic bacterium, Syntrophus aciditrophicus. Applied Environmental and Microbiology. 2015.


5. Ray JR, Tadepalli S, Nergiz SZ, Liu KK, You L, Tang YJ,  Singamaneni S, Jun YS. Hydrophilic, Bactericidal Nanoheater Enabled Reverse Osmosis Membranes to Improve Fouling Resistance. ACS Applied Materials & Interfaces. 2015.


4. Wu SG, He L, Wang Q and Tang YJ. An ancient Chinese wisdom for metabolic engineering: Yin-Yang. Microbial Cell Factories. 2015. 


3. Ruan Z, Hollinshead WD, Isaguirre C, Tang YJ, Liao W, Liu Y. Mortierella isabellina growth tolerance and carbon utilizations under the effect of inhibitory compounds in lignocellulosic hydrolysates. Bioresource Technology. 2015. 


2. You L, He L, Tang YJ. The Photoheterotrophic Fluxome in Synechocystis sp. PCC 6803 and Its Implications for Cyanobacterial Bioenergetics. Journal of Bacteriology. 2015.


1. You L, Liu H, Blankenship RE, Tang YJ. Use Photosystems I as Reporter Protein for 13C-Analysis of Cyanobacterial Coculture. Analytical Biochemistry. 2015.  


List of Joint Projects on nonmodel microbial species



Novel metabolic features


Zhou JZ (OU)

Clostridium & Thermoanaerobacter

Compare different clostridium species’ metabolisms

AEM. 2011

Pakrasi (WUSTL)


Mixotrophic and heterotrophic metabolism; novel pathways for isoleucine synthesis

Microbiology. 2010 (two papers)

Blankenship (WUSTL)


Heliobacterium modesticaldum

(Re)-type citrate synthase in  TCA cycle

J Biol Chem. 2010

Blankenship (WUSTL)




Reversed TCA cycle and active PFOR pathway

J Biol Chem. 2010

Alvarez-Cohen (UBC)


Exogenous amino acids transport and utilization

Discover new pathways

J Bact 2009; AEM. 2011

PNAS 2014

Yixin Chen (WUSTL) Shewanella oneidensis  Develop dynamic flux analysis tool to reveal cell metabolism in bioreactor fermentations Plos Computational Biology 2012

Wei Liao (MSU)

Yan Liu (MSU)

Umbelopsis isabellina

Use of oleaginous fungi  for free fatty acid production; Fungal lipid synthesis using mixed substrates; fungal formate based metabolisms

Bioresource Technology 2013; 2015

Biotech for Biofuel 2016

Moon TS (WUSTL) Rhodococcus opacus Use parallel 13C metabolite fingerprinting to characterize a nonmodel spcies' central pathways Biotech and Bioeng. 2016

Joseph Tang (Clark U)

Chloroflexus aurantiacus

Nutrient and C1 metabolism

Frontier in Microbiology 2015

Pakrasi (WUSTL)

Synechocystis  6803

Mixotrophic metabolism profiled by  inverse labeling

Biotechnology Journal 2014

Blankenship and Liu (WUSTL) Cyanobacteria and E.coli coculture Use photosystems I as the reporter protein for coculture metabolism analysis Analytical Biochemistry 2015
MJ McInerneyc (OU) &
W Buckel (Max-Planck )
Syntrophus aciditrophicus Discover a unique Hydroxybutyrate pathway AEM.2015
Seema Singh (Sandia  Lab) Sphingobium sp. SYK-6 Flux analysis of lignin based metabolism PNAS 2017