Recent Papers 2018~2019 (You can find a complete publication list from my Google Scholar)

1. Oyetunde T, Liu D, Martin HG, Tang YJ. Machine learning framework for robust assessment of microbial factory performance. Plosone. In press.

2. Sarnaik A, Abernathy MH, Han X, Ouyang Y, Xia K, Chen Y, Cress B, Zhang F, Lalia A, Pandita R, Linhardt RJ, Tang YJ, Koffas M. Metabolic engineering of cyanobacteria for photoautotrophic production of heparosan, a pharmaceutical precursor of heparin. Algal Research. 2019. 37, 57-63.

3. Hendry J, Gopalakrishnan S, Ungerer J, Pakrasi H, Tang YJ, and Maranas C. Genome-scale fluxome of Synechococcus elongatus UTEX 2973 using transient 13C-labeling data. Plant Physiology. 2018. pp. 01357.2018.

4. Czajka J, Abernathy MH, Benites VT, Baidoo EE, Deming J, Tang YJ. A model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H. PNAS. 2018. In press.

5. Wan N, Wang H, Ng CK, Mukherjee M, Cao B, Ren D, Tang YJ. Bacterial metabolism during biofilm growth investigated by 13C tracing. Frontier in Microbiology. 2018. Volume 9. Article 2657.

6. Abernathy MH, Zhang Y, Hollinshead W, Wang G,  Baidoo EEK, Liu T, Tang YJ. Comparative studies of glycolytic pathways and channeling under in vitro and in vivo modes. AICHE Journal. 2018. In press.

7. Abernathy M, Wan N, Shui W, Tang YJ. Dynamic 13C labeling of fast turnover metabolites for analysis of metabolic fluxes and metabolite channeling. In Methods Molecular Biology. 2019. SpringerNature. Edward E.K. Baidoo (Eds): Microbial Metabolomics. Chapter 18. Vol. 1859.

8. Czajka JJ, Nathenson JA, Benites VT, Baidoo EEK, Cheng Q, Wang Y and Tang YJ. Engineering the oleaginous yeast Yarrowia lipolytica to produce the aroma compound β-ionone. Microb Cell Fact. 2018. 17(1):136

9. Oyetunde T, Bao FS, Chen JW, Martin HG, Tang YJ. Leveraging knowledge engineering and machine learning for microbial bio-manufacturing. Biotechnology Advances. 2018. 36(4), 1308-1315

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

List of Joint Projects on nonmodel microbial species (2008~2018)



Novel metabolic features


Zhou JZ (OU)

Clostridium & Thermoanaerobacter

Compare different clostridium speciesí 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