Recent Papers (You can find a complete publication list from Google Scholar)

 The Tang lab has worked with different research groups and companies to explore microbial metabolisms (over 20 species).

• Worland AM, Han Z, Maruwan J, Wang Y, Du ZY, Tang YJ, Su WW, Roell G. Elucidation of triacylglycerol catabolism in Yarrowia lipolytica: how cells balance acetyl-CoA and excess reducing equivalents. Metabolic Engineering. 2024. 77, 231-241  

• Long B, Zhang F, Dai S, Tang YJ, Yuan JS. Bioengineering to Empower Next Generation Lignocellulosic Biorefinery. Nature Reviews Bioengineering. 2024.

• Xiao Z, et al. Generative artificial intelligence GPT-4 accelerates knowledge mining and machine learning for synthetic biology. ACS Synthetic Biology. 2023.

• Backman TWH, Schenk C, Radivojevic T, Ando D, Singh J, Czajka JJ, Costello Z, Keasling JD, Tang Y, Akhmatskaya E, Martin HG, BayFlux: A Bayesian method to quantify Fluxes at the Genome Scale. Plos Computational Biology. 2023.

• Han Z, Maruwan J, Tang YJ, Su WW. Conditional protein degradation in Yarrowia lipolytica using the auxin-inducible degron. Frontiers in Bioengineering and Biotechnology. 2023. 11:1188119.

• Roell GW, Schenk C,  Anthony WE, Carr RR,  Ponukumati A, Kim J,  Akhmatskaya E, Foston M, Dantas G, Moon TS, Tang YJ, Martin HG.A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism. ACS Synthetic Biology. 2023. 12, 6, 1632–1644

• Zheng Y, Czajka JC, Daiek C, Yang Z, Sun L, Tang Y, Liu Y, Liao W. An algal-bacterial symbiotic system of carbon fixation using formate as a carbon source. Algal Research. 2023.  103103

• Xiao Z., Connor A.J., Worland A.M., Tang Y.J., Zha R.H., and Koffas M. Silk fibroin production in Escherichia coli is limited by a positive feedback loop between metabolic burden and toxicity stress. Metabolic Engineering. 2023.   

• Tang YJ and Moon TS. Mining microbial metabolism. Nature Chemical Biology. 2023.

• Liu F, Worland A, Tang Y, Moustafa H, Hassouna MSE, He Z. Microbial electrochemical ammonia recovery from anaerobic digester centrate and subsequent application to fertilize Arabidopsis thaliana. Water Research. 2022. 220:118667.

• Zha J, Zhao Z, Xiao Z, Eng T, Mukhopadhyay A, Koffas MAG, Biosystem design of Corynebacterium glutamicum for bioproduction. Current Opinion in Biotechnology 2022. vol 79, 102870.

• Zhao R, Sengupta A, Tan A, Whelan R, Pinkerton T, Menasalvas J, Eng T, Mukhopadhyay A, Jun YS, Pakrasi HB, Tang YJ. Photobiological production of high-value pigments via compartmentalized co-cultures using Ca-alginate hydrogels. Scientific Report.  2022 Article number: 22163

• Huffine C, Zhao R, Tang YJ, Cameron JC. Role of carboxysomes in cyanobacterial CO2 assimilation: CO2 concentrating mechanisms and metabolon implications. Environmental Microbiology. 2022

•  Czajka JJ, Banerjee D, Eng T, Menasalvas J, Yane C, Munoz NM, Poirier BC, Kim YM, Baker SE, Tang YJ, & Mukhopadhyay A. Tuning a High Performing Multiplexed-CRISPRi Pseudomonas putida Strain to Further Enhance Indigoidine Production. Metabolic Engineering Communications.  2022. e00206

• Roell G, Sathish A, Wan N, Wen Z, Tang YJ, Bao F. A comparative evaluation of machine learning algorithms for predicting syngas fermentation outcomes. Biochemical Engineering Journal. 2022. Volume 186, August 2022, 108578.

• Fang Z, Tang YJ, Koffas MAG. Harnessing electrical-to-biochemical conversion for microbial synthesis. Current Opinion in Biotechnology 2022, 75, 102687 

• Liao X, Ma H, Tang YJ. Artificial intelligence: a solution to involution of design-build-test-learn cycle. Current Opinion in Biotechnology 2022, 75, 102712

• Li T, Pang N, He L, Xu Y, Fu X, Tang YJ, Shachar-Hill Y, Chen S. Re-programing glucose catabolism in Microalga Chlorella sorokiniana under light condition. Biomolecules 2022. 12(7), 939.           

• Xiao Z, Tan AX, Xu V, Jun YS and Tang YJ. Mineral-Hydrogel Composites for Mitigating Harmful Algal Bloom and Supplying Phosphorous for Photo-biorefineries. Science of The Total Environment. 2022. V847, 157533. 

• Xiao Z, Zheng Y, Gudi C, Liu Y, Liao W, Tang YJ. Development of a kinetic model to describe siz types of symbiotic interactions in a formate utilizing microalgae-bacteria cultivation system.  Algal Research.  2021. 58, 102372.

• Czajka JJ, Oyetunde T, Tang YJ. Integrated Knowledge mining, genome-scale modeling, and machine learning for predicting Yarrowia lipolytica bioproduction.  Metabolic Engineering.  2021. 67, 227-236

• Worland A, Czajka JJ, Xing Y, Harper W, Moore A, Xiao Z, Wang Y, Han Z, Su WW, Tang YJ, Metabolic analysis, terpenoid biosynthesis, and morphology of Yarrowia lipolytica during utilization of lipid-derived feedstock. Metabolic Engineering Communications. 2020. e00130

• Li N, O'Donnell TJ, Han Z, Kurasaki R, Kajihara L, Williams PG, Tang YJ, Su WW. Production and excretion of astaxanthin by engineered Yarrowia lipolytica using plant oil as both the carbon source and the biocompatible extractant. Applied Microbiology and Biotechnology. Applied Microbiology and Biotechnology. 2020. In press.

• Czajka JJ, Kambhampati S, Tang YJ, Wang Y, Allen DK. Application of stable isotope tracing to elucidate metabolic dynamics during Yarrowia lipolytica α-ionone fermentation. iScience. 2020. 100854

• Worland A, Czajka JJ, Wang Y, Li Y. Tang YJ, Su WW. Biosynthesis of terpene compounds using non-model yeast Yarrowia lipolytica: grand challenges and a few perspectives. Current Opinion in Biotechnology. 2020. 64:134-140.

• 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.

• Worland A, Czajka JJ, Wang Y, Tang YJ, Su WW. Biosynthesis of terpene compounds using non-model yeasts: grand challenges and a few perspectives. Current Opinion in Biotechnology. 2020. Invited reveiw.

• Roell G, Carr R, Campbell T, Shang Z, Henson W, Czajka J, Martin HG, Zhang F, Foston M, Dantas G, Moon TS, Tang YJ. A concerted systems biology analysis of aromatic metabolism in Rhodococcus opacus PD630. Metabolic Engineering. 2019. 55:120-130.

• Roell GW, Zha J, Carr R.R., Koffas M.A., Fong S.S., Tang YJ. Engineering Microbial Consortia by Division of Labor. Microbial Cell Factories. 2019. 18(1): 35.

• Hollinshead W, He L, and Tang YJ.  ¹³C-Fingerprinting and Metabolic Flux Analysis of Bacterial Metabolisms. Microbial Metabolic Engineering. 2019. 215-230 

• Oyetunde T, Liu D, Martin HG, Tang YJ. Machine learning framework for robust assessment of microbial factory performance. Plosone. 2019. 14(1):e0210558.

•  Abernathy MH, Czajka JJ, Allen DK, Hill NC, Cameron JC, Tang YJ. Cyanobacterial carboxysome mutant analysis reveals the influence of enzyme compartmentalization on cellular metabolism and metabolic network rigidity. Metabolic Engineering. 2019. 54, 222-231.

•  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. 2019. pp. 01357.2018.

• 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. 115 (49), 12507-12512

•  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.

•  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. 2019. 483-490.

•  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.

•  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

•  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