Publications

• [75] Y. Li, Y. Lai, and T. Lu
  Coarse-grained modeling elucidates differential metabolism of Saccharomyces cerevisiae under varied nutrient limitations
  submitted.
  
• [74] Y. Xin, X. Huang, J. Shin, Y. Jin, and T. Lu
  Topological structure underpins the resilience of microbial mutualism
  submitted.
  
• [73] C. Ni, H. Rehman, K. Nagarajan, and T. Lu
  Microbial range expansion driven by cellular motility and social interactions
  submitted.
  
• [72] Y. Wu, W. Kong, J. Van Stappen, L. Kong, Z. Huang, Z. Yang, Y. Kuo, Y. Chen, Y. He, H. Yeh, T. Lu, and Y. Lu
  Genetically encoded fluorogenic DNA aptamers for imaging metabolite in living cells
  Journal of the American Chemical Society, doi: 10.1021/jacs.4c09855 (2024).
  
• [71] J. Shin, S Liao, N. Kuanysheva, Y. Xin, T Lu*, and Y. Jin* (*Co-corresponding authors)
  Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium
  Nature Communications, 15: 781 (2024).
  
• [70] Z. Su, W. Zhang, Y. Shi, T. Cui, Y. Xu, R. Yang, M. Huang, C. Zhou, H. Zhang, T. Lu, J. Qu, Z. He, J. Gan, Y. Feng
  A bacterial methyltransferase that initiates biotin synthesis, an attractive anti-ESKAPE druggable pathway
  Science Advances, 10: eadp3954 (2024).
  
• [69] P. Nguyen, X. Huang, D. Collins, J. Collins, and T. Lu
  Harnessing synthetic biology to enhance ocean health
  Trends in Biotechnology, 41: 860-874 (2023).
  
• [68] V. Nyugen, Y. Li, and T. Lu
  Emergence of coordinated and dynamic metabolism of Saccharomyces cerevisiae
  ACS Synthetic Biology, 13: 1442-1453 (2023).
  
• [67] T. Bao, Y. Qian, Y. Xin, J. Collins, and T. Lu
  Engineering microbial division of labor for plastic upcycling
  Nature Communications, 14: 5712 (2023).
  
• [66] V. Nyugen, P. Xu, Y. Li, H. Zhao, and T. Lu
  Controlling circuitry underlines the growth optimization of Saccharomyces cerevisiae
  Metabolic Engineering, 80: 173-183 (2023)
  
• [65] T. Lu and S. Techtmann
  From waste to food: towards the creation of a sustainable food generator
  In Curious Future Insight: Science for a Better Tomorrow (Ulrich A.Z. Betz, ed.), Springer, 97-107 (2023)
  
• [64] C. Liao, P. Priyanka, Y. Lai, C. Rao, and T. Lu
  How does Escherichia coli allocate proteome?
  ACS Synthetic Biology, doi: 10.1021/acssynbio.3c00537 (2022)
  
• [63] Y. Jeong, W. Kong, and T. Lu, and J. Irudayaraj
  Soft hydrogel-shell confinement systems as bacteria-based bioactuators and biosensors
  Biosensors and Bioelectronics, 219:114809 (2022).
  
• [62] C. Ni and T. Lu
  Individual-based modeling of spatial dynamics of chemotactic microbial populations
  ACS Synthetic Biology, 11: 3714–3723 (2022).
  
• [61] K. Nagarajan, C. Ni and T. Lu
  Agent-based modeling of microbial communities
  ACS Synthetic Biology, 11: 3564–3574 (2022).
  
• [60] W. Kong, Y. Qian, P. Stewart, and T. Lu
  De novo engineering of a bacterial lifestyle program
  Nature Chemical Biology, 19: 488–497 (2022).
  
• [59] L. Schaerer, R. Wu, L. Putman, J. Pearce, T. Lu, D. Shonnard, R. Ong, and S. Techtmann
  Killing two birds with one stone: biochemical upcycling of plastics into food
  Trends in Biotechnology, 41: 184-196 (2022).
  
• [58] X. Huang, Y. Xin, and T. Lu
  A systematic, complexity-reduction strategy to dissect the kombucha tea microbiome
  eLife, 11: e76401 (2022).
  
• [57] Y. Xu, J. Yang, W. Li, S. Song, Y. Shi, L. Wu, J. Sun, M. Hou, J. Wang, X. Jia, H. Zhang, M. Huang, T. Lu, J. Gan, and Y. Feng
  Three enigmatic BioH isoenzymes are programmed in the primary step of mycobacterial biotin synthesis
  PLoS Pathogens, 18(7): e1010615 (2022).
  
• [56] H. Deter and T. Lu
  Engineering microbial consortia with rationally designed cellular interactions
  Current Opinion in Biotechnology, 76:102730 (2022).
• [55] Y. Qian, W. Kong and T. Lu
  Precise and reliable control of gene expression in agrobacterium tumefaciens
  Biotechnology and Bioengineering, 118:3962–3972 (2021).
• [54] S. Seo, T. Lu, Y. Jin, and H. Blaschek
  A comparative phenotypic and genomic analysis of Clostridium beijerinckii mutant with enhanced solvent production
  Journal of Biotechnology, 329: 49-55 (2021).
• [53] J. Liu, C. Solem, T. Lu, and P. Jensen
  Harnessing lactic acid bacteria in synthetic microbial consortia
  Trends in Biotechnology, 40: 8-11 (2021).
• [52] Y. Cao, J. Neu, A. Blanchard, T. Lu, and L. You
  Repulsive expansion dynamics in colony growth and gene expression
  PLoS Computational Biology 17(3): e1008168 (2021).
• [51] L. Ibarra-Sánchez, W. Kong, T. Lu, and M. Miller
  Efficacy of nisin derivatives with improved biochemical characteristics, alone and in combination with endolysin PlyP100 to control Listeria monocytogenes in Queso Fresco
  Food Microbiology, 94: 103668 (2020)
• [50] J. Sickle, C. Ni, D. Shen, D. Zhang, M. Jin, and T. Lu
  Integrative circuit-host modeling of a genetic switch in varying environments
  Scientific Reports, 10: 8383 (2020)
• [49] X. Huang, Y. Fan, T. Lu, J. Kang, X. Pang, B. Han, and J. Chen
  Composition and metabolic functions of the microbiome in fermented grain during light-flavor Baijiu fermentation
  Microorganisms, 8: 1281 (2020)
• [48] F. Liu, J. Mao, W. Kong, Y. Feng, Q. Hua, R. Bashir, and T. Lu
  Interaction variability shapes succession of synthetic microbial ecosystems
  Nature Communications, doi: 10.1038/s41467-019-13986-6 (2020)
• [47] F. Liu, J. Mao, T. Lu* and Q. Hua* (*Co-corresponding authors)
  Synthetic, context-dependent microbial consortium of predator and prey
  ACS Synthetic Biology 8: 1713-1722 (2019)
• [46] H. Cheng, D. Cheng, J. Mao, T. Lu, and P. Hong
  Identification and characterization of core sludge and biofilm microbiota in anaerobic membrane bioreactors
  Environmental International 133: 105165 (2019)
• [45] X. Fang, K. Kruse, T. Lu, and J. Wang
  Nonequilibrium physics in biology
  Review of Modern Physics 91: 045004 (2019)
• [44] V. Celik, W. Kong, A. Blanchard, F. Liu, and T. Lu
  Spatial interference scale as a determinant of microbial range expansion
  Science Advances 4: eaau0695 (2018).
• [43] M. A. Khatun, M. A. Hoque, Y. Zhang, T. Lu, L. Cui, N. Zhou, and Y. Feng
  Bacterial consortium-based sensing system for detecting organophosphorus pesticides
  Analytical Chemistry 90 (17): 10577-10584 (2018).
• [42] Q. Tang, T. Lu*, and S. Liu* (*Co-corresponding authors)
  Developing a synthetic biology toolkit for comamonas testosteroni, an emerging cellular chassis for bioremediation
  ACS Synthetic Biology 7: 1753-1762 (2018).
• [41] W. Kong, D. Meldgin, J. Collins, and T. Lu
  Designing microbial consortia with defined social interactions
  Nature Chemical Biology 14: 821–829 (2018).
• [40] Q. Tang, T. Lu*, and S. Liu* (*Co-corresponding authors)
  Engineering the bacterium comamonas testosteroni CNB-1: plasmid curing and genetic manipulation
  Biochemical Engineering Journal 133: 74-82 (2018).
• [39] Z. Zhang, P. Jiménez-Bonilla, S. Seo, T. Lu, Y. Jin, H. Blaschek, and Y. Wang
  Bacterial genome editing with CRISPR-Cas9: taking clostridium beijerinckii as an example
  In Synthetic Biology, Methods in Molecular Biology (Jeff Braman, et al. eds), 1772: 297-325 (2018).
• [38] T. Lu
  Principles of Systems Biology, No. 23
  Cell Systems 5: 428 (2017).
• [37] A. Blanchard, C. Liao, and T. Lu
  Circuit-host coupling induces multifaceted behavioral modulations of a gene switch
  Biophysical Journal 114: 1-10 (2017).
• [36] S. Seo, T. Lu, Y. Jin and H. Blaschek
  Development of an oxygen-independent flavin mononucleotide-based fluorescent reporter system in clostridium beijerinckii and its applications
  Journal of Biotechnology 265: 119-126 (2017)
• [35] C. Liao, A. Blanchard, and T. Lu
  An integrative circuit-host modeling framework for predicting synthetic gene network behaviors
  Nature Microbiology 2: 1658–1666 (2017).
• [34] T. Lu
  What is the role of circuit design in the advancement of synthetic biology?
  Cell Systems 4: 476 (2017)
• [33] S. Seo, H. Janssena, A. Magise, Y. Wang, T. Lu, N. Price, Y. Jin, and H. Blaschek
  Genomic, transcriptional and phenotypic analysis of the acid-crash mutant of clostridium beijerinckii
  Biotechnological Journal 12: 1700182 (2017)
• [32] W. Kong, A. Blanchard, C. Liao, and T. Lu
  Engineering robust and tunable spatial structures with synthetic gene circuits
  Nucleic Acids Research 45: 1005-1014 (2016)
• [31] A. Blanchard, C. Liao, and T. Lu
  An ecological understanding of quorum sensing-controlled bacteriocin production
  Cellular and Molecular Bioengineering 9: 443-454 (2016)
• [30] S. Seo, Y. Wang, T. Lu, Y. Jin, and H. Blaschek
  Characterization of a clostridium beijerinckii spo0A mutant and its application for butyl butyrate production
  Biotechnology and Bioengineering 114: 106-112 (2016)
• [29] C. Liao, S. Seo, and T. Lu
  System-level modeling of acetone-butanol-ethanol fermentation
  FEMS Microbiology Letter 363: fnw074 (2016)
• [28] Y. Wang, Z. Zhang, S. Seo, P. Lynn, T. Lu, Y. Jin, and H. Blaschek
  Gene transcription repression in clostridium beijerinckii using CRISPR-dCas9
  Biotechnology and Bioengineering 113: 2739-2743 (2016)
• [27] Y. Wang, Z. Zhang, S. Seo, P. Lynn, T. Lu, Y. Jin, and H. Blaschek
  Bacterial genome editing with CRISPR/Cas9: deletion, integration, single nucleotide modification, and desirable ‘clean’ mutant selection in clostridium beijerinckii as an example
  ACS Synthetic Biology 5: 721–732 (2016)
• [26] T. Lu
  Piecing together the puzzle of solvent production
  Biofuels International 10: 41-42 (2016)
• [25] J. Mao and T. Lu
  Population-dynamic modeling of bacterial horizontal gene transfer by natural transformation
  Biophysical Journal 110: 258–268 (2015)
• [24] W. Kong, V. Kapuganti, and T. Lu
  A gene network engineering platform for lactic acid bacteria
  Nucleic Acid Research 44(4): e37 (2015)
• [23] A. Blanchard and T. Lu
  Bacterial social interactions drive the emergence of differential spatial colony structures
  BMC Systems Biology 9: 59 (2015)
• [22] C. Liao, S. Seo, V. Celik, H. Liu, W. Kong, Y. Wang, H. Blaschek, Y. Jin, and T. Lu
  Integrated, systems metabolic picture of acetone-butanol-ethanol fermentation by clostridium acetobutylicum
  Proc. Natl. Acad. Sci. 112: 8505–8510 (2015)
• [21] Y. Wang, Z. Zhang, S. Seo, K. Choia, T. Lu, Y. Jin, and H. Blaschek
  Markerless chromosomal gene deletion in clostridium beijerinckii using CRISPR/Cas9 system
  Journal of Biotechnology 200: 1-5 (2015)
• [20] H. Liu and T. Lu
  Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered escherichia coli
  Metabolic Engineering 29: 135-141 (2014)
• [19] W. Kong, V. Celik, C. Liao, Q. Hua, and T. Lu
  Programming the group behaviors of bacterial communities with synthetic cellular communication
  Bioresources and Bioprocessing 1:24 (2014)
• [18] H. Liu, Y. Wang, Q. Tang, W. Kong, W. Chung, and T. Lu
  MEP pathway-mediated isopentenol production in metabolically engineered escherichia coli
  Microbial Cell Factory 13:135 (2014)
• [17] W. Kong and T. Lu
  Cloning and optimization of a nisin biosynthesis pathway for bacteriocin harvest
  ACS Synthetic Biology 3: 439-45 (2014)
• [16] A. Blanchard, V. Celik, and T. Lu
  Extinction, coexistence, and localized patterns of a bacterial population
  BMC Systems Biology 8:23 (2014)
• [15] J. Mao, A. Blanchard, and T. Lu
  Slow and steady wins the race: A bacterial exploitative competition strategy in fluctuating environments
  ACS Synthetic Biology 4: 240–248 (2014)
• [14] C. Liao and T. Lu
  A minimal transcriptional controlling network of regulatory T cell development
  Journal of Physical Chemistry B 117: 12995–13004 (2013)
• [13] H. Qi, A. Blanchard, and T. Lu
  Engineered genetic information processing circuits
  WIREs Systems Biology and Medicine 5: 273–287 (2013)
• [12] W. Fu, T. Lu*, A. Ergun*, J. Hill, S. Haxhinasto, M. Fassett, R. Gazit, S. Adoro, S. Chan, D. Rossi, J. Collins, D. Mathis, and C. Benoist
  A multiply redundant genetic switch 'locks in' the transcriptional signature of Treg cells
  Nature Immunology 13: 972-980 (2012) (*Equal contribution)
• [11] D. Karig, K. Martini, T. Lu, N. DeLateur, N. Goldenfeld, and R. Weiss
  Stochastic Turing patterns in a synthetic bacterial population
  Proc. Natl. Acad. Sci. 115: 6572-6577 (2018)
• [10] W. Ruder*, T. Lu*, and J. J. Collins
  Synthetic biology moving into the clinic
  Science 333: 1248-1252 (2011) (*Equal contribution)
• [9] J. Beal, T. Lu, and R. Weiss
  Automatic compilation from high-level language to genetic regulatory networks
  PLoS One 6: e22490 (2011)
• [8] C. Teuscher, C. Grecu, T. Lu, and R. Weiss
  Challenges and promises of nano and bio communication networks
  Proc. ACM/IEEE Fifth Int’l Symp. Networks-on-Chip, pp. 247-254 (2011)
• [7] T. Lu, M. Ferry, R. Weiss, and J. Hasty
  A molecular noise generator
  Physical Biology 5: 036006 (2008)
• [6] T. Lu, T. Shen, M. Bennett, P. Wolynes, and J. Hasty
  Phenotypic variability of growing cellular populations
  Proc. Natl. Acad. Sci. 104: 18982-18987 (2007)
• [5] T. Lu, J. Hasty, and P. Wolynes
  Effective temperature in stochastic kinetics and gene networks
  Biophysical Journal 91: 84-94 (2006)
• [4] T. Lu, T. Shen, C. Zong, J. Hasty, and P. Wolynes
  Statistics of cellular signal transduction as a race to the nucleus by multiple random walkers in compartment/phosphorylation space
  Proc. Natl. Acad. Sci. 103: 16752-16757 (2006)
• [3] C. Zong, T. Lu, T. Shen, and P. Wolynes
  Nonequilibrium self-assembly of linear fibers: microscopic treatment of growth, decay, catastrophe and rescue
  Physical Biology 3: 83-92 (2006)
• [2] T. Lu, D. Volfson, L. Tsimring and J. Hasty
  Cellular growth and division in the Gillespie algorithm
  IET Systems Biology 1:121-127 (2004)
• [1] T. Lu and Y. Li
  Mesoscopic circuit with linear dissipation
  Modern Physics Letter B, 16: 975-979 (2002)