Publications

At Illinois

• [69] P. Nguyen, X. Huang, D. Collins, J. Collins*, and T. Lu* (*Co-corresponding authors)
  Harnessing synthetic biology to enhance ocean health
  Trends in Biotechnology, 41: 860-874 (2023).
  
• [68] 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 (2023).
  
• [67] V. Nyugen, Y. Li, and T. Lu
  Emergence of coordinated and dynamic metabolism of Saccharomyces cerevisiae, submitted.
  
• [66] T. Bao, Y. Qian, Y. Xin, J. Collins, and T. Lu
  Engineering microbial division of labor for plastic upcycling
  Nature Communications, 14: 5712 (2023).
  
• [65] V. Nyugen, P. Xu, Y. Li, H. Zhao, and T. Lu
  Controlling circuitry underlines the growth optimization of Saccharomyces cerevisiae
  Metabolic Engineering, doi: 10.1016/j.ymben.2023.09.013 (2023)
  
• [64] C. Liao, P. Priyanka, C. Rao, and T. Lu
  How does Escherichia coli allocate proteome?, submitted.
  
• [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, doi: 10.1016 /j.bios.2022.114809 (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)

Prior to joining Illinois

• [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)