Publications

At Illinois

  • [42] V. Celik, W. Kong, A. Blanchard, F. Liu, and T. Lu
    Spatial interference scale as a determinent of microbial community assembly
    Submitted.
  • [41] S. Seo, T. Lu, Y. Jin and H. Blaschek
    Investigation of environmental and genetic factors influencing the acetone-butanol-ethanol (ABE) fermentation by a hyper-butanol producing mutant of Clostridium beijerinckii
    Submitted.
  • [40] W. Kong, D. Meldgin, J. Collins, and T. Lu
    Programming microbial consortia with defined social interactions
    Nature Chemical Biology, in revision.
  • [39] X. Fang, K. Kruse, T. Lu, and J. Wang
    Nonequilibrium physics in biology
    Rev. Mod. Phys. in revision.
  • [38] Q. Tang, T. Lu*, and S. Liu* (*Co-corresponding authors)
    Engineering the soil bacterium Comamonas testosteroni CNB-1: plasmid curing and genetic manipulation
    Biochem. Eng. J. in revision.
  • [37] T. Lu
    Principles of Systems Biology, No. 23
    Cell Systems. in press (2017).
  • [36] A. Blanchard, C. Liao, and T. Lu
    Circuit-host coupling induces multifaceted behavioral modulations of a gene switch
    Biophys. J. (2017).
  • [35] 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
    J. Biotechnol. in press (2017)
  • [34] C. Liao, A. Blanchard, and T. Lu
    An integrative circuit-host modeling framework for predicting synthetic gene network behaviors
    Nature Microbiology, DOI: 10.1038/s41564-017-0022-5 (2017).
  • [33] T. Lu
    What is the role of circuit design in the advancement of synthetic biology?
    Cell Systems. 4: 476 (2017)
  • [32] 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
    Biotechnol. J. DOI: 10.1002/biot.201700182 (2017)
  • [31] W. Kong, A. Blanchard, C. Liao, and T. Lu
    Engineering robust and tunable spatial structures with synthetic gene circuits
    Nucleic Acids Res. DOI: 10.1093/nar/gkw1045 (2016)
  • [30] A. Blanchard, C. Liao, and T. Lu
    An ecological understanding of quorum sensing-controlled bacteriocin production
    Cell Mol Bioeng. 9: 443-454 (2016)
  • [29] 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
    Biotechnol. Bioeng. 114(1): 106-112 (2016)
  • [28] C. Liao, S. Seo, and T. Lu
    System-level modeling of acetone-butanol-ethanol fermentation
    FEMS Microbiol. Lett. 363(9): fnw074 (2016)
  • [27] Y. Wang, Z. Zhang, S. Seo, P. Lynn, T. Lu, Y. Jin, and H. Blaschek
    Gene transcription repression in Clostridium beijerinckii using CRISPR-dCas9
    Biotechnol. Bioeng. 113: 2739-2743 (2016)
  • [26] 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 Synth. Biol. 5: 721–732 (2016)
  • [25] T. Lu
    Piecing together the puzzle of solvent production
    Biofuels International 10: 41-42 (2016)
  • [24] J. Mao and T. Lu
    Population-dynamic modeling of bacterial horizontal gene transfer by natural transformation
    Biophys. J. 110: 258–268 (2015)
  • [23] W. Kong, V. Kapuganti, and T. Lu
    A gene network engineering platform for lactic acid bacteria
    Nucleic Acid Res. DOI:10.1093/nar/gkv1093 (2015)
  • [22] A. Blanchard and T. Lu
    Bacterial social interactions drive the emergence of differential spatial colony structures
    BMC Syst. Biol. 9: 59 (2015)
  • [21] 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)
  • [20] 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
    J. Biotechnol. 200: 1-5 (2015)
  • [19] H. Liu and T. Lu
    Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered escherichia coli
    Metab. Eng. 29: 135-141 (2014)
  • [18] 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)
  • [17] H. Liu, Y. Wang, Q. Tang, W. Kong, W. Chung, and T. Lu
    MEP pathway-mediated isopentenol production in metabolically engineered escherichia coli
    Microb Cell Fact. 13:135 (2014)
  • [16] W. Kong and T. Lu
    Cloning and optimization of a nisin biosynthesis pathway for bacteriocin harvest
    ACS Synth. Biol. 3: 439-45 (2014)
  • [15] A. Blanchard, V. Celik, and T. Lu
    Extinction, coexistence, and localized patterns of a bacterial population
    BMC Syst. Biol. 8:23 (2014)
  • [14] J. Mao, A. Blanchard, and T. Lu
    Slow and steady wins the race: A bacterial exploitative competition strategy in fluctuating environments
    ACS Synth. Biol. 4(3): 240–248 (2014)
  • [13] C. Liao and T. Lu
    A minimal transcriptional controlling network of regulatory T cell development
    J. Phys. Chem. B. 117: 12995–13004 (2013)
  • [12] H. Qi, A. Blanchard, and T. Lu
    Engineered genetic information processing circuits
    WIREs Syst. Biol. Med. 5: 273–287 (2013)
  • [11] 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 (2011 and before)

  • [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(8): e22490 (13pp) (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
    Phys. Biol. 5: 036006 (8pp) (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
    Biophys. J. 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
    Phys. Biol. 3: 83-92 (2006)
  • [2] T. Lu, D. Volfson, L. Tsimring and J. Hasty
    Cellular growth and division in the Gillespie algorithm
    Syst. Biol. 1:121-127 (2004)
  • [1] T. Lu and Y. Li
    Mesoscopic circuit with linear dissipation
    Mod. Phys. Lett. B, 16: 975-979 (2002)