- Synthetic Biology, Systems Biology, and Quantitative Biology
Gene regulatory networks are one of the main cellular infrastructures that confer defined biological functions. Our research focuses on synthetic and systems biology - the analysis, construction, and exploitation of these regulatory networks for cellular functionality programming. This is an interdisciplinary research area that spans the boundary between biology, engineering, and physics. Specifically, we are interested in understanding the architecture and dynamics of naturally existing networks, primarily those in bacteria, and exploring their relationship to cellular function. One interesting example is bacterial communication networks and their roles in enabling cellular collective behaviors. In parallel, we are interested in engineering gene circuits for biomedical applications by assembling and editing genes and genomes inside living cells, very much like building integrated circuits with transistors and other elements for a computer. Along that line, microbiota reengineering is very attractive to us because of its potential for therapeutic interventions. To pursue our interest, we have adopted E. coli and other bacteria as our model organisms, and have also employed an integrated experimental and computational approach. Experimental techniques from molecular biology and theoretical tools from nonlinear dynamics and statistical mechanics are extensively used in our research. Our long-term goal is to uncover nature's design principles of gene regulatory networks and to apply these principles to engineer novel circuits for biomedical applications.
- List of Teachers Ranked as Excellent by Their Students, UIUC (2015)
- Young Investigator Award, Center for Biofilm Engineering at Montana State University (2017)
- Center for Advanced Study Fellow, UIUC (2017)
- NCSA Faculty Fellowship (2016)
- Office of Naval Research Young Investigator Award (2016)
- Young Innovator of Cellular and Molecular Bioengineering (BMES) (2016)
- NSF CAREER Award (2015)
- Ellen Schapiro & Gerald Axelbaum Investigator (BBRF) (2015)
- NARSAD Young Investigator Award (BBRF) (2014)
- National Scientist Development Grant (AHA) (2012)
Selected Articles in Journals
- 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)
- 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. DOI: 10.1002/bit.26057 (2016)
- A. Blanchard, C. Liao, and T. Lu, An ecological understanding of quorum sensing-controlled bacteriocin production, Cell Mol Bioeng. 9: 443-454 (2016)
- 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. in press (2016)
- 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. DOI: 10.1021/acssynbio.6b00060 (2016)
- C. Liao, S. Seo, and T. Lu, System-level modeling of acetone-butanol-ethanol fermentation, FEMS Microbiol. Lett. DOI:10.1093/femsle/fnw074 (2016)
- T. Lu, Piecing together the puzzle of solvent production, Biofuels International, 10: 41-42 (2016)
- J. Mao and T. Lu, Population-dynamic modeling of bacterial horizontal gene transfer by natural transformation, Biophys. J. 110: 258–268 (2015)
- W. Kong, K. Kapuganti, and T. Lu, A gene network engineering platform for lactic acid bacteria, Nucleic Acid Res. DOI: 10.1093/nar/gkv1093 (2015)
- A. Blanchard and T. Lu, Bacterial social interactions drive the emergence of differential spatial colony structures, BMC Syst. Biol. 9: 59 (2015)
- 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)
- 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)
- 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)
- 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)
- 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)
- W. Kong and T. Lu, Construction and optimization of a nisin biosynthesis pathway for bacteriocin harvest, ACS Synth. Biol. 3:439-45 (2014)
- A. Blanchard, V. Celik, and T. Lu, Extinction, coexistence, and localized patterns of a bacterial population, BMC Syst. Biol. 8:23 (2014).
- 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).
- C. Liao and T. Lu, A minimal transcriptional controlling network of regulatory T cell development, J. Phys. Chem. B. 117: 12995–13004 (2013).
- H. Qi, A. Blanchard, and T. Lu, Engineered genetic information processing circuits, WIREs Syst. Biol. Med. 5: 273–287 (2013).
- W. Fu, A. Ergun*, T. Lu*, J. Hill, S. Haxhinasto, M. Fassett, R. Gazit, S. Adoro, L. Glimcher, S. Chan, P. Kastner, D. Rossi, J. Collins, D. Mathis, C. Benoist, A multiply redundant genetic switch locks in the transcriptional signature of Treg cells, Nature Immunology. 13: 972-980 (2012). (*Equal contribution)
- W. Ruder*, T. Lu*, and J. Collins, Synthetic biology moving into the clinic, Science. 333: 1248-1252 (2011). (*Equal contribution)
- J. Beal, T. Lu, and R. Weiss, Automatic compilation from high-level language to genetic regulatory networks, PLoS One. 6(8): e22490 (13pp) (2011).
- 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).
- T. Lu, M. Ferry, R. Weiss, and J. Hasty, A molecular noise generator, Phys. Biol. 5: 036006 (8pp) (2008).
- 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).
- 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).
- 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).
- T. Lu, J. Hasty, and P. Wolynes, Effective temperature in stochastic kinetics and gene networks, Biophys. J. 91: 84-94 (2006).
- T. Lu, D. Volfson, L. Tsimring and J. Hasty, Cellular growth and division in the Gillespie algorithm, Syst. Biol. 1:121-127 (2004).
- T. Lu and Y. Li, Mesoscopic circuit with linear dissipation, Mod. Phys. Lett. B, 16: 975-979 (2002).