Publications

Recent publications

  • Louis C. Dacquay, Derek Tsang, Donny Chan, John Parkinson, Dana J. Philpott, and David R. McMillen (2021). E. coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis. Gut Microbes 13(1), e1994832. https://doi.org/10.1080/19490976.2021.1994832 

  • Louis C. Dacquay and David R. McMillen (2021).  Improving the design of an oxidative stress sensing biosensor in yeast.  Federation of European Microbiological Societies (FEMS) Yeast Research 21, foab025. (https://doi.org/10.1093/femsyr/foab025).

  • Milos Legner, David R. McMillen, and Dennis G. Cvitkovitch (2019). Role of dilution rate and nutrient availability in the formation of microbial biofilms.  Frontiers in Microbiology. (https://doi.org/10.3389/fmicb.2019.00916).

  • Brendan J. Hussey and David R. McMillen (2018). Programmable T7-based synthetic transcription factors.  Nucleic Acids Research 46(18): 9842–9854.
  • Zhe F. Tang and David R. McMillen (2016). Design principles for the analysis and construction of robustly homeostatic biological networks. Journal of Theoretical Biology 408, 274-289.
  • Edouard A. Harris, Eun Jee Koh, Jason Moffat, and David R. McMillen (2016).  Automated inference procedure for the determination of cell growth parameters.  Physical Review E 93: 012402.
  • Mostafizur Mazumder, Katherine E. Brechun, Yongjoo B. Kim, Stefan A. Hoffmann, Yih Yang Chen, Carrie-Lynn Keiski, Katja M. Arndt, David R. McMillen and G. Andrew Woolley (2015).  An E. coli system for evolving improved light-controlled DNA-binding proteins.  Protein Engineering, Design, and Selection 28 (9): 293-302.
  • Mostafizur Mazumder and David R. McMillen (2014).  Design and characterization of a dual-mode promoter with activation and repression capability for tuning gene expression in yeast.  Nucleic Acids Research 42 (14): 9514–9522.  Open access publication
  • Jordan Ang, Edouard Harris, Brendan J. Hussey, Richard Kil, and David R. McMillen (2013). Tuning response curves for synthetic biology.  ACS Synthetic Biology 2, 547-567. Open access publication.
  • Jordan Ang and David R. McMillen (2013). Physical constraints on biological integral control design for homeostasis and sensory adaptation.  Biophysical Journal 104(2): 505-515. Online publication.
  • Jordan Ang, Brian Ingalls, and David R. McMillen (2011). Probing the input-output behavior of biological systems: system identification methods from control theory.  Methods in Enzymology 487 (Computer Methods, Part C): 279-317. Online publication.
  • Sangram Bagh, Mahuya Mandal, Jordan Ang, and David R. McMillen (2011).  An active intracellular device to prevent lethal viral effects in bacteria.   Biotechnology and Bioengineering 108(3): 645-654.  Online publication.
  • Jordan Ang, Sangram Bagh, Brian P. Ingalls, and David R. McMillen (2010).  Considerations for using integral feedback control to construct a perfectly adapting synthetic gene network.  Journal of Theoretical Biology 266(4): 723-738.  Online publication.
  • Sangram Bagh, Mahuya Mandal, and David R. McMillen (2010).  Minimal genetic device with multiple tunable functions.  Physical Review E 82(2): 021911.  Online publication.
  • Sangram Bagh and David R. McMillen (2009).  A synthetic genetic circuit whose signal-response curve is temperature-tunable from band-detection to sigmoidal behaviour. Natural Computing. Online publication.
  • Marco Iafolla, Mostafizur Mazumder, Vandit Sardana, Tharsan Velauthapillai, Karanbir Pannu, and David R. McMillen (2008).  Dark proteins: inclusion body quantification. Proteins: structure, function, and bioinformatics 72: 1233-1242.
  • Sangram Bagh, Mostafizur Mazumder, Tharsan Velauthapillai, Vandit Sardana, Guang Qiang Dong, Ashok B. Movva, Len H. Lim, and David R. McMillen (2008).  Plasmid-borne prokaryotic gene expression: sources of variability and quantitative system characterization.  Physical Review E 77: 021919.
  • Guang Qiang Dong and David R. McMillen (2008).  Effects of protein maturation on the noise in gene expression.  Physical Review E 77: 021908
  • Marco Iafolla, Guang Qiang Dong, and David R. McMillen (2008).  Increasing the accuracy of bacterial transcription simulations: when to exclude the genome without loss of accuracy.  BMC Bioinformatics 9: 373.
  • Guang Qiang Dong, Luke Jakobowski, Marco Iafolla, and David R. McMillen (2007).  Simplification of stochastic chemical reaction models with fast and slow dynamics.  Journal of Biological Physics 32: 67-95.

Less-recent publications

  • Marco A. J. Iafolla and David R. McMillen (2006). Extracting biochemical parameters for cellular modeling: A ‘mean-field’ approach.  Journal of Physical Chemistry-B 110: 22019-22028.
  • Guang Qiang Dong, Luke Jakobowski, and David R. McMillen (2006). Systematic reduction of a stochastic signalling cascade model.  Journal of Biological Physics 32: 173-176.
  • Nicholas Guido, Xiao Wang, David Adalsteinsson, David R. McMillen, Jeff Hasty,  Charles Cantor, Timothy Elston, and James Collins (2006).  A bottom-up approach to gene regulation.  Nature 439: 856-860.
  • David Adalsteinsson, David R. McMillen, and Timothy C Elston (2004). Biochemical Network Stochastic Simulator (BioNetS): Software for Stochastic Modeling of Biochemical Networks.  BioMed Central  (BMC) Bioinformatics  5:24.
  • David R. McMillen and Nancy Kopell (2003). Noise-stabilized long-distance synchronization in populations of model neurons.  Journal of Computational Neuroscience 15: 143-157.
  • Jeff Hasty, David R. McMillen, and J. J. Collins (2002). Engineered gene circuits. Nature 420: 224-230.
  • David R. McMillen, Nancy Kopell, Jeff Hasty, and J. J. Collins (2002). Synchronizing genetic relaxation oscillators by intercell signaling. Proceedings  of the National Academy of Sciences (USA) 99(2):679-84.
  • Jeff Hasty, David R. McMillen, Farren Isaacs, and J. J. Collins (2001). Computational studies of gene regulatory networks: In numero molecular biology. Nature Reviews Genetics 2: 268-279.
  • Jeff Hasty, Farren Isaacs, Milos Dolnik, David R. McMillen, and J. J. Collins (2001). Designer gene networks:  Towards fundamental  cellular control. Chaos 11(1): 207-220.
  • David R. McMillen, Gabriele D'Eleuterio, and Janet Halperin (1999). Simple central pattern generator  model using phasic analog neurons. Physical Review E 59(6): 6994-6999.