Publications

Recent publications

  • 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.