David R. McMillen
Associate Professor | Ph.D.
Research
We apply a combination of experimental and theoretical techniques to study the internal dynamics of cells, with specific reference to processes such as gene expression and regulation. Working in simple organisms as such a bacteria allows us to address simplified systems by constructing our own novel genetic regulatory networks, inserting them into living cells, and comparing their behaviour to that of theoretical/computational models of biochemical reaction kinetics. We also have a program in synthetic biology, where we are interested in using these simplified genetic networks as controllers designed to alter the internal dynamics of cells in predictable ways, with the long-term goal being the ability to carry out medical interventions from inside the cell.
Publications
Marco Iafolla, Guang Qiang Dong, and DAVID R. MCMILLEN (2008). Increasing the efficiency of bacterial transcription simulations: when to exclude the genome without loss of accuracy. BMC Bioinformatics 9:373.
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.
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.
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 (U.S.A.) 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.
