Simulation of E. coli Gene Regulation including Overlapping Cell Cycles, Growth, Division, Time Delays and Noise
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DOI: 10.1371/journal.pone.0062380
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References listed on IDEAS
- Gürol M. Süel & Jordi Garcia-Ojalvo & Louisa M. Liberman & Michael B. Elowitz, 2006. "An excitable gene regulatory circuit induces transient cellular differentiation," Nature, Nature, vol. 440(7083), pages 545-550, March.
- Johan Paulsson, 2004. "Summing up the noise in gene networks," Nature, Nature, vol. 427(6973), pages 415-418, January.
- Erez Dekel & Uri Alon, 2005. "Optimality and evolutionary tuning of the expression level of a protein," Nature, Nature, vol. 436(7050), pages 588-592, July.
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