Uncoupled Analysis of Stochastic Reaction Networks in Fluctuating Environments
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DOI: 10.1371/journal.pcbi.1003942
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- Dmitri Volfson & Jennifer Marciniak & William J. Blake & Natalie Ostroff & Lev S. Tsimring & Jeff Hasty, 2006. "Origins of extrinsic variability in eukaryotic gene expression," Nature, Nature, vol. 439(7078), pages 861-864, February.
- Clive G Bowsher & Margaritis Voliotis & Peter S Swain, 2013. "The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks," PLOS Computational Biology, Public Library of Science, vol. 9(3), pages 1-9, March.
- Ioannis Lestas & Glenn Vinnicombe & Johan Paulsson, 2010. "Fundamental limits on the suppression of molecular fluctuations," Nature, Nature, vol. 467(7312), pages 174-178, September.
- Thomas B. Kepler & Timothy C. Elston, 2001. "Stochasticity in Transcriptional Regulation: Origins, Consequences and Mathematical Representations," Working Papers 01-06-033, Santa Fe Institute.
- K. Giesecke & H. Kakavand & M. Mousavi, 2011. "Exact Simulation of Point Processes with Stochastic Intensities," Operations Research, INFORMS, vol. 59(5), pages 1233-1245, October.
- P. A. W Lewis & G. S. Shedler, 1979. "Simulation of nonhomogeneous poisson processes by thinning," Naval Research Logistics Quarterly, John Wiley & Sons, vol. 26(3), pages 403-413, September.
- Alejandro Colman-Lerner & Andrew Gordon & Eduard Serra & Tina Chin & Orna Resnekov & Drew Endy & C. Gustavo Pesce & Roger Brent, 2005. "Regulated cell-to-cell variation in a cell-fate decision system," Nature, Nature, vol. 437(7059), pages 699-706, September.
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Cited by:
- Margaritis Voliotis & Philipp Thomas & Ramon Grima & Clive G Bowsher, 2016. "Stochastic Simulation of Biomolecular Networks in Dynamic Environments," PLOS Computational Biology, Public Library of Science, vol. 12(6), pages 1-18, June.
- Zhou Fang & Ankit Gupta & Sant Kumar & Mustafa Khammash, 2024. "Advanced methods for gene network identification and noise decomposition from single-cell data," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Deena R Schmidt & Roberto F Galán & Peter J Thomas, 2018. "Stochastic shielding and edge importance for Markov chains with timescale separation," PLOS Computational Biology, Public Library of Science, vol. 14(6), pages 1-35, June.
- Gennady Gorin & John J. Vastola & Meichen Fang & Lior Pachter, 2022. "Interpretable and tractable models of transcriptional noise for the rational design of single-molecule quantification experiments," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
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