Reconciling kinetic and thermodynamic models of bacterial transcription
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DOI: 10.1371/journal.pcbi.1008572
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References listed on IDEAS
- Thomas B. Kepler & Timothy C. Elston, 2001. "Stochasticity in Transcriptional Regulation: Origins, Consequences and Mathematical Representations," Working Papers 01-06-033, Santa Fe Institute.
- Jason Gertz & Eric D. Siggia & Barak A. Cohen, 2009. "Analysis of combinatorial cis-regulation in synthetic and genomic promoters," Nature, Nature, vol. 457(7226), pages 215-218, January.
- Mattias Rydenfelt & Hernan G Garcia & Robert Sidney Cox III & Rob Phillips, 2014. "The Influence of Promoter Architectures and Regulatory Motifs on Gene Expression in Escherichia coli," PLOS ONE, Public Library of Science, vol. 9(12), pages 1-31, December.
- Arjun Raj & Charles S Peskin & Daniel Tranchina & Diana Y Vargas & Sanjay Tyagi, 2006. "Stochastic mRNA Synthesis in Mammalian Cells," PLOS Biology, Public Library of Science, vol. 4(10), pages 1-13, September.
- Niraj Kumar & Abhyudai Singh & Rahul V Kulkarni, 2015. "Transcriptional Bursting in Gene Expression: Analytical Results for General Stochastic Models," PLOS Computational Biology, Public Library of Science, vol. 11(10), pages 1-22, October.
- Bruno MC Martins & Peter S Swain, 2011. "Trade-Offs and Constraints in Allosteric Sensing," PLOS Computational Biology, Public Library of Science, vol. 7(11), pages 1-13, November.
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Cited by:
- Vinodh Kandavalli & Spartak Zikrin & Johan Elf & Daniel Jones, 2025. "Anti-correlation of LacI association and dissociation rates observed in living cells," Nature Communications, Nature, vol. 16(1), pages 1-9, December.
- Tatiana N. Lakhova & Fedor V. Kazantsev & Aleksey M. Mukhin & Nikolay A. Kolchanov & Yury G. Matushkin & Sergey A. Lashin, 2022. "Algorithm for the Reconstruction of Mathematical Frame Models of Bacterial Transcription Regulation," Mathematics, MDPI, vol. 10(23), pages 1-9, November.
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