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Stochastic mRNA Synthesis in Mammalian Cells

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Cited by:

  1. Anton J M Larsson & Christoph Ziegenhain & Michael Hagemann-Jensen & Björn Reinius & Tina Jacob & Tim Dalessandri & Gert-Jan Hendriks & Maria Kasper & Rickard Sandberg, 2021. "Transcriptional bursts explain autosomal random monoallelic expression and affect allelic imbalance," PLOS Computational Biology, Public Library of Science, vol. 17(3), pages 1-16, March.
  2. Mohammad Soltani & Cesar A Vargas-Garcia & Duarte Antunes & Abhyudai Singh, 2016. "Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-23, August.
  3. Samuel M D Oliveira & Antti Häkkinen & Jason Lloyd-Price & Huy Tran & Vinodh Kandavalli & Andre S Ribeiro, 2016. "Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements," PLOS Computational Biology, Public Library of Science, vol. 12(10), pages 1-18, October.
  4. Abhyudai Singh & Mohammad Soltani, 2013. "Quantifying Intrinsic and Extrinsic Variability in Stochastic Gene Expression Models," PLOS ONE, Public Library of Science, vol. 8(12), pages 1-12, December.
  5. Jonathan Liu & Donald Hansen & Elizabeth Eck & Yang Joon Kim & Meghan Turner & Simon Alamos & Hernan Garcia, 2021. "Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage," PLOS Computational Biology, Public Library of Science, vol. 17(5), pages 1-26, May.
  6. Chen, Aimin & Tian, Tianhai & Chen, Yiren & Zhou, Tianshou, 2022. "Stochastic analysis of a complex gene-expression model," Chaos, Solitons & Fractals, Elsevier, vol. 160(C).
  7. Daphne Ezer & Victoria Moignard & Berthold Göttgens & Boris Adryan, 2016. "Determining Physical Mechanisms of Gene Expression Regulation from Single Cell Gene Expression Data," PLOS Computational Biology, Public Library of Science, vol. 12(8), pages 1-28, August.
  8. Namiko Mitarai & Ian B Dodd & Michael T Crooks & Kim Sneppen, 2008. "The Generation of Promoter-Mediated Transcriptional Noise in Bacteria," PLOS Computational Biology, Public Library of Science, vol. 4(7), pages 1-9, July.
  9. Elijah Roberts & Andrew Magis & Julio O Ortiz & Wolfgang Baumeister & Zaida Luthey-Schulten, 2011. "Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study," PLOS Computational Biology, Public Library of Science, vol. 7(3), pages 1-21, March.
  10. Singh, Abhyudai & Vahdat, Zahra & Xu, Zikai, 2019. "Time-triggered stochastic hybrid systems with two timer-dependent resets," OSF Preprints u8fzg, Center for Open Science.
  11. William C. W. Chen & Leonid Gaidukov & Yong Lai & Ming-Ru Wu & Jicong Cao & Michael J. Gutbrod & Gigi C. G. Choi & Rachel P. Utomo & Ying-Chou Chen & Liliana Wroblewska & Manolis Kellis & Lin Zhang & , 2022. "A synthetic transcription platform for programmable gene expression in mammalian cells," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  12. 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.
  13. Amy L. Hughes & Aleksander T. Szczurek & Jessica R. Kelley & Anna Lastuvkova & Anne H. Turberfield & Emilia Dimitrova & Neil P. Blackledge & Robert J. Klose, 2023. "A CpG island-encoded mechanism protects genes from premature transcription termination," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
  14. Alistair N Boettiger & Peter L Ralph & Steven N Evans, 2011. "Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability," PLOS Computational Biology, Public Library of Science, vol. 7(5), pages 1-14, May.
  15. Irene Robles-Rebollo & Sergi Cuartero & Adria Canellas-Socias & Sarah Wells & Mohammad M. Karimi & Elisabetta Mereu & Alexandra G. Chivu & Holger Heyn & Chad Whilding & Dirk Dormann & Samuel Marguerat, 2022. "Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  16. Zachary R Fox & Brian Munsky, 2019. "The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments," PLOS Computational Biology, Public Library of Science, vol. 15(1), pages 1-23, January.
  17. Vendula Rusnakova & Pavel Honsa & David Dzamba & Anders Ståhlberg & Mikael Kubista & Miroslava Anderova, 2013. "Heterogeneity of Astrocytes: From Development to Injury – Single Cell Gene Expression," PLOS ONE, Public Library of Science, vol. 8(8), pages 1-15, August.
  18. Ross D. Jones & Yili Qian & Katherine Ilia & Benjamin Wang & Michael T. Laub & Domitilla Del Vecchio & Ron Weiss, 2022. "Robust and tunable signal processing in mammalian cells via engineered covalent modification cycles," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
  19. Matthieu Wyart & David Botstein & Ned S Wingreen, 2010. "Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data," PLOS Computational Biology, Public Library of Science, vol. 6(11), pages 1-14, November.
  20. Xinyu Hu & Bob van Sluijs & Óscar García-Blay & Yury Stepanov & Koen Rietrae & Wilhelm T. S. Huck & Maike M. K. Hansen, 2024. "ARTseq-FISH reveals position-dependent differences in gene expression of micropatterned mESCs," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
  21. Song, Yi & Xu, Wei & Wei, Wei & Niu, Lizhi, 2023. "Dynamical transition of phenotypic states in breast cancer system with Lévy noise," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 627(C).
  22. Vivekanandan Ramalingam & Xinyang Yu & Brian D. Slaughter & Jay R. Unruh & Kaelan J. Brennan & Anastasiia Onyshchenko & Jeffrey J. Lange & Malini Natarajan & Michael Buck & Julia Zeitlinger, 2023. "Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  23. Muir Morrison & Manuel Razo-Mejia & Rob Phillips, 2021. "Reconciling kinetic and thermodynamic models of bacterial transcription," PLOS Computational Biology, Public Library of Science, vol. 17(1), pages 1-30, January.
  24. Michi Miura & Supravat Dey & Saumya Ramanayake & Abhyudai Singh & David S Rueda & Charles R M Bangham, 2019. "Kinetics of HTLV-1 reactivation from latency quantified by single-molecule RNA FISH and stochastic modelling," PLOS Pathogens, Public Library of Science, vol. 15(11), pages 1-20, November.
  25. Qiwen Sun & Zhaohang Cai & Chunjuan Zhu, 2022. "A Novel Dynamical Regulation of mRNA Distribution by Cross-Talking Pathways," Mathematics, MDPI, vol. 10(9), pages 1-14, May.
  26. Marc S Sherman & Barak A Cohen, 2014. "A Computational Framework for Analyzing Stochasticity in Gene Expression," PLOS Computational Biology, Public Library of Science, vol. 10(5), pages 1-13, May.
  27. Jingyao Wang & Shihe Zhang & Hongfang Lu & Heng Xu, 2022. "Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
  28. Pranidhi Sood & Robert J Johnston Jr. & Edo Kussell, 2012. "Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina," PLOS Computational Biology, Public Library of Science, vol. 8(2), pages 1-13, February.
  29. Anissa Guillemin & Ronan Duchesne & Fabien Crauste & Sandrine Gonin-Giraud & Olivier Gandrillon, 2019. "Drugs modulating stochastic gene expression affect the erythroid differentiation process," PLOS ONE, Public Library of Science, vol. 14(11), pages 1-19, November.
  30. Stuart Aitken & Marie-Cécile Robert & Ross D Alexander & Igor Goryanin & Edouard Bertrand & Jean D Beggs, 2010. "Processivity and Coupling in Messenger RNA Transcription," PLOS ONE, Public Library of Science, vol. 5(1), pages 1-12, January.
  31. Matthew Antel & Romir Raj & Madona Y. G. Masoud & Ziwei Pan & Sheng Li & Barbara G. Mellone & Mayu Inaba, 2022. "Interchromosomal interaction of homologous Stat92E alleles regulates transcriptional switch during stem-cell differentiation," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
  32. Cemal Erdem & Arnab Mutsuddy & Ethan M. Bensman & William B. Dodd & Michael M. Saint-Antoine & Mehdi Bouhaddou & Robert C. Blake & Sean M. Gross & Laura M. Heiser & F. Alex Feltus & Marc R. Birtwistle, 2022. "A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
  33. Rajesh Ramaswamy & Ivo F Sbalzarini & Nélido González-Segredo, 2011. "Noise-Induced Modulation of the Relaxation Kinetics around a Non-Equilibrium Steady State of Non-Linear Chemical Reaction Networks," PLOS ONE, Public Library of Science, vol. 6(1), pages 1-10, January.
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