Summing up the noise in gene networks

Stochastic Gene Expression in a Single Cell

Elowitz, M. B., Levine, A. J., Siggia, E. D., & Swain, P. S. (2002) · Science · doi:10.1126/science.1070919 · Cited by 5,441

Intrinsic and extrinsic contributions to stochasticity in gene expression

Swain, P. S., Elowitz, M. B., & Siggia, E. D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162041399 · Cited by 1,661

Intrinsic noise in gene regulatory networks

Thattai, M., & van Oudenaarden, A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.151588598 · Cited by 1,428

ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON

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Noise in the nervous system

Faisal, A. A., Selen, L. P. J., & Wolpert, D. M. (2008) · Nature Reviews Neuroscience · doi:10.1038/nrn2258 · Cited by 2,883

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Raj, A., & van Oudenaarden, A. (2008) · Cell · doi:10.1016/j.cell.2008.09.050 · Cited by 2,593

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

Taniguchi, Y., Choi, P. J., Li, G.-W., Chen, H., Babu, M., Hearn, J., Emili, A., & Xie, X. S. (2010) · Science · doi:10.1126/science.1188308 · Cited by 1,982

Stochastic mRNA Synthesis in Mammalian Cells

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Real-Time Kinetics of Gene Activity in Individual Bacteria

Golding, I., Paulsson, J., Zawilski, S. M., & Cox, E. C. (2005) · Cell · doi:10.1016/j.cell.2005.09.031 · Cited by 1,468

Roles for MicroRNAs in Conferring Robustness to Biological Processes

Ebert, M. S., & Sharp, P. A. (2012) · Cell · doi:10.1016/j.cell.2012.04.005 · Cited by 1,564

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006) · Nature · doi:10.1038/nature04785 · Cited by 1,483

Control of Stochasticity in Eukaryotic Gene Expression

Raser, J. M., & O'Shea, E. K. (2004) · Science · doi:10.1126/science.1098641 · Cited by 1,425

Gene Regulation at the Single-Cell Level

Rosenfeld, N., Young, J. W., Alon, U., Swain, P. S., & Elowitz, M. B. (2005) · Science · doi:10.1126/science.1106914 · Cited by 1,104

Probing Gene Expression in Live Cells, One Protein Molecule at a Time

Yu, J., Xiao, J., Ren, X., Lao, K., & Xie, X. S. (2006) · Science · doi:10.1126/science.1119623 · Cited by 918

Noise in protein expression scales with natural protein abundance

Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O'Shea, E., Pilpel, Y., & Barkai, N. (2006) · Nature Genetics · doi:10.1038/ng1807 · Cited by 807

Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression

Friedman, N., Cai, L., & Xie, X. S. (2006) · Physical Review Letters · doi:10.1103/physrevlett.97.168302 · Cited by 700

Comparison and evaluation of statistical error models for scRNA-seq

Choudhary, S., & Satija, R. (2022) · Genome Biology · doi:10.1186/s13059-021-02584-9 · Cited by 634

Physicochemical modelling of cell signalling pathways

Aldridge, B. B., Burke, J. M., Lauffenburger, D. A., & Sorger, P. K. (2006) · Nature Cell Biology · doi:10.1038/ncb1497 · Cited by 592

Canalization of development by microRNAs

Hornstein, E., & Shomron, N. (2006) · Nature Genetics · doi:10.1038/ng1803 · Cited by 578

Effects of Molecular Memory and Bursting on Fluctuations in Gene Expression

Pedraza, J. M., & Paulsson, J. (2008) · Science · doi:10.1126/science.1144331 · Cited by 404

Eukaryotic transcriptional dynamics: from single molecules to cell populations

Coulon, A., Chow, C. C., Singer, R. H., & Larson, D. R. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3484 · Cited by 309

Nuclear Retention of mRNA in Mammalian Tissues

Bahar Halpern, K., Caspi, I., Lemze, D., Levy, M., Landen, S., Elinav, E., Ulitsky, I., & Itzkovitz, S. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.11.036 · Cited by 258

Evidence that Fold-Change, and Not Absolute Level, of β-Catenin Dictates Wnt Signaling

Goentoro, L., & Kirschner, M. W. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.017 · Cited by 300

RNA dynamics in live Escherichia coli cells

Golding, I., & Cox, E. C. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0404443101 · Cited by 288

Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation

Kueh, H. Y., Champhekar, A., Nutt, S. L., Elowitz, M. B., & Rothenberg, E. V. (2013) · Science · doi:10.1126/science.1240831 · Cited by 273

From the stochasticity of molecular processes to the variability of synaptic transmission

Ribrault, C., Sekimoto, K., & Triller, A. (2011) · Nature Reviews Neuroscience · doi:10.1038/nrn3025 · Cited by 198

Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae

Stewart-Ornstein, J., Weissman, J. S., & El-Samad, H. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.11.035 · Cited by 177

The Utility of Paradoxical Components in Biological Circuits

Hart, Y., & Alon, U. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.004 · Cited by 151

FISH-ing for captured contacts: towards reconciling FISH and 3C

Fudenberg, G., & Imakaev, M. (2017) · Nature Methods · doi:10.1038/nmeth.4329 · Cited by 141

Stochastic fluctuations in metabolic pathways

Levine, E., & Hwa, T. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610987104 · Cited by 132

Aneuploidy Causes Non-genetic Individuality

Beach, R. R., Ricci-Tam, C., Brennan, C. M., Moomau, C. A., Hsu, P.-H., Hua, B., Silberman, R. E., Springer, M., & Amon, A. (2017) · Cell · doi:10.1016/j.cell.2017.03.021 · Cited by 109

Dissecting the expression dynamics of RNA-binding proteins in posttranscriptional regulatory networks

Mittal, N., Roy, N., Babu, M. M., & Janga, S. C. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0906940106 · Cited by 103

Implementation of Dynamic Bayesian Decision Making by Intracellular Kinetics

Kobayashi, T. J. (2010) · Physical Review Letters · doi:10.1103/physrevlett.104.228104 · Cited by 68

Combined Model of Intrinsic and Extrinsic Variability for Computational Network Design with Application to Synthetic Biology

Toni, T., & Tidor, B. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002960 · Cited by 62

Near-Critical Behavior of Aminoacyl-tRNA Pools in E. coli at Rate-Limiting Supply of Amino Acids

Elf, J., & Ehrenberg, M. (2005) · Biophysical Journal · doi:10.1529/biophysj.104.051383 · Cited by 46

Systems biology: from physiology to gene regulation

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Pathway dynamics can delineate the sources of transcriptional noise in gene expression

Ham, L., Jackson, M., & Stumpf, M. P. (2021) · eLife · doi:10.7554/elife.69324 · Cited by 37

Noise Control in Gene Regulatory Networks with Negative Feedback

Hinczewski, M., & Thirumalai, D. (2016) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.6b02093 · Cited by 15

Variability of the innate immune response is globally constrained by transcriptional bursting

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Theory for optimal estimation and control under resource limitations and its applications to biological information processing and decision-making

Tottori, T., & Kobayashi, T. J. (2025) · Physical Review Research · doi:10.1103/gvl6-cvby · Cited by 6

Exact distributions of threshold crossing times of proteins under post-transcriptional regulation by small RNAs

Ali, S. Y., Prasad, A., & Das, D. (2025) · Physical Review E · doi:10.1103/physreve.111.014405 · Cited by 2

Nearly maximal information gain due to time integration in central dogma reactions

Sarkar, S., & Rammohan, J. (2023) · iScience · doi:10.1016/j.isci.2023.106767