A Stochastic Single-Molecule Event Triggers Phenotype Switching of a Bacterial Cell

Genetic regulatory mechanisms in the synthesis of proteins.

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Stochasticity in gene expression: from theories to phenotypes

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Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-Infected Escherichia coli Cells

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Stochastic protein expression in individual cells at the single molecule level

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Gene Regulation at the Single-Cell Level

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Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell

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Multistability in the lactose utilization network of Escherichia coli

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

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ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON

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Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations

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Epigenetic Ratchet: Spontaneous Adaptation via Stochastic Gene Expression

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Event-triggered feedback in noise-driven phase oscillators

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Origins of Transcriptional Transition: Balance between Upstream and Downstream Regulatory Gene Sequences

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Prions and Prion-like Phenomena in Epigenetic Inheritance

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Molecular-memory-driven phenotypic switching in a genetic toggle switch without cooperative binding

Qiu, B., Zhou, T., & Zhang, J. (2020) · Physical review. E · doi:10.1103/physreve.101.022409 · Cited by 6

Anticipating response function in gene regulatory networks

Gautam, P., & Sinha, S. K. (2021) · Journal of The Royal Society Interface · doi:10.1098/rsif.2021.0206 · Cited by 6

Numbers on the edges: A simplified and scalable method for quantifying the Gene Regulation Function

Fernández-López, R., del Campo, I., Ruiz, R., Lanza, V. F., Vielva, L., & de la Cruz, F. (2010) · BioEssays · doi:10.1002/bies.200900164 · Cited by 6

Modeling the effect of transcriptional noise on switching in gene networks in a genetic bistable switch

Chaudhury, S. (2015) · Journal of Biological Physics · doi:10.1007/s10867-015-9375-2 · Cited by 6

Harnessing microbial heterogeneity for improved biosynthesis fueled by synthetic biology

Cao, Y., Li, J., Liu, L., Du, G., & Liu, Y. (2024) · Synthetic and Systems Biotechnology · doi:10.1016/j.synbio.2024.11.004 · Cited by 4

Irreversible Stochastic Processes, Coupled Diffusions and Systems Biochemistry

Shi, P.-Z., & Qian, H. (2010) · Computational biology · doi:10.1007/978-1-84996-196-7_9 · Cited by 5

Kinetic approaches to lactose operon induction and bimodality

Michel, D. (2013) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2013.02.005 · Cited by 5

Temperature-dependence of the single-cell variability in the kinetics of transcription activation in Escherichia coli

Goncalves, N. S. M., Startceva, S., Palma, C. S. D., Bahrudeen, M. N. M., Oliveira, S. M. D., & Ribeiro, A. S. (2017) · Physical Biology · doi:10.1088/1478-3975/aa9ddf · Cited by 5

Kinetic characteristics of transcriptional bursting in a complex gene model with cyclic promoter structure

Yang, X., Wang, Z., Wu, Y., Zhou, T., & Zhang, J. (2022) · Mathematical Biosciences & Engineering · doi:10.3934/mbe.2022153 · Cited by 5

Technologies for whole‐cell modeling: Genome‐wide reconstruction of a cell in silico

Kaizu, K., & Takahashi, K. (2023) · Development Growth & Differentiation · doi:10.1111/dgd.12897 · Cited by 4

Transcriptional Bursting in the Tryptophan Operon of E. coli and Its Effect on the System Stochastic Dynamics

Salazar-Cavazos, E., & Santill, M. (2012) · InTech eBooks · doi:10.5772/36220 · Cited by 5

Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors

Sala, A., Shoaib, M., Anufrieva, O., Mutharasu, G., Hoque, R., Yli-Harja, O. P., & Kandhavelu, M. (2015) · Physical Biology · doi:10.1088/1478-3975/12/3/036003 · Cited by 5

Epitope-Tagged Autotransporters as Single-Cell Reporters for Gene Expression by a Salmonella Typhimurium wbaP Mutant

Curkić, I., Schütz, M. S., Oberhettinger, P., Diard, M., Claassen, M., Linke, D., & Hardt, W. (2016) · PLoS ONE · doi:10.1371/journal.pone.0154828 · Cited by 5

Rethinking (again) Hardy-Weinberg and genetic drift in undergraduate biology

Klymkowsky, M. W. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1199739 · Cited by 5

The unreasonable effectiveness of equilibrium gene regulation through the cell cycle

Vilar, J. M. G., & Saiz, L. (2024) · Cell Systems · doi:10.1016/j.cels.2024.06.002 · Cited by 4

Effects of elongation delay in transcription dynamics

Zhang, X., Jin, H., Yang, Z., & Lei, J. (2014) · Mathematical Biosciences & Engineering · doi:10.3934/mbe.2014.11.1431 · Cited by 4

Efficient and flexible implementation of Langevin simulation for gene burst production

Yan, C. S., Chepyala, S. R., Yen, C.-M., & Hsu, C. (2017) · Scientific Reports · doi:10.1038/s41598-017-16835-y · Cited by 5

Analytical Expressions and Physics for Single-Cell mRNA Distributions of the lac Operon of E. coli

Choudhary, K., & Narang, A. (2019) · Biophysical Journal · doi:10.1016/j.bpj.2019.06.029 · Cited by 5

Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry

Kalay, Z. (2011) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409238.2011.582081 · Cited by 5

Inference of Kinetic Parameters of Delayed Stochastic Models of Gene Expression Using a Markov Chain Approximation

Mannerström, H., Yli-Harja, O. P., & Ribeiro, A. S. (2010) · EURASIP Journal on Bioinformatics and Systems Biology · doi:10.1155/2011/572876 · Cited by 5

Tracking of individual freely diffusing fluorescent protein molecules in the bacterial cytoplasmPreprint

English, B. P., Sanamrad, A., Tankov, S., Hauryliuk, V., & Elf, J. (2010) · arXiv (Cornell University) · doi:10.48550/arxiv.1003.2110 · Cited by 5

Cell-cycle dependence of transcription dominates noise in gene expression

Zopf, C. J., Quinn, K., Zeidman, J., & Maheshri, N. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003161 · Cited by 4

Quantifying heterogeneity of stochastic gene expression

Iida, K., Obata, N., & Kimura, Y. (2019) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2019.01.003 · Cited by 3

Investigating the Gap between Discrete and Continuous Models of Chemically Reacting Systems

Haruna, T. (2010) · Journal of Computer Chemistry Japan · doi:10.2477/jccj.h2110 · Cited by 4

Nonlocal dynamics in a gene regulatory system with tempered stable Lévy noise

Xiao, Y., & Zeng, C. (2020) · Communications in Nonlinear Science and Numerical Simulation · doi:10.1016/j.cnsns.2020.105178 · Cited by 4

Robustness of DNA looping across multiple cell divisions in individual bacteria

Chang, C., Garcia-Alcala, M., Saiz, L., Vilar, J. M. G., & Cluzel, P. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2200061119 · Cited by 3

Theoretical investigation of functional responses of bio-molecular assembly networks

Gautam, P., & Sinha, S. K. (2023) · Soft Matter · doi:10.1039/d2sm01530g · Cited by 4

Distinguishing the rates of gene activation from phenotypic variations

Chen, Y., Lv, C., Li, F., & Li, T. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0172-0 · Cited by 4

A Mechanism for Stochastic Decision Making by Bacteria

Hensel, Z., & Xiao, J. (2009) · ChemBioChem · doi:10.1002/cbic.200800824 · Cited by 4

The accuracy of biochemical interactions is ensured by endothermic stepwise kinetics

Michel, D., Boutin, B., & Ruelle, P. (2016) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2016.02.001 · Cited by 4

Fluctuating-rate model with multiple gene states

Li, J., Ge, H., & Zhang, Y. (2020) · Journal of Mathematical Biology · doi:10.1007/s00285-020-01538-2 · Cited by 4

Analysis of Fluorescent Proteins for Observing Single Gene Locus in a Live and Fixed Escherichia coli Cell

Son, J. B., Kim, S.-H., Yang, S., Ahn, Y., & Lee, N. K. (2024) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.4c01816 · Cited by 4

Quantifying Waddington landscapes, paths, and kinetics of cell fate decision making of differentiation/development

Xu, L., & Wang, J. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-817996-3.00002-5 · Cited by 3

Phenotypic Heterogeneity inMycobacterium tuberculosis

Dhar, N., McKinney, J. D., & Manina, G. (2017) · ASM Press eBooks · doi:10.1128/9781555819569.ch32 · Cited by 2

Integrated microfluidic systems for genetic analysis

Jakaratanopas, S., Zhuang, B., Gan, W., & Liu, P. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-819971-8.00004-4 · Cited by 3

Quantification of Functional Dynamics of Membrane Proteins Reconstituted in Nanodiscs Membranes by Single Turnover Functional Readout

Moses, M. E., Hedegård, P., & Hatzakis, N. S. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.08.026 · Cited by 3

Single-molecule methods for studying gene regulation in vivo

Hensel, Z., & Xiao, J. (2013) · Pflügers Archiv - European Journal of Physiology · doi:10.1007/s00424-013-1243-y · Cited by 3

Integrated microfluidic systems for genetic analysis

Zhuang, B., Gan, W., & Liu, P. (2013) · Elsevier eBooks · doi:10.1533/9780857097040.4.465 · Cited by 3

molecule precision biological questions in living, functioning cells with single Experimental approaches for addressing fundamental

Lenn, T., & Leake, M. C. (2012) · Cited by 3

Chance Events in Aging

Steinsaltz, D., Christodoulou, M. D., Cohen, A. A., & Steiner, U. K. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11394-7 · Cited by 2

Urn models for stochastic gene expression yield intuitive insights into the probability distributions of single-cell mRNA and protein counts

Choudhary, K., & Narang, A. (2020) · Physical Biology · doi:10.1088/1478-3975/aba50f · Cited by 3

Quantum information processing at the cellular level. Euclidean approachPreprint

Ogryzko, V. V. (2009) · arXiv (Cornell University) · doi:10.48550/arxiv.0906.4279 · Cited by 3

Transcriptional Initiation: Frequency, Bursting, and Transcription Factories

Finan, K., & Cook, P. R. (2011) · Wiley eBooks · doi:10.1002/9783527639991.ch10 · Cited by 4

Natural Agency: An Ecological Approach

Garza, D. L., & Fulda, F. C. (2016) · Cited by 3

Temporal tuning of switch-like virulence expression resolves environmental uncertainty through phenotypic heterogeneity

Spratt, M. R., & Lane, K. M. (2026) · Current Biology · doi:10.1016/j.cub.2026.06.001 · Cited by 3

Noise equals control

DeGiuli, E. (2025) · Physical review. E · doi:10.1103/vlx8-spc6 · Cited by 2

Consensus of multi-agent systems under variable denial-of-service attacks: Noise-based event-triggered protocols

Li, S., Gao, Y., & Li, W. (2025) · Applied Mathematics and Computation · doi:10.1016/j.amc.2025.129842 · Cited by 2

Applications

Érdi, P., & Lente, G. (2014) · Springer series in synergetics · doi:10.1007/978-1-4939-0387-0_3 · Cited by 2

Single molecule investigations of DNA looping using the tethered particle method and translocation by acto-myosin using polarized total internal reflection fluorescence microscopy

Beausang, J. F. (2010) · ScholarlyCommons (University of Pennsylvania) · Cited by 2

Extending the tools of single‐molecule fluorescence imaging to problems in microbiology

Biteen, J. S. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08089.x · Cited by 2

Finite-size effects in dynamics of zero-range processes

Juntunen, J., Pulkkinen, O. I., & Merikoski, J. (2010) · Physical Review E · doi:10.1103/physreve.82.031119 · Cited by 2

Quantitative Single-Cell Gene Expression Measurements in Bacteria Using Time-Lapse Microscopy

Dunlop, M. J. (2014) · Microscopy and Microanalysis · doi:10.1017/s1431927614007600 · Cited by 2

Stochastic Simulation to Visualize Gene Expression and Error Correction in Living Cells

Chen, K. Y., Zuckerman, D. M., & Nelson, P. (2020) · The Biophysicist · doi:10.35459/tbp.2019.000101 · Cited by 2

Wasserstein Distances for Estimating Parameters in Stochastic Reaction Networks

Öcal, K., Grima, R., & Sanguinetti, G. (2019) · Lecture notes in computer science · doi:10.1007/978-3-030-31304-3_24 · Cited by 2

Global quantitative understanding of non-equilibrium cell fate decision-making in response to pheromone

Li, S., Liu, Q., Wang, E., & Wang, J. (2023) · iScience · doi:10.1016/j.isci.2023.107885 · Cited by 2

Time-Lapse Transcription

Nair, G. P., & Raj, A. (2011) · Science · doi:10.1126/science.1205995 · Cited by 2

Potential landscape of high dimensional nonlinear stochastic dynamics and rare transitions with large noisePreprint

Tang, Y., Yuan, R., Wang, G., Zhu, X., & Ao, P. (2016) · arXiv (Cornell University) · Cited by 2

Cell fate determination by Lamarckian molecule-inheritance and chancePreprint

Bruggeman, F. J., Schouten, J., de Groot, D. H., & Planqué, R. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/618199 · Cited by 2

Colony pattern development of a synthetic bistable switchPreprint

Chu, P., Zhu, J., Ma, Z., & Fu, X. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.17.599191 · Cited by 2

Switching off: The phenotypic transition to the uninduced state of the lactose uptake pathway

Bhogale, P. M., Sorg, R. A., Veening, J., & Berg, J. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.12.027 · Cited by 1

Growth phase-dependent ribonucleic acid production dynamics

Shoaib, M., Murugesan, A., Devanesan, S., AlSalhi, M. S., & Kandhavelu, M. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.132457 · Cited by 1

Impact of competition between precursor and mature microRNAs on stochastic gene expression

Adhikary, R., & Das, D. (2026) · Biophysical Journal · doi:10.1016/j.bpj.2026.07.010 · Cited by 1

Stochastic Effects in Quorum Sensing

Weber, M. L., & Buceta, J. (2014) · Biological and medical physics, biomedical engineering · doi:10.1007/978-1-4939-1402-9_3 · Cited by 1

Mechanoenzymatics and Nanoassembly of Single Molecules

Puchner, E. M., & Gaub, H. E. (2009) · Springer series in chemical physics · doi:10.1007/978-3-642-02597-6_15 · Cited by 1

The effect of coupled stochastic processes in a two-state biochemical switch

Graham, G., & Lipan, O. (2011) · Journal of Biological Physics · doi:10.1007/s10867-011-9226-8 · Cited by 1

Tracking translation of single mRNA molecule in live cells

Wang, W., & Chen, C. (2016) · 中国科学通报：英文版 · doi:10.1007/s11434-016-1116-9 · Cited by 1

A systematic study of the determinants of protein abundance memory in cell lineage

Gao, Z., Sun, H., Qin, S., Yang, X., & Tang, C. (2018) · 中国科学通报：英文版 · doi:10.1016/j.scib.2018.07.010 · Cited by 1

Clumped-MCEM: Inference for multistep transcriptional processes

Shetty, K. S., & Annappa, B. (2019) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2019.107092 · Cited by 1

Analysis of Single Bacterium Dynamics in a Stochastic Model of Toxin-Producing Bacteria

Paterson, J., López‐García, M., Gillard, J. J., Laws, T. R., Lythe, G., & Molina-Parı́s, C. (2021) · Lecture notes in computer science · doi:10.1007/978-3-030-91825-5_13 · Cited by 1

A new mechanism of development and differentiation through slow binding/unbinding of regulatory proteins to the genesPreprint

Feng, H., & Wang, J. (2012) · arXiv (Cornell University) · doi:10.48550/arxiv.1202.6274 · Cited by 1

Genome‐Wide Analysis of Single Cells and the Role of Microfluidics

Bose, S., & Sims, P. A. (2016) · Wiley eBooks · doi:10.1002/9783527801312.ch2 · Cited by 1

Cell-to-cell variability in the yeast pheromone response: high throughput screen identifies genes with different effects on transmitted signal and responsePreprint

Pesce, C. G., Peria, W., Zdraljevic, S., Rockwell, D., Yu, R. C., Colman‐Lerner, A., & Brent, R. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/093187 · Cited by 1

Effects of mRNA degradation and site-specific transcriptional pausing on protein expression noisePreprint

Kim, S., & Jacobs, C. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/210401 · Cited by 1

Forecasting when cells die during antibiotic exposure using stochastic gene expressionPreprint

Rossi, N. A., Meouche, I. E., & Dunlop, M. J. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/494161 · Cited by 1

Single-molecule kinetics in living cellsPreprint

Elf, J., & Barkefors, I. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1809.03265 · Cited by 1

Regulatory asymmetry in the negative single-input module network motif: Role of network size, growth rate and binding affinityPreprint

Ali, M. Z., Parisutham, V., Choubey, S., & Brewster, R. C. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/865527 · Cited by 1

Exact computation of growth-rate fluctuations in random environmentPreprint

Unterberger, J. M. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2111.04167 · Cited by 1

Robustness of DNA Looping Across Multiple Divisions in Individual BacteriaPreprint

Chang, C., Garcia-Alcala, M., Saiz, L., Vilar, J. M. G., & Cluzel, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.28.474367 · Cited by 1

Beyond Limit Cycles

MILTON, J. G., & Ohira, T. (2014) · Springer eBooks · doi:10.1007/978-1-4614-9096-8_11

Stochastic modelling of gene expression : from single molecules to populations

Voliotis, M. (2009) · White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York) · Cited by 1

MicroBioRobots for Single Cell Manipulation

Sakar, M. S. (2010)

SIGNAL INTEGRATION IN CELL-TO-CELL COMMUNICATION

Teng, S. (2010)

Single cell RT-qPCR based ocean environmental sensing device development

Shi, X. (2013)

Le hasard au cœur de la cellule

Heams, T. (2011) · Sciences & philosophie · doi:10.3917/edmat.kupie.2011.01.0028

Background: Determinants of membrane protein dual topological orientation are not known. Results: Dual topological conformers of lactose permease co-exist in proportion to membrane phospholipid composition. Post-assembly changes in phospholipid composition alter the proportional amounts. Conclusion: Dual conformations of membrane proteins are determined during and post-assembly by lipid-protein interactions. Significance: A thermodynamic model explains the existence of multiple conformers of …

Bogdanov, M. V., & Dowhan, W. (2012)

Genetic Analysis and Cell Manipulation on Microfluidic Surfaces

Zhu, J. (2014) · doi:10.7916/d8sn0712

Etiology of phenotype switching strategy in time varying stochastic environment

Horváth, D., & Brutovský, B. (2016) · Physica A Statistical Mechanics and its Applications · doi:10.1016/j.physa.2016.05.066

Heterogeneous Folding and Function of Small RNA Motifs: The Hairpin Ribozyme and a Translational Riboswitch.

Marek, M. S. (2014) · Deep Blue (University of Michigan)

Construction of gene circuits to control cell behavior

Hu, H. (2016)

AFTER THEEW "YEAR OF DARWI"

Rossini, L., Rossini, P., Neuroscienze, F., Ospedali, A., & Giacomo, O. S. (2010)

Stochastic models of gene expression and post-transcriptional regulation

Pendar, H., Kulkarni, R., & Jia, T. (2011) · Bulletin of the American Physical Society

Fluorescence Spectroscopy for Cell Membrane Biophysics at the Nanometer and Nanosecond Scales

Rhodes, C. (2012) · eScholarship (California Digital Library)

Evolutionary Systems Biology in Yeast

Wang, G. (2010) · Univ. Duesseldorf: Duesseldorfer Dokumenten- und Publikationsserver

Sliding mode control of decaying-dimerizing system

Lv, H., Zhou, C., & Zhang, Q. (2017) · Chinese Control Conference (CCC) · doi:10.23919/chicc.2017.8027938

Study of signal transduction in reconstituted membranes: Ras activation by SOS and RasGRP1

Tu, H. (2013) · eScholarship (California Digital Library)

Research highlights

(2008) · Nature Chemical Biology · doi:10.1038/nchembio1208-727

A Mechanism for Stochastic Decision Making by Bacteria

Hensel, Z., & Xiao, J. (2009) · ChemBioChem · doi:10.1002/cbic.200800824 · Cited by 4

What makes the lac -pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems

Bhogale, P. M., Sorg, R. A., Veening, J., & Berg, J. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku839 · Cited by 20

Pre‐dispositions and epigenetic inheritance in the Escherichia coli lactose operon bistable switch

Robert, L., Paul, G., Chen, Y., Taddéi, F., Baigl, D., & Lindner, A. B. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.12 · Cited by 75

Switching off: The phenotypic transition to the uninduced state of the lactose uptake pathway

Bhogale, P. M., Sorg, R. A., Veening, J., & Berg, J. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.12.027 · Cited by 1