Stochasticity in gene expression: from theories to phenotypes

Network biology: understanding the cell's functional organization

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Stochastic Gene Expression in a Single Cell

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Bacterial Persistence as a Phenotypic Switch

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Biological robustness

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Intrinsic and extrinsic contributions to stochasticity in gene expression

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Intrinsic noise in gene regulatory networks

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Control of Stochasticity in Eukaryotic Gene Expression

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Multistability in the lactose utilization network of Escherichia coli

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ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON

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Network motifs: theory and experimental approaches

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Persister cells, dormancy and infectious disease

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Persister cells

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Real-Time Kinetics of Gene Activity in Individual Bacteria

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The changing demographic pattern of multiple sclerosis epidemiology

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Computational and analytical challenges in single-cell transcriptomics

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Analytical distributions for stochastic gene expression

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Direct cell reprogramming is a stochastic process amenable to acceleration

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Noise in protein expression scales with natural protein abundance

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What Is Stochastic Resonance? Definitions, Misconceptions, Debates, and Its Relevance to Biology

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Single-RNA counting reveals alternative modes of gene expression in yeast

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Gene regulatory network inference: Data integration in dynamic models—A review

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MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals

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

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Noise in Gene Expression Determines Cell Fate in Bacillus subtilis

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Increased cell-to-cell variation in gene expression in ageing mouse heart

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Bifurcation dynamics in lineage-commitment in bipotent progenitor cells

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Microbial Cell Individuality and the Underlying Sources of Heterogeneity

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Dynamic regulation of transcriptional states by chromatin and transcription factors

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Single-cell analysis tools for drug discovery and development

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Cryptococcus neoformans Overcomes Stress of Azole Drugs by Formation of Disomy in Specific Multiple Chromosomes

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

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Expert performance in sport and the dynamics of talent development

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Robustness: mechanisms and consequences

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Quantification of mRNA and protein and integration with protein turnover in a bacterium

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Nuclear Retention of mRNA in Mammalian Tissues

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Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

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A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

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The Origins of Mesenchymal Stromal Cell Heterogeneity

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Coupling and coordination in gene expression processes: a systems biology view

Komili, S., & Silver, P. A. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2223 · Cited by 218

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

The sorting direct method for stochastic simulation of biochemical systems with varying reaction execution behavior

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Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA–seq

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MiRNAs confer phenotypic robustness to gene networks by suppressing biological noise

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Stochastic fluctuations in metabolic pathways

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Systems biology of stem cells: three useful perspectives to help overcome the paradigm of linear pathways

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Bursts and pulses: Insights from single cell studies into transcriptional mechanisms

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Evaluating stably expressed genes in single cells

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Quantitative single-cell live imaging links HES5 dynamics with cell-state and fate in murine neurogenesis

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Kinetic Modeling of Virus Growth in Cells

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Mouse embryonic fibroblasts exhibit extensive developmental and phenotypic diversity

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Patchy distribution of flexible genetic elements in bacterial populations mediates robustness to environmental uncertainty: Population-level robustness through genome flexibility

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

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A mechanism for the sharp transition of morphogen gradient interpretation in Xenopus

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Epigenetic control of variation and stochasticity in metabolic disease

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Evolution equation of phenotype distribution: general formulation and application to error catastrophe

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Effects of DNA replication on mRNA noise

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Systems analysis of cellular networks under uncertainty

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Effects of cell-cycle-dependent expression on random fluctuations in protein levels

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Lineage marker synchrony in hematopoietic genealogies refutes the PU.1/GATA1 toggle switch paradigm

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What can we learn when fitting a simple telegraph model to a complex gene expression model?

Jiao, F., Li, J., Liu, T., Zhu, Y., Che, W., Bleris, L., & Jia, C. (2024) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1012118 · Cited by 26

Microbial evolution in vivo and in silico: methods and applications

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Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition

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