Stochasticity in gene expression: from theories to phenotypes.

Direct cell reprogramming is a stochastic process amenable to acceleration. Nature (2009) 8.71

Noise in gene expression determines cell fate in Bacillus subtilis. Science (2007) 7.45

Single-RNA counting reveals alternative modes of gene expression in yeast. Nat Struct Mol Biol (2008) 6.09

MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell (2007) 5.67

Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature (2008) 4.63

Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol (2009) 4.60

Oscillations and variability in the p53 system. Mol Syst Biol (2006) 4.59

Cellular decision making and biological noise: from microbes to mammals. Cell (2011) 4.44

Two strategies for gene regulation by promoter nucleosomes. Genome Res (2008) 4.19

Analytical distributions for stochastic gene expression. Proc Natl Acad Sci U S A (2008) 3.48

A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science (2008) 3.46

Variability and robustness in T cell activation from regulated heterogeneity in protein levels. Science (2008) 3.38

Quantitative characteristics of gene regulation by small RNA. PLoS Biol (2007) 3.35

Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet (2009) 3.24

What is stochastic resonance? Definitions, misconceptions, debates, and its relevance to biology. PLoS Comput Biol (2009) 2.98

Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol (2009) 2.93

Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs. Eur Phys J E Soft Matter (2006) 2.88

Bet-hedging and epigenetic inheritance in bacterial cell development. Proc Natl Acad Sci U S A (2008) 2.88

General properties of transcriptional time series in Escherichia coli. Nat Genet (2011) 2.76

Non-genetic heterogeneity--a mutation-independent driving force for the somatic evolution of tumours. Nat Rev Genet (2009) 2.69

Regulatory activity revealed by dynamic correlations in gene expression noise. Nat Genet (2008) 2.49

Non-genetic heterogeneity of cells in development: more than just noise. Development (2009) 2.48

Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A (2005) 2.47

Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc Natl Acad Sci U S A (2009) 2.45

Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A (2007) 2.40

Colored extrinsic fluctuations and stochastic gene expression. Mol Syst Biol (2008) 2.32

Quantification of mRNA and protein and integration with protein turnover in a bacterium. Mol Syst Biol (2011) 2.31

Robustness: mechanisms and consequences. Trends Genet (2009) 2.27

Regulation of phenotypic variability by a threshold-based mechanism underlies bacterial persistence. Proc Natl Acad Sci U S A (2010) 2.20

Input output robustness in simple bacterial signaling systems. Proc Natl Acad Sci U S A (2007) 2.17

The transcriptome of the human pathogen Trypanosoma brucei at single-nucleotide resolution. PLoS Pathog (2010) 2.15

Heritable stochastic switching revealed by single-cell genealogy. PLoS Biol (2007) 2.11

The role of physiological heterogeneity in microbial population behavior. Nat Chem Biol (2010) 2.04

Cryptococcus neoformans overcomes stress of azole drugs by formation of disomy in specific multiple chromosomes. PLoS Pathog (2010) 2.04

Somatodendritic microRNAs identified by laser capture and multiplex RT-PCR. RNA (2007) 2.01

Conflict between noise and plasticity in yeast. PLoS Genet (2010) 1.94

Emergence of noise-induced oscillations in the central circadian pacemaker. PLoS Biol (2010) 1.94

Diffusion of transcription factors can drastically enhance the noise in gene expression. Biophys J (2006) 1.92

Epigenetic and conventional regulation is distributed among activators of FLO11 allowing tuning of population-level heterogeneity in its expression. PLoS Genet (2009) 1.88

The role of incoherent microRNA-mediated feedforward loops in noise buffering. PLoS Comput Biol (2011) 1.84

The three-dimensional structure of human interphase chromosomes is related to the transcriptome map. Mol Cell Biol (2007) 1.82

Regulated noise in the epigenetic landscape of development and disease. Cell (2012) 1.79

Positive feedback in cellular control systems. Bioessays (2008) 1.79

Separating intrinsic from extrinsic fluctuations in dynamic biological systems. Proc Natl Acad Sci U S A (2011) 1.79

Transcription of functionally related constitutive genes is not coordinated. Nat Struct Mol Biol (2010) 1.78

The potential landscape of genetic circuits imposes the arrow of time in stem cell differentiation. Biophys J (2010) 1.76

Decision making at a subcellular level determines the outcome of bacteriophage infection. Cell (2010) 1.76

A continuum of cell states spans pluripotency and lineage commitment in human embryonic stem cells. PLoS One (2009) 1.74

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol (2009) 1.73

Bursty gene expression in the intact mammalian liver. Mol Cell (2015) 1.72

Evolution under canalization and the dual roles of microRNAs: a hypothesis. Genome Res (2009) 1.72

Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci U S A (2006) 1.70

Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade. Biophys J (2005) 1.69

Dynamics of single-cell gene expression. Mol Syst Biol (2006) 1.69

Fold-change detection and scalar symmetry of sensory input fields. Proc Natl Acad Sci U S A (2010) 1.67

Isolation and characterization of superdormant spores of Bacillus species. J Bacteriol (2009) 1.65

Stochastic models for regulatory networks of the genetic toggle switch. Proc Natl Acad Sci U S A (2006) 1.65

Bone marrow mesenchymal stem cells: historical overview and concepts. Hum Gene Ther (2010) 1.63

Optimal noise filtering in the chemotactic response of Escherichia coli. PLoS Comput Biol (2006) 1.61

Histone H3 acetylation and H3 K4 methylation define distinct chromatin regions permissive for transgene expression. Mol Cell Biol (2006) 1.60

Transient heterogeneity in extracellular protease production by Bacillus subtilis. Mol Syst Biol (2008) 1.60

Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res (2011) 1.58

A model of immune regulation as a consequence of randomized lymphocyte division and death times. Proc Natl Acad Sci U S A (2007) 1.57

Multistable and multistep dynamics in neutrophil differentiation. BMC Cell Biol (2006) 1.56

Myt1 and Ngn3 form a feed-forward expression loop to promote endocrine islet cell differentiation. Dev Biol (2008) 1.55

Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol Cell (2012) 1.53

Revealing static and dynamic modular architecture of the eukaryotic protein interaction network. Mol Syst Biol (2007) 1.53

Non-Darwinian dynamics in therapy-induced cancer drug resistance. Nat Commun (2013) 1.52

Apomictic and sexual ovules of Boechera display heterochronic global gene expression patterns. Plant Cell (2010) 1.52

Noise-driven stem cell and progenitor population dynamics. PLoS One (2008) 1.52

Evolution of robustness to noise and mutation in gene expression dynamics. PLoS One (2007) 1.51

Alternative promoter use in eye development: the complex role and regulation of the transcription factor MITF. Development (2008) 1.50

Impact of microRNA regulation on variation in human gene expression. Genome Res (2012) 1.49

Computational modeling of the hematopoietic erythroid-myeloid switch reveals insights into cooperativity, priming, and irreversibility. PLoS Comput Biol (2009) 1.48

Cellular asymmetry and individuality in directional sensing. Proc Natl Acad Sci U S A (2006) 1.47

Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell (2013) 1.47

Visualization of individual Scr mRNAs during Drosophila embryogenesis yields evidence for transcriptional bursting. Curr Biol (2009) 1.46

Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci U S A (2011) 1.46

An information-theoretic characterization of the optimal gradient sensing response of cells. PLoS Comput Biol (2007) 1.45

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. Nat Methods (2014) 1.44

Noise contributions in an inducible genetic switch: a whole-cell simulation study. PLoS Comput Biol (2011) 1.44

Single TNFalpha trimers mediating NF-kappaB activation: stochastic robustness of NF-kappaB signaling. BMC Bioinformatics (2007) 1.44

Noise in gene expression is coupled to growth rate. Genome Res (2015) 1.44

The pharmacodynamics of the p53-Mdm2 targeting drug Nutlin: the role of gene-switching noise. PLoS Comput Biol (2014) 1.42

Timing and dynamics of single cell gene expression in the arabinose utilization system. Biophys J (2008) 1.41

Ectopic expression of peripheral-tissue antigens in the thymic epithelium: probabilistic, monoallelic, misinitiated. Proc Natl Acad Sci U S A (2008) 1.41

Stochastic fluctuations in metabolic pathways. Proc Natl Acad Sci U S A (2007) 1.39

Gene expression variability within and between human populations and implications toward disease susceptibility. PLoS Comput Biol (2010) 1.39

Intracellular growth of Mycobacterium tuberculosis after macrophage cell death leads to serial killing of host cells. Elife (2017) 1.39

A fluctuation method to quantify in vivo fluorescence data. Biophys J (2006) 1.39

Effect of promoter architecture on the cell-to-cell variability in gene expression. PLoS Comput Biol (2011) 1.37

Screening for noise in gene expression identifies drug synergies. Science (2014) 1.37

Transcriptional control of noise in gene expression. Proc Natl Acad Sci U S A (2008) 1.36

Quantifying origins of cell-to-cell variations in gene expression. Biophys J (2008) 1.36

Altered RNA editing in mice lacking ADAR2 autoregulation. Mol Cell Biol (2006) 1.36

Fluctuations, pauses, and backtracking in DNA transcription. Biophys J (2007) 1.34

Computational morphodynamics: a modeling framework to understand plant growth. Annu Rev Plant Biol (2010) 1.33

Quantitative time-lapse fluorescence microscopy in single cells. Annu Rev Cell Dev Biol (2009) 1.32

Mathematical models of specificity in cell signaling. Biophys J (2007) 1.31

Positive feedback and noise activate the stringent response regulator rel in mycobacteria. PLoS One (2008) 1.30

Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell (2010) 14.18

A common mechanism of cellular death induced by bactericidal antibiotics. Cell (2007) 12.92

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46

Inferring genetic networks and identifying compound mode of action via expression profiling. Science (2003) 9.10

Synthetic biology: applications come of age. Nat Rev Genet (2010) 6.96

Wisdom of crowds for robust gene network inference. Nat Methods (2012) 6.91

Sublethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis. Mol Cell (2010) 5.33

Reverse engineering gene networks using singular value decomposition and robust regression. Proc Natl Acad Sci U S A (2002) 5.29

Engineered riboregulators enable post-transcriptional control of gene expression. Nat Biotechnol (2004) 5.07

Phenotypic consequences of promoter-mediated transcriptional noise. Mol Cell (2006) 4.93

Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc Natl Acad Sci U S A (2003) 4.89

Programmable cells: interfacing natural and engineered gene networks. Proc Natl Acad Sci U S A (2004) 4.72

How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol (2010) 4.65

Synthetic gene networks that count. Science (2009) 4.54

Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell (2008) 4.47

Cellular decision making and biological noise: from microbes to mammals. Cell (2011) 4.44

Metabolite-enabled eradication of bacterial persisters by aminoglycosides. Nature (2011) 4.06

A bottom-up approach to gene regulation. Nature (2006) 4.03

Gyrase inhibitors induce an oxidative damage cellular death pathway in Escherichia coli. Mol Syst Biol (2007) 3.98

Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nat Biotechnol (2005) 3.89

Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat Biotechnol (2009) 3.86

Bacterial charity work leads to population-wide resistance. Nature (2010) 3.50

Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc Natl Acad Sci U S A (2014) 3.50

Vibrating insoles and balance control in elderly people. Lancet (2003) 3.48

RNA synthetic biology. Nat Biotechnol (2006) 3.37

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells. Nat Biotechnol (2011) 3.25

Origins of extrinsic variability in eukaryotic gene expression. Nature (2005) 3.18

Next-generation synthetic gene networks. Nat Biotechnol (2009) 3.12

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature (2013) 3.02

Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc Natl Acad Sci U S A (2009) 3.01

Signaling-mediated bacterial persister formation. Nat Chem Biol (2012) 2.96

Reprogramming of T cells from human peripheral blood. Cell Stem Cell (2010) 2.93

Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A (2007) 2.87

A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell (2007) 2.83

Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature (2011) 2.81

Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli. Mol Cell (2009) 2.74

Oxidation of the guanine nucleotide pool underlies cell death by bactericidal antibiotics. Science (2012) 2.72

Antibiotic-induced bacterial cell death exhibits physiological and biochemical hallmarks of apoptosis. Mol Cell (2012) 2.56

beta2-adrenergic receptor signaling and desensitization elucidated by quantitative modeling of real time cAMP dynamics. J Biol Chem (2007) 2.42

Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A (2007) 2.40

MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. Proc Natl Acad Sci U S A (2009) 2.37

Synthetic biology moving into the clinic. Science (2011) 2.36

A synthetic biology framework for programming eukaryotic transcription functions. Cell (2012) 2.32

Oncogenic NRAS signaling differentially regulates survival and proliferation in melanoma. Nat Med (2012) 2.26

Synthetic gene network for entraining and amplifying cellular oscillations. Phys Rev Lett (2002) 2.24

A network biology approach to prostate cancer. Mol Syst Biol (2007) 2.07

Noise-enhanced balance control in patients with diabetes and patients with stroke. Ann Neurol (2006) 2.06

Regulation of cell signaling dynamics by the protein kinase-scaffold Ste5. Mol Cell (2008) 2.00

The transcriptional landscape of hematopoietic stem cell ontogeny. Cell Stem Cell (2012) 1.96

microRNA regulatory network inference identifies miR-34a as a novel regulator of TGF-β signaling in glioblastoma. Cancer Discov (2012) 1.94

Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways. Biophys J (2007) 1.93

A multiply redundant genetic switch 'locks in' the transcriptional signature of regulatory T cells. Nat Immunol (2012) 1.93

Role of reactive oxygen species in antibiotic action and resistance. Curr Opin Microbiol (2009) 1.92

Aging, muscle activity, and balance control: physiologic changes associated with balance impairment. Gait Posture (2003) 1.84

The engineering of gene regulatory networks. Annu Rev Biomed Eng (2003) 1.73

Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade. Biophys J (2005) 1.69

Induction of multipotential hematopoietic progenitors from human pluripotent stem cells via respecification of lineage-restricted precursors. Cell Stem Cell (2013) 1.68

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc Natl Acad Sci U S A (2010) 1.66

Genetic switchboard for synthetic biology applications. Proc Natl Acad Sci U S A (2012) 1.60

Potentiating antibacterial activity by predictably enhancing endogenous microbial ROS production. Nat Biotechnol (2013) 1.59

Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics (2004) 1.54

Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res (2010) 1.52

Heterogeneous bacterial persisters and engineering approaches to eliminate them. Curr Opin Microbiol (2011) 1.47

A systems-biology analysis of feedback inhibition in the Sho1 osmotic-stress-response pathway. Curr Biol (2007) 1.47

Tunable signal processing in synthetic MAP kinase cascades. Cell (2011) 1.45

Negative feedback enhances robustness in the yeast polarity establishment circuit. Cell (2012) 1.42

Antibiotics and the gut microbiota. J Clin Invest (2014) 1.39

Tracking shallow chemical gradients by actin-driven wandering of the polarization site. Curr Biol (2012) 1.37

Microbial persistence and the road to drug resistance. Cell Host Microbe (2013) 1.37

Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks. Proc Natl Acad Sci U S A (2007) 1.36

Salmonella typhimurium intercepts Escherichia coli signaling to enhance antibiotic tolerance. Proc Natl Acad Sci U S A (2013) 1.29

Regulators of G protein signaling and transient activation of signaling: experimental and computational analysis reveals negative and positive feedback controls on G protein activity. J Biol Chem (2003) 1.29

Fluctuations in transcription factor binding can explain the graded and binary responses observed in inducible gene expression. J Theor Biol (2004) 1.27

Dose-to-duration encoding and signaling beyond saturation in intracellular signaling networks. PLoS Comput Biol (2008) 1.26

A robust numerical algorithm for studying biomolecular transport processes. J Theor Biol (2003) 1.20

Fungicidal drugs induce a common oxidative-damage cellular death pathway. Cell Rep (2013) 1.19

Transcriptome analysis identifies regulators of hematopoietic stem and progenitor cells. Stem Cell Reports (2013) 1.19

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation. J Chem Phys (2006) 1.18

Roles for the transcription elongation factor NusA in both DNA repair and damage tolerance pathways in Escherichia coli. Proc Natl Acad Sci U S A (2010) 1.18

Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat Methods (2012) 1.17

Unraveling the physiological complexities of antibiotic lethality. Annu Rev Pharmacol Toxicol (2014) 1.16

Control of MAPK specificity by feedback phosphorylation of shared adaptor protein Ste50. J Biol Chem (2008) 1.16

Noise-enhanced balance control in older adults. Neuroreport (2002) 1.16

Functional characterization of bacterial sRNAs using a network biology approach. Proc Natl Acad Sci U S A (2011) 1.14

A network biology approach to aging in yeast. Proc Natl Acad Sci U S A (2009) 1.11

Valproic acid extends Caenorhabditis elegans lifespan. Aging Cell (2008) 1.10

Regulation of physiologic actions of LRRK2: focus on autophagy. Neurodegener Dis (2011) 1.07

Functional genomic characterization of neoblast-like stem cells in larval Schistosoma mansoni. Elife (2013) 1.07

Genomic approaches to deconstruct pluripotency. Annu Rev Genomics Hum Genet (2011) 1.06

Noise-enhanced vibrotactile sensitivity in older adults, patients with stroke, and patients with diabetic neuropathy. Arch Phys Med Rehabil (2002) 1.06

Mathematical model of nucleotide regulation on airway epithelia. Implications for airway homeostasis. J Biol Chem (2008) 1.05

CellGeo: a computational platform for the analysis of shape changes in cells with complex geometries. J Cell Biol (2014) 1.04

A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophys J (2007) 1.04

Variable-free exploration of stochastic models: a gene regulatory network example. J Chem Phys (2007) 1.03

Silencing HoxA1 by intraductal injection of siRNA lipidoid nanoparticles prevents mammary tumor progression in mice. Sci Transl Med (2014) 1.03

Compression and dilation of the membrane-cortex layer generates rapid changes in cell shape. J Cell Biol (2013) 1.02

Reliability and validity of the Stanford Presenteeism Scale. J Occup Environ Med (2004) 1.02

Yeast dynamically modify their environment to achieve better mating efficiency. Sci Signal (2011) 1.01

Microbial environments confound antibiotic efficacy. Nat Chem Biol (2011) 0.99

A structural model reveals energy transduction in dynein. Proc Natl Acad Sci U S A (2006) 0.98