Published in Science on February 01, 2013
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood (2013) 2.12
Recapitulation of the forward nuclear auxin response pathway in yeast. Proc Natl Acad Sci U S A (2014) 1.17
Aro: a machine learning approach to identifying single molecules and estimating classification error in fluorescence microscopy images. BMC Bioinformatics (2015) 1.04
Stimulus-induced modulation of transcriptional bursting in a single mammalian gene. Proc Natl Acad Sci U S A (2013) 1.01
Sexually-dimorphic targeting of functionally-related genes in COPD. BMC Syst Biol (2014) 0.94
Designing experiments to understand the variability in biochemical reaction networks. J R Soc Interface (2013) 0.91
ODE constrained mixture modelling: a method for unraveling subpopulation structures and dynamics. PLoS Comput Biol (2014) 0.90
Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression. PLoS One (2015) 0.89
Single-cell analysis of transcription kinetics across the cell cycle. Elife (2016) 0.88
Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods (2014) 0.87
Analytic approaches to stochastic gene expression in multicellular systems. Biophys J (2013) 0.86
Cell-to-cell variability in the propensity to transcribe explains correlated fluctuations in gene expression. Cell Syst (2015) 0.85
Iterative experiment design guides the characterization of a light-inducible gene expression circuit. Proc Natl Acad Sci U S A (2015) 0.85
What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast. PLoS Comput Biol (2016) 0.84
Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics. Methods (2015) 0.83
Combining Spinach-tagged RNA and gene localization to image gene expression in live yeast. Nat Commun (2015) 0.82
Stochastic holin expression can account for lysis time variation in the bacteriophage λ. J R Soc Interface (2014) 0.82
Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance. PLoS Comput Biol (2014) 0.82
MAPK feedback encodes a switch and timer for tunable stress adaptation in yeast. Sci Signal (2015) 0.82
A computational framework for analyzing stochasticity in gene expression. PLoS Comput Biol (2014) 0.81
Osmostress-induced gene expression--a model to understand how stress-activated protein kinases (SAPKs) regulate transcription. FEBS J (2015) 0.79
Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks. ACS Synth Biol (2014) 0.78
A novel role for lncRNAs in cell cycle control during stress adaptation. Curr Genet (2014) 0.78
Casein kinase II regulation of the Hot1 transcription factor promotes stochastic gene expression. J Biol Chem (2014) 0.78
Finite state projection based bounds to compare chemical master equation models using single-cell data. J Chem Phys (2016) 0.78
A method for detecting single mRNA molecules in Arabidopsis thaliana. Plant Methods (2016) 0.78
Inference for Stochastic Chemical Kinetics Using Moment Equations and System Size Expansion. PLoS Comput Biol (2016) 0.77
Phenotypic signatures arising from unbalanced bacterial growth. PLoS Comput Biol (2014) 0.77
Real-time quantification of protein expression at the single-cell level via dynamic protein synthesis translocation reporters. Nat Commun (2016) 0.77
Intercellular Variability in Protein Levels from Stochastic Expression and Noisy Cell Cycle Processes. PLoS Comput Biol (2016) 0.77
Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response. Mol Syst Biol (2015) 0.76
Multiscale analysis of the murine intestine for modeling human diseases. Integr Biol (Camb) (2015) 0.76
What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems. Nucleic Acids Res (2014) 0.76
A novel splice variant of XIAP-associated factor 1 (XAF1) is expressed in peripheral blood containing gastric cancer-derived circulating tumor cells. Gastric Cancer (2014) 0.76
From analog to digital models of gene regulation. Phys Biol (2015) 0.76
Stochasticity in the miR-9/Hes1 oscillatory network can account for clonal heterogeneity in the timing of differentiation. Elife (2016) 0.76
Effects of cell-cycle-dependent expression on random fluctuations in protein levels. R Soc Open Sci (2016) 0.75
Systems biology: the role of engineering in the reverse engineering of biological signaling. Cells (2013) 0.75
Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures. J R Soc Interface (2015) 0.75
An integrated microfluidic device for rapid and high-sensitivity analysis of circulating tumor cells. Sci Rep (2017) 0.75
Signaling in T cells - is anything the m(a)TOR with the picture(s)? F1000Res (2016) 0.75
Modeling stem cell induction processes. PLoS One (2013) 0.75
Build to understand: synthetic approaches to biology. Integr Biol (Camb) (2015) 0.75
Pluralistic and stochastic gene regulation: examples, models and consistent theory. Nucleic Acids Res (2016) 0.75
Stochastic Kinetics of Nascent RNA. Phys Rev Lett (2016) 0.75
The finite state projection approach to analyze dynamics of heterogeneous populations. Phys Biol (2017) 0.75
Multiplexed gene control reveals rapid mRNA turnover. Sci Adv (2017) 0.75
Control of stochasticity in eukaryotic gene expression. Science (2004) 12.85
Stochastic mRNA synthesis in mammalian cells. PLoS Biol (2006) 12.58
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Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods (2008) 10.40
Osmotic stress signaling and osmoadaptation in yeasts. Microbiol Mol Biol Rev (2002) 8.02
Defining network topologies that can achieve biochemical adaptation. Cell (2009) 5.49
The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science (2008) 4.94
The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys (2006) 4.68
Regulated nucleo/cytoplasmic exchange of HOG1 MAPK requires the importin beta homologs NMD5 and XPO1. EMBO J (1998) 3.87
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. Science (2009) 3.60
Using gene expression noise to understand gene regulation. Science (2012) 3.49
Effects of molecular memory and bursting on fluctuations in gene expression. Science (2008) 3.20
The dose dependence of glucocorticoid-inducible gene expression results from changes in the number of transcriptionally active templates. EMBO J (1990) 3.04
A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell (2009) 2.91
Signal processing by the HOG MAP kinase pathway. Proc Natl Acad Sci U S A (2008) 2.56
Principles of MAP kinase signaling specificity in Saccharomyces cerevisiae. Annu Rev Genet (2004) 2.54
Inducible gene expression: diverse regulatory mechanisms. Nat Rev Genet (2010) 2.53
Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell (2008) 2.47
A decade of systems biology. Annu Rev Cell Dev Biol (2010) 2.30
Structural basis of RNA polymerase II backtracking, arrest and reactivation. Nature (2011) 2.19
Osmostress-induced transcription by Hot1 depends on a Hog1-mediated recruitment of the RNA Pol II. EMBO J (2003) 1.90
Automated reverse engineering of nonlinear dynamical systems. Proc Natl Acad Sci U S A (2007) 1.76
Listening to the noise: random fluctuations reveal gene network parameters. Mol Syst Biol (2009) 1.71
Moment-based inference predicts bimodality in transient gene expression. Proc Natl Acad Sci U S A (2012) 1.58
Transient activation of the HOG MAPK pathway regulates bimodal gene expression. Science (2011) 1.54
Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol Cell (2012) 1.53
A member of the sugar transporter family, Stl1p is the glycerol/H+ symporter in Saccharomyces cerevisiae. Mol Biol Cell (2005) 1.27
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
Regulation of noise in the expression of a single gene. Nat Genet (2002) 14.93
Nature, nurture, or chance: stochastic gene expression and its consequences. Cell (2008) 12.13
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods (2008) 10.40
Direct cell reprogramming is a stochastic process amenable to acceleration. Nature (2009) 8.71
Noise propagation in gene networks. Science (2005) 8.19
Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase. Cell (2012) 7.17
Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res (2002) 6.65
Enhancement of cellular memory by reducing stochastic transitions. Nature (2005) 6.01
Stochastic switching as a survival strategy in fluctuating environments. Nat Genet (2008) 5.87
Variability in gene expression underlies incomplete penetrance. Nature (2010) 5.85
MicroRNA-mediated feedback and feedforward loops are recurrent network motifs in mammals. Mol Cell (2007) 5.67
The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science (2008) 4.94
Slug and Sox9 cooperatively determine the mammary stem cell state. Cell (2012) 4.77
The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys (2006) 4.68
Cellular decision making and biological noise: from microbes to mammals. Cell (2011) 4.44
Stochastic gene expression in fluctuating environments. Genetics (2004) 4.23
Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet (2005) 4.07
MicroRNAs can generate thresholds in target gene expression. Nat Genet (2011) 3.90
Gramene: a resource for comparative grass genomics. Nucleic Acids Res (2002) 3.72
The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers. EMBO J (2012) 3.70
Snowdrift game dynamics and facultative cheating in yeast. Nature (2009) 3.66
Using gene expression noise to understand gene regulation. Science (2012) 3.49
Dll1+ secretory progenitor cells revert to stem cells upon crypt damage. Nat Cell Biol (2012) 3.30
Gramene, a tool for grass genomics. Plant Physiol (2002) 3.14
A systems-level analysis of perfect adaptation in yeast osmoregulation. Cell (2009) 2.91
Stochastic gene expression: from single molecules to the proteome. Curr Opin Genet Dev (2007) 2.81
RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol (2011) 2.77
Single-molecule approaches to stochastic gene expression. Annu Rev Biophys (2009) 2.75
Single-molecule transcript counting of stem-cell markers in the mouse intestine. Nat Cell Biol (2011) 2.72
Attenuation of noise in ultrasensitive signaling cascades. Biophys J (2002) 2.42
Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A (2013) 2.33
Gramene: development and integration of trait and gene ontologies for rice. Comp Funct Genomics (2002) 2.16
Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus. Cell (2010) 2.15
Validating transcripts with probes and imaging technology. Nat Methods (2011) 2.15
A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet (2007) 2.14
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood (2013) 2.12
Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol Cell (2010) 2.12
Heritable stochastic switching revealed by single-cell genealogy. PLoS Biol (2007) 2.11
Genetic and phenotypic diversity in breast tumor metastases. Cancer Res (2014) 1.96
Probing polymerization forces by using actin-propelled lipid vesicles. Proc Natl Acad Sci U S A (2003) 1.92
Parameter estimation and model selection in computational biology. PLoS Comput Biol (2010) 1.91
Identifying the stem cell of the intestinal crypt: strategies and pitfalls. Cell Stem Cell (2012) 1.88
A novel sperm-delivered toxin causes late-stage embryo lethality and transmission ratio distortion in C. elegans. PLoS Biol (2011) 1.84
A system of counteracting feedback loops regulates Cdc42p activity during spontaneous cell polarization. Dev Cell (2005) 1.81
The diffusive finite state projection algorithm for efficient simulation of the stochastic reaction-diffusion master equation. J Chem Phys (2010) 1.74
Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock. Nature (2007) 1.74
Listening to the noise: random fluctuations reveal gene network parameters. Mol Syst Biol (2009) 1.71
Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol (2012) 1.70
Predicting stochastic gene expression dynamics in single cells. Proc Natl Acad Sci U S A (2006) 1.70
Synthetic biology: understanding biological design from synthetic circuits. Nat Rev Genet (2009) 1.70
Optimality in the development of intestinal crypts. Cell (2012) 1.67
Circadian gating of the cell cycle revealed in single cyanobacterial cells. Science (2010) 1.62
Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast. Cell (2012) 1.61
A general mechanism for network-dosage compensation in gene circuits. Science (2010) 1.59
Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. Mol Cell (2012) 1.53
In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol (2011) 1.49
Cellular asymmetry and individuality in directional sensing. Proc Natl Acad Sci U S A (2006) 1.47
A critical role for the Wnt effector Tcf4 in adult intestinal homeostatic self-renewal. Mol Cell Biol (2012) 1.34
A physical sciences network characterization of non-tumorigenic and metastatic cells. Sci Rep (2013) 1.33
Quantitative time-lapse fluorescence microscopy in single cells. Annu Rev Cell Dev Biol (2009) 1.32
Transcript counting in single cells reveals dynamics of rDNA transcription. Mol Syst Biol (2010) 1.32
Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks. Biophys J (2006) 1.31
Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.) (supplement). DNA Res (2002) 1.29
Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing. Genome Res (2009) 1.28
Growth landscape formed by perception and import of glucose in yeast. Nature (2009) 1.26
Biomimetic systems for studying actin-based motility. Curr Biol (2003) 1.25
Reduction and solution of the chemical master equation using time scale separation and finite state projection. J Chem Phys (2006) 1.25
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev (2012) 1.24
Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol (2006) 1.23
Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer. J Clin Invest (2011) 1.23
Cell lineage branching as a strategy for proliferative control. BMC Biol (2015) 1.22
Single-molecule mRNA detection and counting in mammalian tissue. Nat Protoc (2013) 1.18
Efficient computation of parameter sensitivities of discrete stochastic chemical reaction networks. J Chem Phys (2010) 1.13
Identification of molecular compartments and genetic circuitry in the developing mammalian kidney. Development (2012) 1.13
Dampening of expression oscillations by synchronous regulation of a microRNA and its target. Nat Genet (2013) 1.11
Neuroblast migration along the anteroposterior axis of C. elegans is controlled by opposing gradients of Wnts and a secreted Frizzled-related protein. Development (2011) 1.09
Spatial stochastic dynamics enable robust cell polarization. PLoS Comput Biol (2013) 1.08
Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol (2010) 1.07
Amplitude control of cell-cycle waves by nuclear import. Nat Cell Biol (2004) 1.07
Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression. Proc Natl Acad Sci U S A (2011) 1.04
Stochastic cytokine expression induces mixed T helper cell States. PLoS Biol (2013) 1.04
Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos. WormBook (2012) 1.03
Allele-specific detection of single mRNA molecules in situ. Nat Methods (2013) 1.02
Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway. Cell (2013) 0.97
A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes. Mol Biol Cell (2012) 0.96
The simplicity of completion time distributions for common complex biochemical processes. Phys Biol (2009) 0.95
Elastic instability in growing yeast colonies. Biophys J (2004) 0.94
Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation. Dev Cell (2013) 0.93
The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinformatics (2013) 0.91
The thrombospondin repeat containing protein MIG-21 controls a left-right asymmetric Wnt signaling response in migrating C. elegans neuroblasts. Dev Biol (2011) 0.91
A pathwise derivative approach to the computation of parameter sensitivities in discrete stochastic chemical systems. J Chem Phys (2012) 0.91
Studying Lineage Decision-Making In Vitro: Emerging Concepts and Novel Tools. Annu Rev Cell Dev Biol (2015) 0.90
Analysis of stochastic strategies in bacterial competence: a master equation approach. PLoS Comput Biol (2010) 0.88
Actin polymerization: forcing flat faces forward. Curr Biol (2004) 0.87
Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Phys Biol (2013) 0.87
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks. Bioinformatics (2012) 0.87
The Caenorhabditis elegans synthetic multivulva genes prevent ras pathway activation by tightly repressing global ectopic expression of lin-3 EGF. PLoS Genet (2011) 0.87