Dynamic regulation of transcriptional states by chromatin and transcription factors

Stochastic Gene Expression in a Single Cell

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Network motifs: theory and experimental approaches

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A decade of exploring the cancer epigenome—biological and translational implications

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The accessible chromatin landscape of the human genome

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The biology of chromatin remodeling complexes.

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Stochasticity in gene expression: from theories to phenotypes

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Transcription factors: from enhancer binding to developmental control

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Stability and flexibility of epigenetic gene regulation in mammalian development

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Stochastic mRNA Synthesis in Mammalian Cells

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Intrinsic and extrinsic contributions to stochasticity in gene expression

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Cofactor Dynamics and Sufficiency in Estrogen Receptor–Regulated Transcription

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Noise in eukaryotic gene expression

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Pioneer transcription factors: establishing competence for gene expression

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The long-range interaction landscape of gene promoters

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Real-Time Kinetics of Gene Activity in Individual Bacteria

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Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

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Estrogen Receptor-α Directs Ordered, Cyclical, and Combinatorial Recruitment of Cofactors on a Natural Target Promoter

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Control of Stochasticity in Eukaryotic Gene Expression

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High-Resolution Mapping and Characterization of Open Chromatin across the Genome

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The Myc/Max/Mad Network and the Transcriptional Control of Cell Behavior

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Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

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Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression

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Dynamics of the p53-Mdm2 feedback loop in individual cells

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FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

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Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

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Mammalian genes are transcribed with widely different bursting kinetics

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ATP-dependent chromatin remodeling: genetics, genomics and mechanisms

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Circuitry of nuclear factor κB signaling

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Optimized localization analysis for single-molecule tracking and super-resolution microscopy

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The glucocorticoid receptor: rapid exchange with regulatory sites in living cells

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p53 Dynamics Control Cell Fate

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Time of feeding and the intrinsic circadian clock drive rhythms in hepatic gene expression.

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An expansive human regulatory lexicon encoded in transcription factor footprints

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Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor

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Transcriptional Pulsing of a Developmental Gene

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From Silencing to Gene Expression

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Harmonics of Circadian Gene Transcription in Mammals

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In vivo dynamics of RNA polymerase II transcription

Darzacq, X., Shav-Tal, Y., de Turris, V., Brody, Y., Shenoy, S. M., Phair, R. D., & Singer, R. H. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1280 · Cited by 665 · see citing works

DNase I sensitivity QTLs are a major determinant of human expression variation

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Probing protein heterogeneity in the plasma membrane using PALM and pair correlation analysis

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Stochastic modelling for quantitative description of heterogeneous biological systems

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Delay-induced stochastic oscillations in gene regulation

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Mapping Human Epigenomes

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Pulsatile Stimulation Determines Timing and Specificity of NF-κB-Dependent Transcription

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Insights from genomic profiling of transcription factors

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Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

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A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

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Mapping the Number of Molecules and Brightness in the Laser Scanning Microscope

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Frequency-modulated nuclear localization bursts coordinate gene regulation

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An encyclopedia of mouse DNA elements (Mouse ENCODE)

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Combinatorial binding predicts spatio-temporal cis-regulatory activity

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General properties of transcriptional time series in Escherichia coli

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Epigenetic signatures of stem-cell identity

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Ultradian hormone stimulation induces glucocorticoid receptor-mediated pulses of gene transcription

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Extensive chromatin remodelling and establishment of transcription factor ‘hotspots’ during early adipogenesis

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Nucleosome-mediated cooperativity between transcription factors

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Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors

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Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

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Eukaryotic transcriptional dynamics: from single molecules to cell populations

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Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism

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An Epigenetic Signature for Monoallelic Olfactory Receptor Expression

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A benchmark for chromatin binding measurements in live cells

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Signal-dependent dynamics of transcription factor translocation controls gene expression

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Separating intrinsic from extrinsic fluctuations in dynamic biological systems

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Pioneer factors in hormone-dependent cancers

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Impulse Control: Temporal Dynamics in Gene Transcription

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Removal of Promoter Nucleosomes by Disassembly Rather Than Sliding In Vivo

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In vivo footprinting of rat TAT gene: Dynamic interplay between the glucocorticoid receptor and a liver-specific factor

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Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

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Rapid Periodic Binding and Displacement of the Glucocorticoid Receptor during Chromatin Remodeling

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Genomic approaches towards finding cis-regulatory modules in animals

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Finding distal regulatory elements in the human genome

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Chromatin remodeling: insights and intrigue from single-molecule studies

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Motivations and Methods for Analyzing Pulsatile Hormone Secretion

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Dynamic Analysis of Stochastic Transcription Cycles

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Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

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Dynamic behavior of transcription factors on a natural promoter in living cells

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Long-term model predictive control of gene expression at the population and single-cell levels

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Genome-Wide Analysis of Estrogen Receptor α DNA Binding and Tethering Mechanisms Identifies Runx1 as a Novel Tethering Factor in Receptor-Mediated Transcriptional Activation

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A hyper‐dynamic equilibrium between promoter‐bound and nucleoplasmic dimers controls NF‐κB‐dependent gene activity

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FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

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The dose dependence of glucocorticoid‐inducible gene expression results from changes in the number of transcriptionally active templates.

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Dynamics of heat shock factor association with native gene loci in living cells

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Raster image correlation spectroscopy (RICS) for measuring fast protein dynamics and concentrations with a commercial laser scanning confocal microscope

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Transcriptional Regulatory Circuits: Predicting Numbers from Alphabets

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Collaborative Competition Mechanism for Gene Activation In Vivo

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Revisiting the central dogma one molecule at a time

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Dynamic nucleosomes and gene transcription

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Nucleosome Retention and the Stochastic Nature of Promoter Chromatin Remodeling for Transcription

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Pioneer factors: directing transcriptional regulators within the chromatin environment

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Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions

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Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter

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Nuclear Receptor DHR4 Controls the Timing of Steroid Hormone Pulses During Drosophila Development

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Chromatin Opening and Stable Perturbation of Core Histone:DNA Contacts by FoxO1

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Early chromatin unfolding by RUNX1: a molecular explanation for differential requirements during specification versus maintenance of the hematopoietic gene expression program

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Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

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Sustained Oscillations of NF-κB Produce Distinct Genome Scanning and Gene Expression Profiles

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