Multimodal transcriptional control of pattern formation in embryonic development

Optimal Decoding of Cellular Identities in a Genetic Network

(2019) Mariela D. Petkova et al.   CELL

The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output

(2019) Shigehiro Yamada et al.   CURRENT BIOLOGY

Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

(2019) Jeehae Park et al.   eLife

LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos

(2018) Jacques P. Bothma et al.   CELL

Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos

(2018) Ben J. Vincent et al.   PLoS Genetics

Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting

(2018) Benjamin Zoller et al.   CELL

Temporal control of gene expression by the pioneer factor Zelda through transient interactions in hubs

(2018) Jeremy Dufourt et al.   Nature Communications

Precision in a rush: Trade-offs between reproducibility and steepness of the hunchback expression pattern

(2018) Huy Tran et al.   PLoS Computational Biology

3 minutes to precisely measure morphogen concentration

(2018) Tanguy Lucas et al.   PLoS Genetics

Differential context-specific impact of individual core promoter elements on transcriptional dynamics

(2017) Oliver Hendy et al.   MOLECULAR BIOLOGY OF THE CELL

Decoding temporal interpretation of the morphogen Bicoid in the early Drosophila embryo

(2017) Anqi Huang et al.   eLife

Transcriptional bursting in Drosophila development: Stochastic dynamics of eve stripe 2 expression

(2017) David M. Holloway et al.   PLoS One

Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells

(2016) Chong Wang et al.   CELL

Dynamics of Translation of Single mRNA Molecules In Vivo

(2016) Xiaowei Yan et al.   CELL

Enhancer Control of Transcriptional Bursting

(2016) Takashi Fukaya et al.   CELL

The appeasement of Doug: a synthetic approach to enhancer biology

(2016) Ben J. Vincent et al.   Integrative Biology

Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping

(2016) Caroline R. Bartman et al.   MOLECULAR CELL

Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors

(2016) Justin Crocker et al.   NATURE GENETICS

Stochastic Kinetics of Nascent RNA

(2016) Heng Xu et al.   PHYSICAL REVIEW LETTERS

Translation dynamics of single mRNAs in live cells and neurons

(2016) B. Wu et al.   SCIENCE

Real-time quantification of single RNA translation dynamics in living cells

(2016) T. Morisaki et al.   SCIENCE

Precision of Readout at the hunchback Gene: Analyzing Short Transcription Time Traces in Living Fly Embryos

(2016) Jonathan Desponds et al.   PLoS Computational Biology

Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei

(2016) T. Niroshini Senaratne et al.   PLoS Genetics

Quantitative perturbation-based analysis of gene expression predicts enhancer activity in early Drosophila embryo

(2016) Rupinder Sayal et al.   eLife

Spatially coordinated dynamic gene transcription in living pituitary tissue

(2016) Karen Featherstone et al.   eLife

Single-cell analysis of transcription kinetics across the cell cycle

(2016) Samuel O Skinner et al.   eLife

A continuum model of transcriptional bursting

(2016) Adam M Corrigan et al.   eLife

A stochastic transcriptional switch model for single cell imaging data

(2015) Kirsty L. Hey et al.   BIOSTATISTICS

Bayesian inference of reaction kinetics from single-cell recordings across a heterogeneous cell population

(2015) L. Bronstein et al.   METHODS

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Structure of silent transcription intervals and noise characteristics of mammalian genes

(2015) B. Zoller et al.   Molecular Systems Biology

Combining protein and mRNA quantification to decipher transcriptional regulation

(2015) Heng Xu et al.   NATURE METHODS

Napoleon Is in Equilibrium

(2015) Rob Phillips   Annual Review of Condensed Matter Physics

Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

(2015) Sandeep Choubey et al.   PLoS Computational Biology

Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings

(2014) Christoph Zechner et al.   NATURE METHODS

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos

(2014) J. P. Bothma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promoter architecture dictates cell-to-cell variability in gene expression

(2014) Daniel L. Jones et al.   SCIENCE

Transcription Factors Modulate c-Fos Transcriptional Bursts

(2014) Adrien Senecal et al.   Cell Reports

Kinetic competition during the transcription cycle results in stochastic RNA processing

(2014) Antoine Coulon et al.   eLife

Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity

(2013) Shawn C. Little et al.   CELL

Live Imaging of Bicoid-Dependent Transcription in Drosophila Embryos

(2013) Tanguy Lucas et al.   CURRENT BIOLOGY

Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning

(2013) Hernan G. Garcia et al.   CURRENT BIOLOGY

Stimulus-induced modulation of transcriptional bursting in a single mammalian gene

(2013) N. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Transcription Fosters Coordinate snail Expression in the Drosophila Embryo

(2013) Alistair Nicol Boettiger et al.   Cell Reports

Cellular resolution models for even skipped regulation in the entire Drosophila embryo

(2013) Garth R Ilsley et al.   eLife

The transcription cycle in eukaryotes: From productive initiation to RNA polymerase II recycling

(2012) Jayasha Shandilya et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

A model of spatially restricted transcription in opposing gradients of activators and repressors

(2012) Michael A White et al.   Molecular Systems Biology

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

A transgenic mouse for in vivo detection of endogenous labeled mRNA

(2011) Timothée Lionnet et al.   NATURE METHODS

Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics

(2011) D. M. Suter et al.   SCIENCE

Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene

(2011) D. R. Larson et al.   SCIENCE

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

Consequences of Eukaryotic Enhancer Architecture for Gene Expression Dynamics, Development, and Fitness

(2011) Michael Z. Ludwig et al.   PLoS Genetics

Developmental Control of Late Replication and S Phase Length

(2010) Antony W. Shermoen et al.   CURRENT BIOLOGY

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

(2010) Walid D Fakhouri et al.   Molecular Systems Biology

Learning Rates and States from Biophysical Time Series: A Bayesian Approach to Model Selection and Single-Molecule FRET Data

(2009) Jonathan E. Bronson et al.   BIOPHYSICAL JOURNAL

Visualization of Individual Scr mRNAs during Drosophila Embryogenesis Yields Evidence for Transcriptional Bursting

(2009) Adam Paré et al.   CURRENT BIOLOGY

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

(2009) Manu et al.   PLoS Computational Biology

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

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

(2008) Daniel Zenklusen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Characterization of the Drosophila segment determination morphome

(2007) Svetlana Surkova et al.   DEVELOPMENTAL BIOLOGY