Response to Nodal morphogen gradient is determined by the kinetics of target gene induction

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

(2014) Sun Melody Foo et al.   CURRENT BIOLOGY

Encoding of Temporal Signals by the TGF-β Pathway and Implications for Embryonic Patterning

(2014) Benoit Sorre et al.   DEVELOPMENTAL CELL

Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila

(2014) Z. Xu et al.   GENES & DEVELOPMENT

Construction of a Vertebrate Embryo from Two Opposing Morphogen Gradients

(2014) P.-F. Xu et al.   SCIENCE

TGFβ signaling in establishing left–right asymmetry

(2014) Hidetaka Shiratori et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Specified Neural Progenitors Sort to Form Sharp Domains after Noisy Shh Signaling

(2013) Fengzhu Xiong et al.   CELL

Morphogen interpretation: the transcriptional logic of neural tube patterning

(2013) Michael Cohen et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Functional evaluation of ES cell-derived endodermal populations reveals differences between Nodal and Activin A-guided differentiation

(2013) A. E. Chen et al.   DEVELOPMENT

Morphogen transport

(2013) P. Muller et al.   DEVELOPMENT

Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus

(2013) Qiang Tu et al.   DEVELOPMENTAL BIOLOGY

Eukaryotic transcriptional dynamics: from single molecules to cell populations

(2013) Antoine Coulon et al.   NATURE REVIEWS GENETICS

Full Transcriptome Analysis of Early Dorsoventral Patterning in Zebrafish

(2013) Erika Fodor et al.   PLoS One

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals

(2013) T. Oosterveen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Controlling Long-Term Signaling: Receptor Dynamics Determine Attenuation and Refractory Behavior of the TGF-  Pathway

(2013) P. Vizan et al.   Science Signaling

In Vivo T-Box Transcription Factor Profiling Reveals Joint Regulation of Embryonic Neuromesodermal Bipotency

(2013) George E. Gentsch et al.   Cell Reports

Pattern Formation by Graded and Uniform Signals in the Early Drosophila Embryo

(2012) Jitendra S. Kanodia et al.   BIOPHYSICAL JOURNAL

Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube

(2012) Nikolaos Balaskas et al.   CELL

A System of Repressor Gradients Spatially Organizes the Boundaries of Bicoid-Dependent Target Genes

(2012) Hongtao Chen et al.   CELL

The Harmonies Played by TGF-β in Stem Cell Biology

(2012) Naoki Oshimori et al.   Cell Stem Cell

Patterning embryos with oscillations: structure, function and dynamics of the vertebrate segmentation clock

(2012) A. C. Oates et al.   DEVELOPMENT

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning

(2012) K. A. Peterson et al.   GENES & DEVELOPMENT

TGFβ signalling in context

(2012) Joan Massagué   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Barcoded DNA-Tag Reporters for Multiplex Cis-Regulatory Analysis

(2012) Jongmin Nam et al.   PLoS One

Massively parallel measurements of molecular interaction kinetics on a microfluidic platform

(2012) M. Geertz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential Diffusivity of Nodal and Lefty Underlies a Reaction-Diffusion Patterning System

(2012) P. Muller et al.   SCIENCE

Morphogen Gradients: From Generation to Interpretation

(2011) Katherine W. Rogers et al.   Annual Review of Cell and Developmental Biology

A Poised Chromatin Platform for TGF-β Access to Master Regulators

(2011) Qiaoran Xi et al.   CELL

HEB and E2A function as SMAD/FOXH1 cofactors

(2011) S.-J. Yoon et al.   GENES & DEVELOPMENT

Global Identification of SMAD2 Target Genes Reveals a Role for Multiple Co-regulatory Factors in Zebrafish Early Gastrulas

(2011) Zhaoting Liu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Quantitative analysis of transient and sustained transforming growth factor-  signaling dynamics

(2011) Z. Zi et al.   Molecular Systems Biology

Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast

(2011) C. Miller et al.   Molecular Systems Biology

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

The time to measure positional information: maternal Hunchback is required for the synchrony of the Bicoid transcriptional response at the onset of zygotic transcription

(2010) A. Porcher et al.   DEVELOPMENT

Histone Demethylase JmjD2A Regulates Neural Crest Specification

(2010) Pablo Hernan Strobl-Mazzulla et al.   DEVELOPMENTAL CELL

Classic and contemporary approaches to modeling biochemical reactions

(2010) W. W. Chen et al.   GENES & DEVELOPMENT

Information processing at the foxa node of the sea urchin endomesoderm specification network

(2010) S. B.-T. de-Leon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling the spatio-temporal network that drives patterning in the vertebrate central nervous system

(2009) Yuichi Nishi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Nodal and BMP2/4 pattern the mesoderm and endoderm during development of the sea urchin embryo

(2009) Véronique Duboc et al.   DEVELOPMENT

A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo

(2009) Yi-Hsien Su et al.   DEVELOPMENTAL BIOLOGY

Transcription Dynamics

(2009) Gordon L. Hager et al.   MOLECULAR CELL

Graded Smad2/3 Activation Is Converted Directly into Levels of Target Gene Expression in Embryonic Stem Cells

(2009) Marcela Guzman-Ayala et al.   PLoS One

Anterior-posterior positional information in the absence of a strong Bicoid gradient

(2009) A. Ochoa-Espinosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Robust Generation and Decoding of Morphogen Gradients

(2009) N. Barkai et al.   Cold Spring Harbor Perspectives in Biology

Nodal Morphogens

(2009) A. F. Schier   Cold Spring Harbor Perspectives in Biology

Visualisation and Quantification of Morphogen Gradient Formation in the Zebrafish

(2009) Steven A Harvey et al.   PLOS BIOLOGY

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

(2008) Mathieu Lupien et al.   CELL

Regulation of Canonical Wnt Signaling by Brachyury Is Essential for Posterior Mesoderm Formation

(2008) Benjamin L. Martin et al.   DEVELOPMENTAL CELL

Nodal signalling is involved in left–right asymmetry in snails

(2008) Cristina Grande et al.   NATURE

Direct multiplexed measurement of gene expression with color-coded probe pairs

(2008) Gary K Geiss et al.   NATURE BIOTECHNOLOGY

Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system

(2008) B. Schmierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY