Communication codes in developmental signaling pathways

Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo

(2019) Heath E. Johnson et al.   DEVELOPMENTAL CELL

Mechanisms of Notch signaling: a simple logic deployed in time and space

(2019) Domingos Henrique et al.   DEVELOPMENT

Cell-autonomous and redundant roles of Hey1 and HeyL in muscle stem cells: HeyL requires Hes1 to bind diverse DNA sites

(2019) Yu-taro Noguchi et al.   DEVELOPMENT

Modulation of Phase Shift between Wnt and Notch Signaling Oscillations Controls Mesoderm Segmentation

(2018) Katharina F. Sonnen et al.   CELL

Dynamic Ligand Discrimination in the Notch Signaling Pathway

(2018) Nagarajan Nandagopal et al.   CELL

Enteroid Monolayers Reveal an Autonomous WNT and BMP Circuit Controlling Intestinal Epithelial Growth and Organization

(2018) Curtis A. Thorne et al.   DEVELOPMENTAL CELL

Cell‐specific responses to the cytokine TGFβ are determined by variability in protein levels

(2018) Jette Strasen et al.   Molecular Systems Biology

Morphogen gradient reconstitution reveals Hedgehog pathway design principles

(2018) Pulin Li et al.   SCIENCE

Programming self-organizing multicellular structures with synthetic cell-cell signaling

(2018) Satoshi Toda et al.   SCIENCE

A molecular mechanism for Wnt ligand-specific signaling

(2018) Marie Eubelen et al.   SCIENCE

Network Motifs Capable of Decoding Transcription Factor Dynamics

(2018) Zongmao Gao et al.   Scientific Reports

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning

(2018) Sophie M Morgani et al.   eLife

Encoding Growth Factor Identity in the Temporal Dynamics of FOXO3 under the Combinatorial Control of ERK and AKT Kinases

(2018) Somponnat Sampattavanich et al.   Cell Systems

Self-organization of a human organizer by combined Wnt and Nodal signalling

(2018) I. Martyn et al.   NATURE

Synthetic mammalian pattern formation driven by differential diffusivity of Nodal and Lefty

(2018) Ryoji Sekine et al.   Nature Communications

WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids

(2018) Anna Yoney et al.   eLife

An immediate–late gene expression module decodes ERK signal duration

(2017) Florian Uhlitz et al.   Molecular Systems Biology

Planar cell polarity in development and disease

(2017) Mitchell T. Butler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Sensing relative signal in the Tgf-β/Smad pathway

(2017) Christopher L. Frick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of an optimized synthetic Notch receptor as an in vivo cell–cell contact sensor

(2017) Li He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Decoding of position in the developing neural tube from antiparallel morphogen gradients

(2017) Marcin Zagorski et al.   SCIENCE

Tracing neuronal circuits in transgenic animals by transneuronal control of transcription (TRACT)

(2017) Ting-hao Huang et al.   eLife

Optimal Regulatory Circuit Topologies for Fold-Change Detection

(2017) Miri Adler et al.   Cell Systems

Self-Organization of Embryonic Genetic Oscillators into Spatiotemporal Wave Patterns

(2016) Charisios D. Tsiairis et al.   CELL

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors

(2016) Kole T. Roybal et al.   CELL

Monitoring cell-cell contactsin vivoin transgenic animals

(2016) Ting-Hao Huang et al.   DEVELOPMENT

Frequency modulation of ERK activation dynamics rewires cell fate

(2016) H. Ryu et al.   Molecular Systems Biology

BMP signalling in skeletal development, disease and repair

(2016) Valerie S. Salazar et al.   Nature Reviews Endocrinology

Notch signalling in context

(2016) Sarah J. Bray   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Allosteric proteins as logarithmic sensors

(2016) Noah Olsman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistence, period and precision of autonomous cellular oscillators from the zebrafish segmentation clock

(2016) Alexis B Webb et al.   eLife

Morphogen rules: design principles of gradient-mediated embryo patterning

(2015) J. Briscoe et al.   DEVELOPMENT

The intracellular domains of Notch1 and Notch2 are functionally equivalent during development and carcinogenesis

(2015) Z. Liu et al.   DEVELOPMENT

Combinatorial gene regulation by modulation of relative pulse timing

(2015) Yihan Lin et al.   NATURE

Galactose metabolic genes in yeast respond to a ratio of galactose and glucose

(2015) Renan Escalante-Chong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic lateral inhibition governs cell-type bifurcation with robust ratios

(2015) Mitsuhiro Matsuda et al.   Nature Communications

Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms

(2015) Michael Cohen et al.   Nature Communications

High-Sensitivity Measurements of Multiple Kinase Activities in Live Single Cells

(2014) Sergi Regot et al.   CELL

Pulsatile Dynamics in the Yeast Proteome

(2014) Chiraj K. Dalal 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

Fold Change of Nuclear NF-κB Determines TNF-Induced Transcription in Single Cells

(2014) Robin E.C. Lee et al.   MOLECULAR CELL

A method to recapitulate early embryonic spatial patterning in human embryonic stem cells

(2014) Aryeh Warmflash et al.   NATURE METHODS

Signalling dynamics in vertebrate segmentation

(2014) Alexis Hubaud et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Doppler effect in embryonic pattern formation

(2014) D. Soroldoni et al.   SCIENCE

Correction: Fringe proteins modulate Notch-ligand cis and trans interactions to specify signaling states

(2014) Lauren LeBon et al.   eLife

Scaling of Dorsal-Ventral Patterning by Embryo Size-Dependent Degradation of Spemann’s Organizer Signals

(2013) Hidehiko Inomata et al.   CELL

Using Optogenetics to Interrogate the Dynamic Control of Signal Transmission by the Ras/Erk Module

(2013) Jared E. Toettcher et al.   CELL

Encoding and Decoding Cellular Information through Signaling Dynamics

(2013) Jeremy E. Purvis et al.   CELL

Mechanisms of scaling in pattern formation

(2013) D. M. Umulis et al.   DEVELOPMENT

Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression

(2013) A. S. Hansen et al.   Molecular Systems Biology

The mechanisms of Hedgehog signalling and its roles in development and disease

(2013) James Briscoe et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rate of environmental change determines stress response specificity

(2013) J. W. Young et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

Tunable Signal Processing Through Modular Control of Transcription Factor Translocation

(2013) N. Hao et al.   SCIENCE

Oscillatory Control of Factors Determining Multipotency and Fate in Mouse Neural Progenitors

(2013) I. Imayoshi et al.   SCIENCE

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

(2013) P. Vizan et al.   Science Signaling

Creating gradients by morphogen shuttling

(2013) Ben-Zion Shilo et al.   TRENDS IN GENETICS

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

(2012) Nikolaos Balaskas et al.   CELL

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

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

Dynamic Response Diversity of NFAT Isoforms in Individual Living Cells

(2012) Nissan Yissachar et al.   MOLECULAR CELL

Frequency-Modulated Pulses of ERK Activity Transmit Quantitative Proliferation Signals

(2012) John G. Albeck et al.   MOLECULAR CELL

Scaling of embryonic patterning based on phase-gradient encoding

(2012) Volker M. Lauschke et al.   NATURE

Dynamics of TGF-  signaling reveal adaptive and pulsatile behaviors reflected in the nuclear localization of transcription factor Smad4

(2012) A. Warmflash et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors

(2012) Julia Heisig et al.   PLoS Genetics

Morphogen Gradients: From Generation to Interpretation

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

Expansion-Repression Mechanism for Scaling the Dpp Activation Gradient in Drosophila Wing Imaginal Discs

(2011) Danny Ben-Zvi et al.   CURRENT BIOLOGY

A Two-Dimensional ERK-AKT Signaling Code for an NGF-Triggered Cell-Fate Decision

(2011) Jia-Yun Chen et al.   MOLECULAR CELL

Signal-dependent dynamics of transcription factor translocation controls gene expression

(2011) Nan Hao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli

(2010) Thomas S Shimizu et al.   Molecular Systems Biology

Build life to understand it

(2010) Michael Elowitz et al.   NATURE

Structural and mechanistic insights into cooperative assembly of dimeric Notch transcription complexes

(2010) Kelly L Arnett et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Fold-change detection and scalar symmetry of sensory input fields

(2010) O. Shoval et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BMP and BMP receptor expression during murine organogenesis

(2009) Shahab M. Danesh et al.   GENE EXPRESSION PATTERNS

Dynamics and Variability of ERK2 Response to EGF in Individual Living Cells

(2009) Cellina Cohen-Saidon et al.   MOLECULAR CELL

Evidence that Fold-Change, and Not Absolute Level, of β-Catenin Dictates Wnt Signaling

(2009) Lea Goentoro et al.   MOLECULAR CELL

The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation

(2009) Lea Goentoro et al.   MOLECULAR CELL

Rapid and sustained nuclear–cytoplasmic ERK oscillations induced by epidermal growth factor

(2009) Harish Shankaran et al.   Molecular Systems Biology

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

(2009) L. Ashall et al.   SCIENCE

Frequency-modulated nuclear localization bursts coordinate gene regulation

(2008) Long Cai et al.   NATURE

Oscillations in Notch Signaling Regulate Maintenance of Neural Progenitors

(2008) Hiromi Shimojo et al.   NEURON