Controlling spatiotemporal pattern formation in a concentration gradient with a synthetic toggle switch

A Simple and Flexible Computational Framework for Inferring Sources of Heterogeneity from Single-Cell Dynamics

(2019) Lekshmi Dharmarajan et al.   Cell Systems

Synthetic Pattern Formation

(2019) Nan Luo et al.   BIOCHEMISTRY

Light‐Controlled, High‐Resolution Patterning of Living Engineered Bacteria Onto Textiles, Ceramics, and Plastic

(2019) Felix Moser et al.   ADVANCED FUNCTIONAL MATERIALS

Synthetic Bistability and Differentiation in Yeast

(2019) Yaoyu Yang et al.   ACS Synthetic Biology

A multiscale model of epigenetic heterogeneity-driven cell fate decision-making

(2019) Núria Folguera-Blasco et al.   PLoS Computational Biology

Genetic circuits to engineer tissues with alternative functions

(2019) C. P. Healy et al.   Journal of Biological Engineering

Modularity, criticality, and evolvability of a developmental gene regulatory network

(2019) Berta Verd et al.   eLife

Communicating Structure and Function in Synthetic Biology Diagrams

(2019) Jacob Beal et al.   ACS Synthetic Biology

Beyond networks: mechanism and process in evo-devo

(2019) James DiFrisco et al.   BIOLOGY & PHILOSOPHY

Synthetic developmental biology: build and control multicellular systems

(2019) Mo R Ebrahimkhani et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Engineered Living Materials: Prospects and Challenges for Using Biological Systems to Direct the Assembly of Smart Materials

(2018) Peter Q. Nguyen et al.   ADVANCED MATERIALS

Understanding Biological Regulation Through Synthetic Biology

(2018) Caleb J. Bashor et al.   Annual Review of Biophysics

Estimating the Diffusion Coefficients of Sugars Using Diffusion Experiments in Agar-Gel and Computer Simulations

(2018) Shuichi Miyamoto et al.   CHEMICAL & PHARMACEUTICAL BULLETIN

Mathematical model of a serine integrase-controlled toggle switch with a single input

(2018) Alexandra Pokhilko et al.   Journal of the Royal Society Interface

Designing cell function: assembly of synthetic gene circuits for cell biology applications

(2018) Mingqi Xie et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Programming gene and engineered-cell therapies with synthetic biology

(2018) Tasuku Kitada et al.   SCIENCE

Morphogen gradient reconstitution reveals Hedgehog pathway design principles

(2018) Pulin Li et al.   SCIENCE

Programmed hierarchical patterning of bacterial populations

(2018) Christian R. Boehm et al.   Nature Communications

Combining a Toggle Switch and a Repressilator within the AC-DC Circuit Generates Distinct Dynamical Behaviors

(2018) Ruben Perez-Carrasco et al.   Cell Systems

Programmable protein circuits in living cells

(2018) Xiaojing J. Gao et al.   SCIENCE

Cellular checkpoint control using programmable sequential logic

(2018) Lauren B. Andrews et al.   SCIENCE

Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties

(2018) Charlie Gilbert et al.   ACS Synthetic Biology

Programmable assembly of pressure sensors using pattern-forming bacteria

(2017) Yangxiaolu Cao et al.   NATURE BIOTECHNOLOGY

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

(2017) Marcin Zagorski et al.   SCIENCE

Balancing a genetic toggle switch by real-time feedback control and periodic forcing

(2017) Jean-Baptiste Lugagne et al.   Nature Communications

Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation

(2017) Erik Clark   PLOS BIOLOGY

Morphogen interpretation: concentration, time, competence, and signaling dynamics

(2017) Andreas Sagner et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Synthetic biology meets tissue engineering

(2016) J. A. Davies et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Mammalian synthetic biology for studying the cell

(2016) Melina Mathur et al.   JOURNAL OF CELL BIOLOGY

The cellular Ising model: a framework for phase transitions in multicellular environments

(2016) Marc Weber et al.   Journal of the Royal Society Interface

Orthogonal intercellular signaling for programmed spatial behavior

(2016) P. K. Grant et al.   Molecular Systems Biology

Synchronous long-term oscillations in a synthetic gene circuit

(2016) Laurent Potvin-Trottier et al.   NATURE

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

Quorum-Sensing Synchronization of Synthetic Toggle Switches: A Design Based on Monotone Dynamical Systems Theory

(2016) Evgeni V. Nikolaev et al.   PLoS Computational Biology

Intrinsic Noise Profoundly Alters the Dynamics and Steady State of Morphogen-Controlled Bistable Genetic Switches

(2016) Ruben Perez-Carrasco et al.   PLoS Computational Biology

Positional information and reaction-diffusion: two big ideas in developmental biology combine

(2015) J. B. A. Green et al.   DEVELOPMENT

Morphogen rules: design principles of gradient-mediated embryo patterning

(2015) J. Briscoe et al.   DEVELOPMENT

Motif for controllable toggle switch in gene regulatory networks

(2015) Chen Zhao et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms

(2015) Michael Cohen et al.   Nature Communications

Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network

(2015) Kevin Axelrod et al.   eLife

Classification of transient behaviours in a time-dependent toggle switch model

(2014) Berta Verd et al.   BMC Systems Biology

Synthetic analog and digital circuits for cellular computation and memory

(2014) Oliver Purcell et al.   CURRENT OPINION IN BIOTECHNOLOGY

A theoretical framework for the regulation of Shh morphogen-controlled gene expression

(2014) M. Cohen et al.   DEVELOPMENT

A Predictive Model of Bifunctional Transcription Factor Signaling during Embryonic Tissue Patterning

(2014) Jan Philipp Junker et al.   DEVELOPMENTAL CELL

Principles of genetic circuit design

(2014) Jennifer A N Brophy et al.   NATURE METHODS

A brief history of synthetic biology

(2014) D. Ewen Cameron et al.   NATURE REVIEWS MICROBIOLOGY

A bistable genetic switch based on designable DNA-binding domains

(2014) Tina Lebar et al.   Nature Communications

A unified design space of synthetic stripe-forming networks

(2014) Yolanda Schaerli et al.   Nature Communications

A BMP-FGF Morphogen Toggle Switch Drives the Ultrasensitive Expression of Multiple Genes in the Developing Forebrain

(2014) Shyam Srinivasan et al.   PLoS Computational Biology

An improved Escherichia coli strain to host gene regulatory networks involving both the AraC and LacI inducible transcription factors

(2014) Manjunatha Kogenaru et al.   Journal of Biological Engineering

Mathematical model of a gene regulatory network reconciles effects of genetic perturbations on hematopoietic stem cell emergence

(2013) Jatin Narula et al.   DEVELOPMENTAL BIOLOGY

Stochastic Stabilization of Phenotypic States: The Genetic Bistable Switch as a Case Study

(2013) Marc Weber et al.   PLoS One

Engineering of regulated stochastic cell fate determination

(2013) M. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A gene regulatory motif that generates oscillatory or multiway switch outputs

(2012) J. Panovska-Griffiths et al.   Journal of the Royal Society Interface

Noise drives sharpening of gene expression boundaries in the zebrafish hindbrain

(2012) Lei Zhang et al.   Molecular Systems Biology

Sequestration-based bistability enables tuning of the switching boundaries and design of a latch

(2012) David Chen et al.   Molecular Systems Biology

Iterative plug-and-play methodology for constructing and modifying synthetic gene networks

(2012) Kevin D Litcofsky et al.   NATURE METHODS

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Bottom-up construction of in vitro switchable memories

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

Mutual Repression Enhances the Steepness and Precision of Gene Expression Boundaries

(2012) Thomas R. Sokolowski et al.   PLoS Computational Biology

Morphogen Gradients: From Generation to Interpretation

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

Robust synthetic gene network design via library-based search method

(2011) Chih-Hung Wu et al.   BIOINFORMATICS

What's all the noise about developmental stochasticity?

(2011) A. C. Oates   DEVELOPMENT

Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling

(2011) R. Sekine et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-dimensional posterior exploration of hydrologic models using multiple-try DREAM(ZS) and high-performance computing

(2011) Eric Laloy et al.   WATER RESOURCES RESEARCH

Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch

(2010) Chunbo Lou et al.   Molecular Systems Biology

Bistable switches control memory and plasticity in cellular differentiation

(2009) L. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multistable Decision Switches for Flexible Control of Epigenetic Differentiation

(2008) Raúl Guantes et al.   PLoS Computational Biology

Spatial Bistability Generates hunchback Expression Sharpness in the Drosophila Embryo

(2008) Francisco J. P. Lopes et al.   PLoS Computational Biology