Optogenetic characterization methods overcome key challenges in synthetic and systems biology

Rapid and tunable post-translational coupling of genetic circuits

(2014) Arthur Prindle et al.   NATURE

Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals

(2014) Evan J Olson et al.   NATURE METHODS

Principles of genetic circuit design

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

Programmable bacteria detect and record an environmental signal in the mammalian gut

(2014) Jonathan W. Kotula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineered temperature compensation in a synthetic genetic clock

(2014) F. Hussain et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Programmed Allee effect in bacteria causes a tradeoff between population spread and survival

(2014) Robert Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Secreting and Sensing the Same Molecule Allows Cells to Achieve Versatile Social Behaviors

(2014) H. Youk et al.   SCIENCE

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

(2013) Jared E. Toettcher et al.   CELL

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Temporal control of self-organized pattern formation without morphogen gradients in bacteria

(2013) S. Payne et al.   Molecular Systems Biology

Synthetic analog computation in living cells

(2013) Ramiz Daniel et al.   NATURE

Synthetic circuits integrating logic and memory in living cells

(2013) Piro Siuti et al.   NATURE BIOTECHNOLOGY

Genomic mining of prokaryotic repressors for orthogonal logic gates

(2013) Brynne C Stanton et al.   Nature Chemical Biology

Precise and reliable gene expression via standard transcription and translation initiation elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

Rapid, modular and reliable construction of complex mammalian gene circuits

(2013) Patrick Guye et al.   NUCLEIC ACIDS RESEARCH

Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

(2013) Joseph P. Torella et al.   NUCLEIC ACIDS RESEARCH

Direct observation of single stationary-phase bacteria reveals a surprisingly long period of constant protein production activity

(2013) O. Gefen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amplifying Genetic Logic Gates

(2013) J. Bonnet et al.   SCIENCE

Modular Design of a Synthetic Payload Delivery Device

(2013) Jin H. Huh et al.   ACS Synthetic Biology

Retroactivity Controls the Temporal Dynamics of Gene Transcription

(2013) Shridhar Jayanthi et al.   ACS Synthetic Biology

Effects of Genetic Variation on the E. coli Host-Circuit Interface

(2013) Stefano Cardinale et al.   Cell Reports

Optogenetic control of cell function using engineered photoreceptors

(2012) Gopal P. Pathak et al.   BIOLOGY OF THE CELL

Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems

(2012) Stefano Cardinale et al.   Biotechnology Journal

Designing Synthetic Regulatory Networks Capable of Self-Organizing Cell Polarization

(2012) Angela H. Chau et al.   CELL

Successes and failures in modular genetic engineering

(2012) Joshua T Kittleson et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Synthetic memory circuits for tracking human cell fate

(2012) D. R. Burrill et al.   GENES & DEVELOPMENT

Mode of Regulation and the Insulation of Bacterial Gene Expression

(2012) Vered Sasson et al.   MOLECULAR CELL

Genetic programs constructed from layered logic gates in single cells

(2012) Tae Seok Moon et al.   NATURE

RNA processing enables predictable programming of gene expression

(2012) Lei Qi et al.   NATURE BIOTECHNOLOGY

Ribozyme-based insulator parts buffer synthetic circuits from genetic context

(2012) Chunbo Lou et al.   NATURE BIOTECHNOLOGY

Optimality and robustness in quorum sensing (QS)-mediated regulation of a costly public good enzyme

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

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

(2012) J. Uhlendorf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors

(2012) Felix Moser et al.   ACS Synthetic Biology

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

The use of light for engineered control and reprogramming of cellular functions

(2011) William Bacchus et al.   CURRENT OPINION IN BIOTECHNOLOGY

Recent advances in computational protein design

(2011) Robert J Pantazes et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template

(2011) L. Bleris et al.   Molecular Systems Biology

Queueing up for enzymatic processing: correlated signaling through coupled degradation

(2011) N. A. Cookson et al.   Molecular Systems Biology

A sensing array of radically coupled genetic ‘biopixels’

(2011) Arthur Prindle et al.   NATURE

In silico feedback for in vivo regulation of a gene expression circuit

(2011) Andreas Milias-Argeitis et al.   NATURE BIOTECHNOLOGY

Light-based feedback for controlling intracellular signaling dynamics

(2011) Jared E Toettcher et al.   NATURE METHODS

Versatile RNA-sensing transcriptional regulators for engineering genetic networks

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequential Establishment of Stripe Patterns in an Expanding Cell Population

(2011) C. Liu et al.   SCIENCE

Synthetic Biology: Integrated Gene Circuits

(2011) N. Nandagopal et al.   SCIENCE

Stochastic Pulse Regulation in Bacterial Stress Response

(2011) J. C. W. Locke et al.   SCIENCE

Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells

(2011) Z. Xie et al.   SCIENCE

Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology

(2011) Baojun Wang et al.   Nature Communications

Multichromatic Control of Gene Expression in Escherichia coli

(2010) Jeffrey J. Tabor et al.   JOURNAL OF MOLECULAR BIOLOGY

Distributed biological computation with multicellular engineered networks

(2010) Sergi Regot et al.   NATURE

Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’

(2010) Alvin Tamsir et al.   NATURE

Optogenetics

(2010) Karl Deisseroth   NATURE METHODS

Logic integration of mRNA signals by an RNAi-based molecular computer

(2010) Zhen Xie et al.   NUCLEIC ACIDS RESEARCH

Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins

(2010) S. J. Culler et al.   SCIENCE

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits

(2009) Tolga Çağatay et al.   CELL

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

Growth Rate-Dependent Global Effects on Gene Expression in Bacteria

(2009) Stefan Klumpp et al.   CELL

Spatiotemporal control of cell signalling using a light-switchable protein interaction

(2009) Anselm Levskaya et al.   NATURE

The second wave of synthetic biology: from modules to systems

(2009) Priscilla E. M. Purnick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression

(2009) D. Nevozhay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic Gene Networks That Count

(2009) A. E. Friedland et al.   SCIENCE

Engineering stochasticity in gene expression

(2008) Jeffrey J. Tabor et al.   Molecular BioSystems

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

Regulatory activity revealed by dynamic correlations in gene expression noise

(2008) Mary J Dunlop et al.   NATURE GENETICS

Signal processing by the HOG MAP kinase pathway

(2008) P. Hersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using Engineered Scaffold Interactions to Reshape MAP Kinase Pathway Signaling Dynamics

(2008) C. J. Bashor et al.   SCIENCE

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE