Foundations for the design and implementation of synthetic genetic circuits

The Development and Application of Optogenetics

(2011) Lief Fenno et al.   Annual Review of Neuroscience

Cellular Decision Making and Biological Noise: From Microbes to Mammals

(2011) Gábor Balázsi et al.   CELL

DARPins and other repeat protein scaffolds: advances in engineering and applications

(2011) Ykelien L Boersma et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA assembly for synthetic biology: from parts to pathways and beyond

(2011) Tom Ellis et al.   Integrative Biology

Computational design approaches and tools for synthetic biology

(2011) James T. MacDonald et al.   Integrative Biology

Light-Activated Kinases Enable Temporal Dissection of Signaling Networks in Living Cells

(2011) Arnaud Gautier et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Neocortical excitation/inhibition balance in information processing and social dysfunction

(2011) Ofer Yizhar et al.   NATURE

MicroRNAs can generate thresholds in target gene expression

(2011) Shankar Mukherji et al.   NATURE GENETICS

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

De Novo Enzyme Design Using Rosetta3

(2011) Florian Richter et al.   PLoS One

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

(2011) Jacob Beal et al.   PLoS One

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

Chemical and Genetic Engineering of Selective Ion Channel-Ligand Interactions

(2011) C. J. Magnus et al.   SCIENCE

Synthetic Biology Moving into the Clinic

(2011) W. C. Ruder et al.   SCIENCE

A Synthetic Optogenetic Transcription Device Enhances Blood-Glucose Homeostasis in Mice

(2011) H. Ye et al.   SCIENCE

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

(2011) Z. Xie et al.   SCIENCE

Applications of Aptamers as Sensors

(2010) Eun Jeong Cho et al.   Annual Review of Analytical Chemistry

The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation

(2010) Aaron Klug   Annual Review of Biochemistry

Noise and Robustness in Prokaryotic Regulatory Networks

(2010) Rafael Silva-Rocha et al.   Annual Review of Microbiology

Characterization of combinatorial patterns generated by multiple two-component sensors in E. coli that respond to many stimuli

(2010) Elizabeth J. Clarke et al.   BIOTECHNOLOGY AND BIOENGINEERING

Making Cellular Memories

(2010) Devin R. Burrill et al.   CELL

Use of two-component signal transduction systems in the construction of synthetic genetic networks

(2010) Alexander J Ninfa   CURRENT OPINION IN MICROBIOLOGY

Multichromatic Control of Gene Expression in Escherichia coli

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

A comparative analysis of synthetic genetic oscillators

(2010) O. Purcell et al.   Journal of the Royal Society Interface

A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression

(2010) Simon Ausländer et al.   Molecular BioSystems

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

A synchronized quorum of genetic clocks

(2010) Tal Danino et al.   NATURE

A TALE nuclease architecture for efficient genome editing

(2010) Jeffrey C Miller et al.   NATURE BIOTECHNOLOGY

The promise of optogenetics in cell biology: interrogating molecular circuits in space and time

(2010) Jared E Toettcher et al.   NATURE METHODS

Rationally designed logic integration of regulatory signals in mammalian cells

(2010) Madeleine Leisner et al.   Nature Nanotechnology

Ultrafast optogenetic control

(2010) Lisa A Gunaydin et al.   NATURE NEUROSCIENCE

Directed molecular evolution of DREADDs: a generic approach to creating next-generation RASSLs

(2010) Shuyun Dong et al.   Nature Protocols

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

Designing customized cell signalling circuits

(2010) Wendell A. Lim   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Strategies for protein synthetic biology

(2010) Raik Grünberg et al.   NUCLEIC ACIDS RESEARCH

A synthetic low-frequency mammalian oscillator

(2010) Marcel Tigges et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Zhen Xie et al.   NUCLEIC ACIDS RESEARCH

Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors

(2010) R. Morbitzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reprogramming Cellular Behavior with RNA Controllers Responsive to Endogenous Proteins

(2010) S. J. Culler et al.   SCIENCE

Rapid Diversification of Cell Signaling Phenotypes by Modular Domain Recombination

(2010) S. G. Peisajovich et al.   SCIENCE

ProMoT: modular modeling for systems biology

(2009) Sebastian Mirschel et al.   BIOINFORMATICS

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

An RNA Aptamer that Induces Transcription

(2009) Anke Hunsicker et al.   CHEMISTRY & BIOLOGY

Engineering multicellular systems by cell–cell communication

(2009) Anand Pai et al.   CURRENT OPINION IN BIOTECHNOLOGY

Towards programming languages for genetic engineering of living cells

(2009) M. Pedersen et al.   Journal of the Royal Society Interface

A synthetic metabolite-based mammalian inter-cell signaling system

(2009) Wilfried Weber et al.   Molecular BioSystems

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

(2009) Anselm Levskaya et al.   NATURE

Temporally precise in vivo control of intracellular signalling

(2009) Raag D. Airan et al.   NATURE

A genetically encoded photoactivatable Rac controls the motility of living cells

(2009) Yi I. Wu et al.   NATURE

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Genome engineering

(2009) Peter A Carr et al.   NATURE BIOTECHNOLOGY

Diversity-based, model-guided construction of synthetic gene networks with predicted functions

(2009) Tom Ellis et al.   NATURE BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

The second wave of synthetic biology: from modules to systems

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

Writing DNA with GenoCADTM

(2009) M. J. Czar et al.   NUCLEIC ACIDS RESEARCH

DNA Binding Made Easy

(2009) D. F. Voytas et al.   SCIENCE

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Synthetic Gene Networks That Count

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

TinkerCell: modular CAD tool for synthetic biology

(2009) Deepak Chandran et al.   Journal of Biological Engineering

A Combinatorial Polymer Library Approach Yields Insight into Nonviral Gene Delivery

(2008) Jordan J. Green et al.   ACCOUNTS OF CHEMICAL RESEARCH

SynBioSS: the synthetic biology modeling suite

(2008) Anthony D. Hill et al.   BIOINFORMATICS

OptCircuit: an optimization based method for computational design of genetic circuits

(2008) Madhukar S Dasika et al.   BMC Systems Biology

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

Intron length increases oscillatory periods of gene expression in animal cells

(2008) I. A. Swinburne et al.   GENES & DEVELOPMENT

Picomolar Affinity Fibronectin Domains Engineered Utilizing Loop Length Diversity, Recursive Mutagenesis, and Loop Shuffling

(2008) Benjamin J. Hackel et al.   JOURNAL OF MOLECULAR BIOLOGY

Modular cell biology: retroactivity and insulation

(2008) Domitilla Del Vecchio et al.   Molecular Systems Biology

Kemp elimination catalysts by computational enzyme design

(2008) Daniela Röthlisberger et al.   NATURE

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

Engineered GPCRs as Tools to Modulate Signal Transduction

(2008) Ying Pei et al.   PHYSIOLOGY

Design and Construction of a Double Inversion Recombination Switch for Heritable Sequential Genetic Memory

(2008) Timothy S. Ham et al.   PLoS One

CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks

(2008) A. Funahashi et al.   PROCEEDINGS OF THE IEEE

A synthetic mammalian gene circuit reveals antituberculosis compounds

(2008) W. Weber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE

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

Engineering microbial consortia: a new frontier in synthetic biology

(2008) Katie Brenner et al.   TRENDS IN BIOTECHNOLOGY

Construction of an artificial intercellular communication network using the nitric oxide signaling elements in mammalian cells

(2007) Wei-Dong Wang et al.   EXPERIMENTAL CELL RESEARCH