Digital and analog gene circuits for biotechnology

Expanding the scope of site-specific recombinases for genetic and metabolic engineering

(2013) Thomas Gaj et al.   BIOTECHNOLOGY AND BIOENGINEERING

Large-scale production of diesel-like biofuels - process design as an inherent part of microorganism development

(2013) Maria C. Cuellar et al.   Biotechnology Journal

A Decade of Riboswitches

(2013) Alexander Serganov et al.   CELL

Towards a whole-cell modeling approach for synthetic biology

(2013) Oliver Purcell et al.   CHAOS

Genetically Encoded Light-Activated Transcription for Spatiotemporal Control of Gene Expression and Gene Silencing in Mammalian Cells

(2013) James Hemphill et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien 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

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

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

(2013) Vivek K Mutalik et al.   NATURE METHODS

A red/far-red light-responsive bi-stable toggle switch to control gene expression in mammalian cells

(2013) Konrad Müller et al.   NUCLEIC ACIDS RESEARCH

Multi-chromatic control of mammalian gene expression and signaling

(2013) Konrad Müller et al.   NUCLEIC ACIDS RESEARCH

Amplifying Genetic Logic Gates

(2013) J. Bonnet et al.   SCIENCE

Ultrasensitive response motifs: basic amplifiers in molecular signalling networks

(2013) Q. Zhang et al.   Open Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Light-Inducible Spatiotemporal Control of Gene Activation by Customizable Zinc Finger Transcription Factors

(2012) Lauren R. Polstein et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

(2012) David Chen et al.   Molecular Systems Biology

A regulatory role for repeated decoy transcription factor binding sites in target gene expression

(2012) Tek-Hyung Lee et al.   Molecular Systems Biology

Genetic programs constructed from layered logic gates in single cells

(2012) Tae Seok Moon et al.   NATURE

Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids

(2012) Fuzhong Zhang et al.   NATURE BIOTECHNOLOGY

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

Rationally designed families of orthogonal RNA regulators of translation

(2012) Vivek K Mutalik et al.   Nature Chemical Biology

De novo design of a synthetic riboswitch that regulates transcription termination

(2012) M. Wachsmuth et al.   NUCLEIC ACIDS RESEARCH

Rewritable digital data storage in live cells via engineered control of recombination directionality

(2012) J. Bonnet 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

Synthetic biology: advancing biological frontiers by building synthetic systems

(2012) Yvonne Y Chen et al.   GENOME BIOLOGY

Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol

(2011) Cong T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Negative auto-regulation increases the input dynamic-range of the arabinose system of Escherichia coli

(2011) Daniel Madar et al.   BMC Systems Biology

Robust Spindle Alignment in Drosophila Neuroblasts by Ultrasensitive Activation of Pins

(2011) Nicholas R. Smith et al.   MOLECULAR CELL

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

MicroRNAs can generate thresholds in target gene expression

(2011) Shankar Mukherji et al.   NATURE GENETICS

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

Model-Driven Engineering of RNA Devices to Quantitatively Program Gene Expression

(2011) J. M. Carothers 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

Microbial production of bulk chemicals: development of anaerobic processes

(2011) Ruud A. Weusthuis et al.   TRENDS IN BIOTECHNOLOGY

Biosensors and their applications in microbial metabolic engineering

(2011) Fuzhong Zhang et al.   TRENDS IN MICROBIOLOGY

Engineering Static and Dynamic Control of Synthetic Pathways

(2010) William J. Holtz et al.   CELL

Construction of a Genetic Multiplexer to Toggle between Chemosensory Pathways in Escherichia coli

(2010) Tae Seok Moon et al.   JOURNAL OF MOLECULAR BIOLOGY

Multichromatic Control of Gene Expression in Escherichia coli

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

Noncooperative Interactions between Transcription Factors and Clustered DNA Binding Sites Enable Graded Transcriptional Responses to Environmental Inputs

(2010) Luca Giorgetti et al.   MOLECULAR CELL

A tunable dual-promoter integrator for targeting of cancer cells

(2010) Lior Nissim et al.   Molecular Systems 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

Design, construction and characterization of a set of insulated bacterial promoters

(2010) J. H. Davis et al.   NUCLEIC ACIDS RESEARCH

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

(2010) J. M. Callura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

Yeast flocculation: New story in fuel ethanol production

(2009) X.Q. Zhao et al.   BIOTECHNOLOGY ADVANCES

Protein sequestration generates a flexible ultrasensitive response in a genetic network

(2009) Nicolas E Buchler et al.   Molecular Systems Biology

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

(2009) Anselm Levskaya et al.   NATURE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Next-generation synthetic gene networks

(2009) Timothy K Lu et al.   NATURE BIOTECHNOLOGY

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

Design and Signaling Mechanism of Light-Regulated Histidine Kinases

(2008) Andreas Möglich et al.   JOURNAL OF MOLECULAR BIOLOGY

Dynamic metabolic engineering for increasing bioprocess productivity

(2008) Nikolaos Anesiadis et al.   METABOLIC ENGINEERING

Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes

(2008) Shai Kaplan et al.   MOLECULAR CELL

Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels

(2008) Shota Atsumi et al.   NATURE

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

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

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE