A versatile framework for microbial engineering using synthetic non-coding RNAs

The Cellular Environment Stabilizes Adenine Riboswitch RNA Structure

(2013) Jillian Tyrrell et al.   BIOCHEMISTRY

The centrality of RNA for engineering gene expression

(2013) James Chappell et al.   Biotechnology Journal

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

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

(2013) Lei S. Qi et al.   CELL

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

CRISPR/Cas9-Targeted Mutagenesis in Caenorhabditis elegans

(2013) Selma Waaijers et al.   GENETICS

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

Targeted genome modification of crop plants using a CRISPR-Cas system

(2013) Qiwei Shan et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

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

(2013) Vivek K Mutalik et al.   NATURE METHODS

Quantitative estimation of activity and quality for collections of functional genetic elements

(2013) Vivek K Mutalik et al.   NATURE METHODS

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

A modular strategy for engineering orthogonal chimeric RNA transcription regulators

(2013) Melissa K. Takahashi et al.   NUCLEIC ACIDS RESEARCH

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Engineering modular ‘ON’ RNA switches using biological components

(2013) Pablo Ceres et al.   NUCLEIC ACIDS RESEARCH

Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems

(2013) James E. DiCarlo et al.   NUCLEIC ACIDS RESEARCH

Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9

(2013) X. Ren 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

Dynamically Reshaping Signaling Networks to Program Cell Fate via Genetic Controllers

(2013) K. E. Galloway et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Synthetic Biology: Advancing the Design of Diverse Genetic Systems

(2013) Yen-Hsiang Wang et al.   Annual Review of Chemical and Biomolecular Engineering

Tunable and Multifunctional Eukaryotic Transcription Factors Based on CRISPR/Cas

(2013) Fahim Farzadfard et al.   ACS Synthetic Biology

Full Design Automation of Multi-State RNA Devices to Program Gene Expression Using Energy-Based Optimization

(2013) Guillermo Rodrigo et al.   PLoS Computational Biology

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

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

(2012) David Chen et al.   Molecular Systems Biology

Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells

(2012) Ping Wei et al.   NATURE

Microbial engineering for the production of advanced biofuels

(2012) Pamela P. Peralta-Yahya et al.   NATURE

Genetic programs constructed from layered logic gates in single cells

(2012) Tae Seok Moon et al.   NATURE

RNA-guided genetic silencing systems in bacteria and archaea

(2012) Blake Wiedenheft 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

An adaptor from translational to transcriptional control enables predictable assembly of complex regulation

(2012) Chang C Liu et al.   NATURE METHODS

Engineering naturally occurring trans -acting non-coding RNAs to sense molecular signals

(2012) Lei Qi et al.   NUCLEIC ACIDS RESEARCH

A high-throughput, quantitative cell-based screen for efficient tailoring of RNA device activity

(2012) Joe C. Liang et al.   NUCLEIC ACIDS RESEARCH

Multi-Target Regulation by Small RNAs Synchronizes Gene Expression Thresholds and May Enhance Ultrasensitive Behavior

(2012) Jörn Matthias Schmiedel et al.   PLoS One

De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells

(2012) G. Rodrigo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic switchboard for synthetic biology applications

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

Engineering robust control of two-component system phosphotransfer using modular scaffolds

(2012) W. R. Whitaker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Site-Specific Labeling of DNA and RNA Using an Efficiently Replicated and Transcribed Class of Unnatural Base Pairs

(2011) Young Jun Seo et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineering Biological Systems with Synthetic RNA Molecules

(2011) Joe C. Liang et al.   MOLECULAR CELL

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

A two-dimensional mutate-and-map strategy for non-coding RNA structure

(2011) Wipapat Kladwang et al.   Nature Chemistry

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Modeling and automation of sequencing-based characterization of RNA structure

(2011) S. Aviran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

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

Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors

(2011) A. Ogawa   RNA

Organization of Intracellular Reactions with Rationally Designed RNA Assemblies

(2011) C. J. Delebecque et al.   SCIENCE

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

(2011) J. M. Carothers et al.   SCIENCE

Synthetic Biology Moving into the Clinic

(2011) W. C. Ruder et al.   SCIENCE

Scaling Up Digital Circuit Computation with DNA Strand Displacement Cascades

(2011) L. Qian et al.   SCIENCE

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

(2011) Z. Xie et al.   SCIENCE

Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli

(2011) Vandana Sharma et al.   ACS Synthetic Biology

Synthetic Riboswitches That Induce Gene Expression in Diverse Bacterial Species

(2010) S. Topp et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Self versus non-self discrimination during CRISPR RNA-directed immunity

(2010) Luciano A. Marraffini et al.   NATURE

Microbial production of fatty-acid-derived fuels and chemicals from plant biomass

(2010) Eric J. Steen et al.   NATURE

A synchronized quorum of genetic clocks

(2010) Tal Danino et al.   NATURE

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems

(2010) Y. Y. Chen 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

The Structural and Functional Diversity of Metabolite-Binding Riboswitches

(2009) Adam Roth et al.   Annual Review of Biochemistry

The Centrality of RNA

(2009) Phillip A. Sharp   CELL

RNA-Guided RNA Cleavage by a CRISPR RNA-Cas Protein Complex

(2009) Caryn R. Hale et al.   CELL

A Synthetic Genetic Edge Detection Program

(2009) Jeffrey J. Tabor et al.   CELL

A tunable synthetic mammalian oscillator

(2009) Marcel Tigges et al.   NATURE

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

Synthetic protein scaffolds provide modular control over metabolic flux

(2009) John E Dueber et al.   NATURE BIOTECHNOLOGY

Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?

(2009) Hal Alper et al.   NATURE REVIEWS MICROBIOLOGY

Synthetic Gene Networks That Count

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

Design Principles for Ligand-Sensing, Conformation-Switching Ribozymes

(2009) Xi Chen et al.   PLoS Computational Biology

RNAi mechanisms and applications

(2008) Daniel H. Kim et al.   BIOTECHNIQUES

Toward scalable parts families for predictable design of biological circuits

(2008) Julius B Lucks et al.   CURRENT OPINION IN MICROBIOLOGY

Engineering Complex Riboswitch Regulation by Dual Genetic Selection

(2008) Vandana Sharma et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Small Toxic Proteins and the Antisense RNAs That Repress Them

(2008) E. M. Fozo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Modular cell biology: retroactivity and insulation

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

A fast, robust and tunable synthetic gene oscillator

(2008) Jesse Stricker et al.   NATURE

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

(2008) Shota Atsumi et al.   NATURE

A flow cytometry-based screen for synthetic riboswitches

(2008) Sean A. Lynch et al.   NUCLEIC ACIDS RESEARCH

Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

(2008) S. J. J. Brouns et al.   SCIENCE

Higher-Order Cellular Information Processing with Synthetic RNA Devices

(2008) M. N. Win et al.   SCIENCE