Multiplex transcriptional characterizations across diverse bacterial species using cell‐free systems

Deconstructing cell-free extract preparation for in vitro activation of transcriptional genetic circuitry

(2019) Adam Silverman et al.   ACS Synthetic Biology

Cell-free gene-regulatory network engineering with synthetic transcription factors

(2019) Zoe Swank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli

(2018) Guillaume Urtecho et al.   BIOCHEMISTRY

Synthesis of (R,R)-2,3-butanediol from starch in a hybrid cell-free reaction system

(2018) Tong Yi et al.   JOURNAL OF INDUSTRIAL AND ENGINEERING CHEMISTRY

Rapid and Scalable Characterization of CRISPR Technologies Using an E. coli Cell-Free Transcription-Translation System

(2018) Ryan Marshall et al.   MOLECULAR CELL

Metagenomic mining of regulatory elements enables programmable species-selective gene expression

(2018) Nathan I Johns et al.   NATURE METHODS

Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

(2018) Nathan M. Belliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid acquisition and model-based analysis of cell-free transcription–translation reactions from nonmodel bacteria

(2018) Simon J. Moore et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell-free prediction of protein expression costs for growing cells

(2018) Olivier Borkowski et al.   Nature Communications

Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors

(2018) Ye Chen et al.   Nature Communications

Single-pot glycoprotein biosynthesis using a cell-free transcription-translation system enriched with glycosylation machinery

(2018) Thapakorn Jaroentomeechai et al.   Nature Communications

Cell-free protein synthesis from genomically recoded bacteria enables multisite incorporation of noncanonical amino acids

(2018) Rey W. Martin et al.   Nature Communications

Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli

(2018) Guillaume Cambray et al.   NATURE BIOTECHNOLOGY

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers

(2018) Melissa K. Takahashi et al.   Nature Communications

Predicting Transcriptional Output of Synthetic Multi-input Promoters

(2018) David M. Zong et al.   ACS Synthetic Biology

Establishing a Cell-Free Vibrio natriegens Expression System

(2018) Daniel J. Wiegand et al.   ACS Synthetic Biology

Establishing a High-Yielding Cell-Free Protein Synthesis Platform Derived from Vibrio natriegens

(2018) Benjamin J. Des Soye et al.   ACS Synthetic Biology

Measuring cis-regulatory energetics in living cells using allelic manifolds

(2018) Talitha L Forcier et al.   eLife

Genetic circuit characterization and debugging using RNA‐seq

(2017) Thomas E Gorochowski et al.   Molecular Systems Biology

Synthetic microbial consortia enable rapid assembly of pure translation machinery

(2017) Fernando Villarreal et al.   Nature Chemical Biology

A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants

(2017) Eva Yus et al.   Nature Communications

Development of a CHO-Based Cell-Free Platform for Synthesis of Active Monoclonal Antibodies

(2017) Rey W. Martin et al.   ACS Synthetic Biology

Streptomyces venezuelae TX-TL - a next generation cell-free synthetic biology tool

(2017) Simon J. Moore et al.   Biotechnology Journal

Biophysical Constraints Arising from Compositional Context in Synthetic Gene Networks

(2017) Enoch Yeung et al.   Cell Systems

BBMerge – Accurate paired shotgun read merging via overlap

(2017) Brian Bushnell et al.   PLoS One

Ribosome-mediated synthesis of natural product-like peptides via cell-free translation

(2016) Rumit Maini et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Principles for designing synthetic microbial communities

(2016) Nathan I Johns et al.   CURRENT OPINION IN MICROBIOLOGY

A cell-free framework for rapid biosynthetic pathway prototyping and enzyme discovery

(2016) Ashty S. Karim et al.   METABOLIC ENGINEERING

Development of a Bacillus subtilis cell-free transcription-translation system for prototyping regulatory elements

(2016) Richard Kelwick et al.   METABOLIC ENGINEERING

Synthetic biology to access and expand nature's chemical diversity

(2016) Michael J. Smanski et al.   NATURE REVIEWS MICROBIOLOGY

The All E. coli TX-TL Toolbox 2.0: A Platform for Cell-Free Synthetic Biology

(2016) Jonathan Garamella et al.   ACS Synthetic Biology

Cell-Free Mixing of Escherichia coli Crude Extracts to Prototype and Rationally Engineer High-Titer Mevalonate Synthesis

(2016) Quentin M. Dudley et al.   ACS Synthetic Biology

Massively Systematic Transcript End Readout, “MASTER”: Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields

(2015) Irina O. Vvedenskaya et al.   MOLECULAR CELL

High-throughput preparation methods of crude extract for robust cell-free protein synthesis

(2015) Yong-Chan Kwon et al.   Scientific Reports

Rapid cell-free forward engineering of novel genetic ring oscillators

(2015) Henrike Niederholtmeyer et al.   eLife

Cell-free metabolic engineering: Biomanufacturing beyond the cell

(2014) Quentin M. Dudley et al.   Biotechnology Journal

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Paper-Based Synthetic Gene Networks

(2014) Keith Pardee et al.   CELL

Broccoli: Rapid Selection of an RNA Mimic of Green Fluorescent Protein by Fluorescence-Based Selection and Directed Evolution

(2014) Grigory S. Filonov et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

(2014) I. Farasat et al.   Molecular Systems Biology

Functional optimization of gene clusters by combinatorial design and assembly

(2014) Michael J Smanski et al.   NATURE BIOTECHNOLOGY

Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard”

(2014) Dan Siegal-Gaskins et al.   ACS Synthetic Biology

Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription–Translation (TX-TL) Systems

(2014) Melissa K. Takahashi et al.   ACS Synthetic Biology

Optimized extract preparation methods and reaction conditions for improved yeast cell-free protein synthesis

(2013) C. Eric Hodgman et al.   BIOTECHNOLOGY AND BIOENGINEERING

Design of orthogonal genetic switches based on a crosstalk map of  s, anti- s, and promoters

(2013) V. A. Rhodius et al.   Molecular Systems Biology

In vitro integration of ribosomal RNA synthesis, ribosome assembly, and translation

(2013) M. C. Jewett et al.   Molecular Systems Biology

Genomic mining of prokaryotic repressors for orthogonal logic gates

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

Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology

(2013) James Chappell et al.   NUCLEIC ACIDS RESEARCH

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

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

(2013) D. B. Goodman et al.   SCIENCE

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

RNA snap ™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria

(2012) Mark B. Stead et al.   NUCLEIC ACIDS RESEARCH

Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli

(2012) K. Kitahara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed in Vivo His-Tagging of Enzyme Pathways for in Vitro Single-Pot Multienzyme Catalysis

(2012) Harris H. Wang et al.   ACS Synthetic Biology

Genome Replication, Synthesis, and Assembly of the Bacteriophage T7 in a Single Cell-Free Reaction

(2012) Jonghyeon Shin et al.   ACS Synthetic Biology

Transforming biochemical engineering with cell-free biology

(2011) James R. Swartz   AICHE JOURNAL

Cell-free synthetic biology: Thinking outside the cell

(2011) C. Eric Hodgman et al.   METABOLIC ENGINEERING

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

Development of an artificial cell, from self-organization to computation and self-reproduction

(2011) Vincent Noireaux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS RESEARCH

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

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

Predicting strength and function for promoters of the Escherichia coli alternative sigma factor,  E

(2010) V. A. Rhodius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of high-yield autofluorescent protein microarrays using hybrid cell-free expression with combined Escherichia coli S30 and wheat germ extracts

(2010) Xristo Zárate et al.   Proteome Science

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Fermentative hydrogen production by the new marine Pantoea agglomerans isolated from the mangrove sludge

(2008) D ZHU et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

An integrated cell-free metabolic platform for protein production and synthetic biology

(2008) Michael C Jewett et al.   Molecular Systems Biology

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH