Tailor-made transcriptional biosensors for optimizing microbial cell factories

Structural Basis of Selective Aromatic Pollutant Sensing by the Effector Binding Domain of MopR, an NtrC Family Transcriptional Regulator

(2016) Shamayeeta Ray et al.   ACS Chemical Biology

Screening of an Escherichia coli promoter library for a phenylalanine biosensor

(2016) Regina Mahr et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Development and substrate specificity screening of an in vivo biosensor for the detection of biomass derived aromatic chemical building blocks

(2016) Leopoldo F. M. Machado et al.   CHEMICAL COMMUNICATIONS

New and improved tools and methods for enhanced biosynthesis of natural products in microorganisms

(2016) Zhiqing Wang et al.   CURRENT OPINION IN BIOTECHNOLOGY

Biosensor-based engineering of biosynthetic pathways

(2016) Jameson K Rogers et al.   CURRENT OPINION IN BIOTECHNOLOGY

Sensing new chemicals with bacterial transcription factors

(2016) Vincent Libis et al.   CURRENT OPINION IN MICROBIOLOGY

Next stop for the CRISPR revolution: RNA-guided epigenetic regulators

(2016) Suhani Vora et al.   FEBS Journal

Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis

(2016) Yi Xiao et al.   Nature Chemical Biology

Local and global regulation of transcription initiation in bacteria

(2016) Douglas F. Browning et al.   NATURE REVIEWS MICROBIOLOGY

Weighted enrichment method for prediction of transcription regulators from transcriptome and global chromatin immunoprecipitation data

(2016) Eiryo Kawakami et al.   NUCLEIC ACIDS RESEARCH

A microbial sensor for organophosphate hydrolysis exploiting an engineered specificity switch in a transcription factor

(2016) Ramesh K. Jha et al.   NUCLEIC ACIDS RESEARCH

Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes inEscherichia coli

(2016) Brady F. Cress et al.   NUCLEIC ACIDS RESEARCH

SensiPath: computer-aided design of sensing-enabling metabolic pathways

(2016) Baudoin Delépine et al.   NUCLEIC ACIDS RESEARCH

Genetically encoded sensors enable real-time observation of metabolite production

(2016) Jameson K. Rogers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic circuit design automation

(2016) A. A. K. Nielsen et al.   SCIENCE

Multiplexed Engineering in Biology

(2016) Jameson K. Rogers et al.   TRENDS IN BIOTECHNOLOGY

Synthetic Evolution of Metabolic Productivity Using Biosensors

(2016) Thomas C. Williams et al.   TRENDS IN BIOTECHNOLOGY

A Parts Database with Consensus Parameter Estimation for Synthetic Circuit Design

(2016) Linh Huynh et al.   ACS Synthetic Biology

Development of Colorimetric-Based Whole-Cell Biosensor for Organophosphorus Compounds by Engineering Transcription Regulator DmpR

(2016) Huiqing Chong et al.   ACS Synthetic Biology

Expanding Biosensing Abilities through Computer-Aided Design of Metabolic Pathways

(2016) Vincent Libis et al.   ACS Synthetic Biology

Transcription factor-based biosensors in biotechnology: current state and future prospects

(2015) Regina Mahr et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice

(2015) Gert Peters et al.   BIOTECHNOLOGY ADVANCES

A review of ensemble methods for de novo motif discovery in ChIP-Seq data

(2015) A. Lihu et al.   BRIEFINGS IN BIOINFORMATICS

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

The functional landscape bound to the transcription factors of Escherichia coli K-12

(2015) Ernesto Pérez-Rueda et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Complex systems in metabolic engineering

(2015) James D Winkler et al.   CURRENT OPINION IN BIOTECHNOLOGY

Novel screening methods—biosensors

(2015) Lothar Eggeling et al.   CURRENT OPINION IN BIOTECHNOLOGY

Development of biosensors and their application in metabolic engineering

(2015) Jie Zhang et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Biosensor-driven adaptive laboratory evolution of l -valine production in Corynebacterium glutamicum

(2015) Regina Mahr et al.   METABOLIC ENGINEERING

Design of an ectoine-responsive AraC mutant and its application in metabolic engineering of ectoine biosynthesis

(2015) Wei Chen et al.   METABOLIC ENGINEERING

Applications and advances of metabolite biosensors for metabolic engineering

(2015) Di Liu et al.   METABOLIC ENGINEERING

Engineering an allosteric transcription factor to respond to new ligands

(2015) Noah D Taylor et al.   NATURE METHODS

Amplification of small molecule-inducible gene expression via tuning of intracellular receptor densities

(2015) Baojun Wang et al.   NUCLEIC ACIDS RESEARCH

Synthetic biosensors for precise gene control and real-time monitoring of metabolites

(2015) Jameson K. Rogers et al.   NUCLEIC ACIDS RESEARCH

Rosetta comparative modeling for library design: Engineering alternative inducer specificity in a transcription factor

(2015) Ramesh K. Jha et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Engineering Transcriptional Regulator Effector Specificity Using Computational Design and In Vitro Rapid Prototyping: Developing a Vanillin Sensor

(2015) Emmanuel L. C. de los Santos et al.   ACS Synthetic Biology

Transcription factor-based biosensors enlightened by the analyte

(2015) Raul Fernandez-López et al.   Frontiers in Microbiology

The Transcription Factor Titration Effect Dictates Level of Gene Expression

(2014) Robert C. Brewster et al.   CELL

Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors

(2014) Marcus Schallmey et al.   CURRENT OPINION IN BIOTECHNOLOGY

Principles of genetic circuit design

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

Engineering anAcinetobacterregulon for biosensing and high-throughput enzyme screening inE. colivia flow cytometry

(2014) Ramesh K. Jha et al.   NUCLEIC ACIDS RESEARCH

Engineering modular and tunable genetic amplifiers for scaling transcriptional signals in cascaded gene networks

(2014) Baojun Wang et al.   NUCLEIC ACIDS RESEARCH

Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration

(2014) Mattias Rydenfelt et al.   PHYSICAL REVIEW E

Evolution-guided optimization of biosynthetic pathways

(2014) Srivatsan Raman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering allostery

(2014) Srivatsan Raman et al.   TRENDS IN GENETICS

Design, Construction, and Characterization of a Set of Biosensors for Aromatic Compounds

(2014) Haoran Xue et al.   ACS Synthetic Biology

Modular, Multi-Input Transcriptional Logic Gating with Orthogonal LacI/GalR Family Chimeras

(2014) David L. Shis et al.   ACS Synthetic Biology

RegTransBase – a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes

(2013) Michael J Cipriano et al.   BMC GENOMICS

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

(2013) Pavel S Novichkov et al.   BMC GENOMICS

Screening for Enhanced Triacetic Acid Lactone Production by Recombinant Escherichia coli Expressing a Designed Triacetic Acid Lactone Reporter

(2013) Shuang-Yan Tang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The TetR Family of Regulators

(2013) L. Cuthbertson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Tuning the dials of Synthetic Biology

(2013) J. A. J. Arpino et al.   MICROBIOLOGY-SGM

Engineering dynamic pathway regulation using stress-response promoters

(2013) Robert H Dahl et al.   NATURE BIOTECHNOLOGY

Genomic mining of prokaryotic repressors for orthogonal logic gates

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

Small-molecule ligand docking into comparative models with Rosetta

(2013) Steven A Combs et al.   Nature Protocols

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

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Programming adaptive control to evolve increased metabolite production

(2013) Howard H. Chou et al.   Nature Communications

Engineering Multicellular Logic in Bacteria with Metabolic Wires

(2013) Rafael Silva-Rocha et al.   ACS Synthetic Biology

SoxR as a Single-Cell Biosensor for NADPH-Consuming Enzymes in Escherichia coli

(2013) Solvej Siedler et al.   ACS Synthetic Biology

Tuning Response Curves for Synthetic Biology

(2013) Jordan Ang et al.   ACS Synthetic Biology

Taking Control over Control: Use of Product Sensing in Single Cells to Remove Flux Control at Key Enzymes in Biosynthesis Pathways

(2013) Georg Schendzielorz et al.   ACS Synthetic Biology

Negative Feedback Regulation of Fatty Acid Production Based on a Malonyl-CoA Sensor–Actuator

(2013) Di Liu et al.   ACS Synthetic Biology

Cooperative Binding

(2013) Melanie I. Stefan et al.   PLoS Computational Biology

The Next Generation of Transcription Factor Binding Site Prediction

(2013) Anthony Mathelier et al.   PLoS Computational Biology

Evolution of an alkane-inducible biosensor for increased responsiveness to short-chain alkanes

(2012) Ben Reed et al.   JOURNAL OF BIOTECHNOLOGY

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

(2012) Fuzhong Zhang et al.   NATURE BIOTECHNOLOGY

Mechanism of promoter repression by Lac repressor–DNA loops

(2012) Nicole A. Becker et al.   NUCLEIC ACIDS RESEARCH

Regulatory consequences of gene translocation in bacteria

(2012) Dena H. S. Block et al.   NUCLEIC ACIDS RESEARCH

Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription repression

(2012) Sarah Meinhardt et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Directed Evolution of the Transcriptional Regulator DntR: Isolation of Mutants with Improved DNT-Response

(2012) Rosa Lönneborg et al.   PLoS One

An Effective Strategy for a Whole-Cell Biosensor Based on Putative Effector Interaction Site of the Regulatory DmpR Protein

(2012) Saurabh Gupta et al.   PLoS One

Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria

(2012) Hernan G. Garcia et al.   Cell Reports

A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level

(2012) Stephan Binder et al.   GENOME BIOLOGY

Structures of the TetR-like Simocyclinone Efflux Pump Repressor, SimR, and the Mechanism of Ligand-Mediated Derepression

(2011) Tung B.K. Le et al.   JOURNAL OF MOLECULAR BIOLOGY

Biosensors and their applications in microbial metabolic engineering

(2011) Fuzhong Zhang et al.   TRENDS IN MICROBIOLOGY

Design and Application of a Mevalonate-Responsive Regulatory Protein

(2010) Shuang-Yan Tang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection

(2010) Jeffrey A. Dietrich et al.   Annual Review of Biochemistry

Development of highly-sensitive microbial biosensors by mutation of the nahR regulatory gene

(2010) Hae Ja Shin   JOURNAL OF BIOTECHNOLOGY

Gene repression by minimal lac loops in vivo

(2010) Laura M. Bond et al.   NUCLEIC ACIDS RESEARCH

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units)

(2010) S. Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

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

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

A modular positive feedback-based gene amplifier

(2010) Goutam J Nistala et al.   Journal of Biological Engineering

An efficient algorithm for multistate protein design based on FASTER

(2009) Benjamin D. Allen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation

(2009) S. A. F. T. van Hijum et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Automated design of synthetic ribosome binding sites to control protein expression

(2009) Howard M Salis et al.   NATURE BIOTECHNOLOGY

Improved tetracycline repressors for gene silencing in mycobacteria

(2009) Marcus Klotzsche et al.   NUCLEIC ACIDS RESEARCH

Engineering transcription factors with novel DNA-binding specificity using comparative genomics

(2009) Tasha A. Desai et al.   NUCLEIC ACIDS RESEARCH

Elucidating residue roles in engineered variants of AraC regulatory protein

(2009) Shuang-Yan Tang et al.   PROTEIN SCIENCE

Measuring the activity of BioBrick promoters using an in vivo reference standard

(2009) Jason R Kelly et al.   Journal of Biological Engineering

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry

Subdividing Repressor Function: DNA Binding Affinity, Selectivity, and Allostery Can Be Altered by Amino Acid Substitution of Nonconserved Residues in a LacI/GalR Homologue†

(2008) Hongli Zhan et al.   BIOCHEMISTRY

AraC Regulatory Protein Mutants with Altered Effector Specificity

(2008) Shuang-Yan Tang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes

(2008) A. Grote et al.   NUCLEIC ACIDS RESEARCH

Bionemo: molecular information on biodegradation metabolism

(2008) G. Carbajosa et al.   NUCLEIC ACIDS RESEARCH

Evolving Lac repressor for enhanced inducibility

(2008) O. Satya Lakshmi et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: Bioinformatics-based predictions generate true positives and false negatives

(2008) Sarah Meinhardt et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

À la carte transcriptional regulators: unlocking responses of the prokaryotic enhancer-binding protein XylR to non-natural effectors

(2003) Junkal Garmendia et al.   MOLECULAR MICROBIOLOGY