Trade-Offs in Biosensor Optimization for Dynamic Pathway Engineering

Opportunities at the Interface of Network Science and Metabolic Modeling

(2021) Varshit Dusad et al.   Frontiers in Bioengineering and Biotechnology

Tuning the Binding Affinity of Heme-Responsive Biosensor for Precise and Dynamic Pathway Regulation

(2020) Jian Zhang et al.   iScience

Extended Metabolic Biosensor Design for Dynamic Pathway Regulation of Cell Factories

(2020) Yadira Boada et al.   iScience

Layered and multi-input autonomous dynamic control strategies for metabolic engineering

(2020) Christina V Dinh et al.   CURRENT OPINION IN BIOTECHNOLOGY

Dynamic control in metabolic engineering: Theories, tools, and applications

(2020) Christopher J. Hartline et al.   METABOLIC ENGINEERING

Pyruvate-responsive genetic circuits for dynamic control of central metabolism

(2020) Xianhao Xu et al.   Nature Chemical Biology

Characterization and mitigation of gene expression burden in mammalian cells

(2020) Timothy Frei et al.   Nature Communications

Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism

(2020) Jie Zhang et al.   Nature Communications

Growth defects and loss-of-function in synthetic gene circuits

(2019) Evangelos-Marios Nikolados et al.   ACS Synthetic Biology

Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis

(2019) Yaokang Wu et al.   NUCLEIC ACIDS RESEARCH

Engineering and application of synthetic nar promoter for fine-tuning the expression of metabolic pathway genes in Escherichia coli

(2018) Hee Jin Hwang et al.   Biotechnology for Biofuels

Current and future modalities of dynamic control in metabolic engineering

(2018) Makoto A Lalwani et al.   CURRENT OPINION IN BIOTECHNOLOGY

Dynamic metabolic control: towards precision engineering of metabolism

(2018) Di Liu et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

In vivo biosensors: mechanisms, development, and applications

(2018) Shuobo Shi et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Recent advances in metabolic engineering of Saccharomyces cerevisiae : New tools and their applications

(2018) Jiazhang Lian et al.   METABOLIC ENGINEERING

Layered dynamic regulation for improving metabolic pathway productivity inEscherichia coli

(2018) Stephanie J. Doong 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

Metabolic Feedback Circuits Provide Rapid Control of Metabolite Dynamics

(2018) Di Liu et al.   ACS Synthetic Biology

Modularization and Response Curve Engineering of a Naringenin-Responsive Transcriptional Biosensor

(2018) Brecht De Paepe et al.   ACS Synthetic Biology

Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction

(2018) Manuel Razo-Mejia et al.   Cell Systems

Repurposing type III polyketide synthase as a malonyl-CoA biosensor for metabolic engineering in bacteria

(2018) Dongsoo Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering a Glucosamine-6-phosphate Responsive glmS Ribozyme Switch Enables Dynamic Control of Metabolic Flux in Bacillus subtilis for Overproduction of N-Acetylglucosamine

(2018) Tengfei Niu et al.   ACS Synthetic Biology

An Optimized Bistable Metabolic Switch To Decouple Phenotypic States during Anaerobic Fermentation

(2018) Naveen Venayak et al.   ACS Synthetic Biology

A real-time control system of gene expression using ligand-bound nucleic acid aptamer for metabolic engineering

(2017) Jing Wang et al.   METABOLIC ENGINEERING

Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit

(2017) Apoorv Gupta et al.   NATURE BIOTECHNOLOGY

Fundamental Design Principles for Transcription-Factor-Based Metabolite Biosensors

(2017) Ahmad A. Mannan et al.   ACS Synthetic Biology

A Glucose-Sensing Toggle Switch for Autonomous, High Productivity Genetic Control

(2017) William Bothfeld et al.   ACS Synthetic Biology

Automated Design Framework for Synthetic Biology Exploiting Pareto Optimality

(2017) Irene Otero-Muras et al.   ACS Synthetic Biology

Multi-objective optimization framework to obtain model-based guidelines for tuning biological synthetic devices: an adaptive network case

(2016) Yadira Boada et al.   BMC Systems Biology

Overloaded and stressed: whole-cell considerations for bacterial synthetic biology

(2016) Olivier Borkowski et al.   CURRENT OPINION IN MICROBIOLOGY

Control theory meets synthetic biology

(2016) Domitilla Del Vecchio et al.   Journal of the Royal Society Interface

Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis

(2016) Yi Xiao et al.   Nature Chemical Biology

Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast

(2016) Mette L Skjoedt et al.   Nature Chemical Biology

Rapid Diversification of BetI-Based Transcriptional Switches for the Control of Biosynthetic Pathways and Genetic Circuits

(2016) Kazuya Saeki et al.   ACS Synthetic Biology

Fourteen Ways to Reroute Cooperative Communication in the Lactose Repressor: Engineering Regulatory Proteins with Alternate Repressive Functions

(2016) David H. Richards et al.   ACS Synthetic Biology

Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations

(2016) Jonathan M Burg et al.   Current Opinion in Chemical Engineering

Isocost Lines Describe the Cellular Economy of Genetic Circuits

(2015) Andras Gyorgy et al.   BIOPHYSICAL JOURNAL

Engineering metabolism through dynamic control

(2015) Naveen Venayak et al.   CURRENT OPINION IN BIOTECHNOLOGY

Design of a bistable switch to control cellular uptake

(2015) Diego A. Oyarzún et al.   Journal of the Royal Society Interface

Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production

(2015) Yuki Soma et al.   METABOLIC ENGINEERING

Sequential control of biosynthetic pathways for balanced utilization of metabolic intermediates in Saccharomyces cerevisiae

(2015) Wenping Xie et al.   METABOLIC ENGINEERING

Engineering an allosteric transcription factor to respond to new ligands

(2015) Noah D Taylor et al.   NATURE METHODS

Quantifying cellular capacity identifies gene expression designs with reduced burden

(2015) Francesca Ceroni et al.   NATURE METHODS

Dealing with the genetic load in bacterial synthetic biology circuits: convergences with the Ohm's law

(2015) M. Carbonell-Ballestero et al.   NUCLEIC ACIDS RESEARCH

Mechanistic links between cellular trade-offs, gene expression, and growth

(2015) Andrea Y. Weiße et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

(2014) P. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Designing RNA-Based Genetic Control Systems for Efficient Production from Engineered Metabolic Pathways

(2014) Jason T. Stevens et al.   ACS Synthetic Biology

Quantitative Assessment of Thermodynamic Constraints on the Solution Space of Genome-Scale Metabolic Models

(2013) Joshua J. Hamilton et al.   BIOPHYSICAL JOURNAL

(Im)Perfect robustness and adaptation of metabolic networks subject to metabolic and gene-expression regulation: marrying control engineering with metabolic control analysis

(2013) Fei He et al.   BMC Systems Biology

Analysis and Design of a Genetic Circuit for Dynamic Metabolic Engineering

(2013) Nikolaos Anesiadis et al.   ACS Synthetic Biology

Promoter engineering: Recent advances in controlling transcription at the most fundamental level

(2012) John Blazeck et al.   Biotechnology Journal

Synthetic gene circuits for metabolic control: design trade-offs and constraints

(2012) D. A. Oyarzun et al.   Journal of the Royal Society Interface

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

(2012) Fuzhong Zhang et al.   NATURE BIOTECHNOLOGY

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Regulatory architecture determines optimal regulation of gene expression in metabolic pathways

(2012) V. Chubukov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters

(2011) Arren Bar-Even et al.   BIOCHEMISTRY

Optimal control of metabolic networks with saturable enzyme kinetics

(2011) D.A. Oyarzún   IET Systems Biology

Identification and microbial production of a terpene-based advanced biofuel

(2011) Pamela P. Peralta-Yahya et al.   Nature Communications

Sequential Activation of Metabolic Pathways: a Dynamic Optimization Approach

(2009) Diego A. Oyarzún et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Production of Glucaric Acid from a Synthetic Pathway in Recombinant Escherichia coli

(2008) T. S. Moon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network

(2008) Gal Chechik et al.   NATURE BIOTECHNOLOGY