Engineering Microbial Metabolite Dynamics and Heterogeneity

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

(2017) Apoorv Gupta et al.   NATURE BIOTECHNOLOGY

Taking control over microbial populations: Current approaches for exploiting biological noise in bioprocesses

(2017) Frank Delvigne et al.   Biotechnology Journal

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis

(2016) Yi Xiao et al.   Nature Chemical Biology

A dynamic pathway analysis approach reveals a limiting futile cycle in N-acetylglucosamine overproducing Bacillus subtilis

(2016) Yanfeng Liu et al.   Nature Communications

Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi)

(2016) Sara Cleto et al.   ACS Synthetic Biology

Quorum Sensing Desynchronization Leads to Bimodality and Patterned Behaviors

(2016) David N. Quan et al.   PLoS Computational Biology

Constructing kinetic models of metabolism at genome-scales: A review

(2015) Shyam Srinivasan et al.   Biotechnology Journal

Engineering metabolism through dynamic control

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

How to train your microbe: methods for dynamically characterizing gene networks

(2015) Sebastian M Castillo-Hair et al.   CURRENT OPINION IN MICROBIOLOGY

Microbial individuality: how single-cell heterogeneity enables population level strategies

(2015) Bruno MC Martins et al.   CURRENT OPINION IN MICROBIOLOGY

Spatiotemporal microbial single-cell analysis using a high-throughput microfluidics cultivation platform

(2015) Alexander Grünberger et al.   CYTOMETRY PART A

Making variability less variable: matching expression system and host for oxygenase-based biotransformations

(2015) Martin Lindmeyer et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Applications and advances of metabolite biosensors for metabolic engineering

(2015) Di Liu et al.   METABOLIC ENGINEERING

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

Imaging metabolite dynamics in living cells using a Spinach-based riboswitch

(2015) Mingxu You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation

(2015) Otto Pulkkinen et al.   Scientific Reports

Constructing kinetic models of metabolism at genome-scales: A review

(2015) Shyam Srinivasan et al.   Biotechnology Journal

Stochasticity of metabolism and growth at the single-cell level

(2014) Daniel J. Kiviet et al.   NATURE

Application of a Genetically Encoded Biosensor for Live Cell Imaging of L-Valine Production in Pyruvate Dehydrogenase Complex-Deficient Corynebacterium glutamicum Strains

(2014) Nurije Mustafi et al.   PLoS One

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

Changes in intracellular metabolite pools during growth of adherent MDCK cells in two different media

(2013) M. Rehberg et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Microbial heterogeneity affects bioprocess robustness: Dynamic single-cell analysis contributes to understanding of microbial populations

(2013) Frank Delvigne et al.   Biotechnology Journal

Changes in substrate availability in Escherichia coli lead to rapid metabolite, flux and growth rate responses

(2013) Hilal Taymaz-Nikerel et al.   METABOLIC ENGINEERING

Transcriptional regulation is insufficient to explain substrate-induced flux changes in Bacillus subtilis

(2013) V. Chubukov et al.   Molecular Systems Biology

Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols

(2013) José L Avalos et al.   NATURE BIOTECHNOLOGY

Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo

(2013) Hannes Link et al.   NATURE BIOTECHNOLOGY

Heterogeneity in protein expression induces metabolic variability in a modeledEscherichia colipopulation

(2013) Piyush Labhsetwar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass spectrometry-based metabolomics of single yeast cells

(2013) A. J. Ibanez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Metabolomics: Analytical and Biological Perspectives

(2013) R. Zenobi   SCIENCE

Optimization of a Yeast RNA Interference System for Controlling Gene Expression and Enabling Rapid Metabolic Engineering

(2013) Nathan C. Crook 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

Bridging the gap between systems biology and synthetic biology

(2013) Di Liu et al.   Frontiers in Microbiology

Construction of microbial cell factories for industrial bioprocesses

(2012) Michael Sauer et al.   JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY

The development and application of a single-cell biosensor for the detection of l-methionine and branched-chain amino acids

(2012) Nurije Mustafi et al.   METABOLIC ENGINEERING

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

(2012) Fuzhong Zhang et al.   NATURE BIOTECHNOLOGY

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Optimality and robustness in quorum sensing (QS)-mediated regulation of a costly public good enzyme

(2012) A. Pai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noise regulation by quorum sensing in low mRNA copy number systems

(2011) Marc Weber et al.   BMC Systems Biology

Impulse Control: Temporal Dynamics in Gene Transcription

(2011) Nir Yosef et al.   CELL

Regulation and control of metabolic fluxes in microbes

(2011) Luca Gerosa et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA

(2011) Peng Xu et al.   METABOLIC ENGINEERING

An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data

(2011) André B. Canelas et al.   METABOLIC ENGINEERING

Parts plus pipes: Synthetic biology approaches to metabolic engineering

(2011) Patrick M. Boyle et al.   METABOLIC ENGINEERING

Biosensors and their applications in microbial metabolic engineering

(2011) Fuzhong Zhang et al.   TRENDS IN MICROBIOLOGY

Fast dynamic 3D MR spectroscopic imaging with compressed sensing and multiband excitation pulses for hyperpolarized 13C studies

(2010) Peder E. Z. Larson et al.   MAGNETIC RESONANCE IN MEDICINE

Catching prompt metabolite dynamics in Escherichia coli with the BioScope at oxygen rich conditions

(2010) Marjan De Mey et al.   METABOLIC ENGINEERING

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Achieving Optimal Growth through Product Feedback Inhibition in Metabolism

(2010) Sidhartha Goyal et al.   PLoS Computational Biology

Microfluidic Confinement of Single Cells of Bacteria in Small Volumes Initiates High-Density Behavior of Quorum Sensing and Growth and Reveals Its Variability

(2009) James Q. Boedicker et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Rapid sampling devices for metabolic engineering applications

(2009) Friederike Schädel et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Metabolic flux analysis in mammalian cell culture

(2009) Lake-Ee Quek et al.   METABOLIC ENGINEERING

Heterogeneity in quorum sensing-regulated bioluminescence ofVibrio harveyi

(2009) Claudia Anetzberger et al.   MOLECULAR MICROBIOLOGY

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Synthetic Biology for Synthetic Chemistry

(2008) Jay D. Keasling   ACS Chemical Biology

Diel Shifts in Carboxylation Pathway and Metabolite Dynamics in the CAM Bromeliad Aechmea ‘Maya’ in Response to Elevated CO2

(2008) J. Ceusters et al.   ANNALS OF BOTANY

System estimation from metabolic time-series data

(2008) Gautam Goel et al.   BIOINFORMATICS

Timing and Dynamics of Single Cell Gene Expression in the Arabinose Utilization System

(2008) Judith A. Megerle et al.   BIOPHYSICAL JOURNAL

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Fermentation of cocoa beans: influence of microbial activities and polyphenol concentrations on the flavour of chocolate

(2008) Nicholas Camu et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Dynamic metabolic engineering for increasing bioprocess productivity

(2008) Nikolaos Anesiadis et al.   METABOLIC ENGINEERING

Structural insights into amino acid binding and gene control by a lysine riboswitch

(2008) Alexander Serganov et al.   NATURE

Dynamics and Design Principles of a Basic Regulatory Architecture Controlling Metabolic Pathways

(2008) Chen-Shan Chin et al.   PLOS BIOLOGY