Mitigation of host cell mutations and regime shift during microbial fermentation: a perspective from flux memory

A modular autoinduction device for control of gene expression in Bacillus subtilis

(2020) Graciely Gomes Correa et al.   METABOLIC ENGINEERING

Application of combinatorial optimization strategies in synthetic biology

(2020) Gita Naseri et al.   Nature Communications

Expanding Toolbox for Genes Expression of Yarrowia lipolytica to Include Novel Inducible, Repressible, and Hybrid Promoters

(2020) Xiaochao Xiong et al.   ACS Synthetic Biology

Coupling metabolic addiction with negative autoregulation to improve strain stability and pathway yield

(2020) Yongkun Lv et al.   METABOLIC ENGINEERING

OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling

(2019) Fangzhou Shen et al.   PLoS Computational Biology

Engineering Robust Production Microbes for Large-Scale Cultivation

(2019) Maren Wehrs et al.   TRENDS IN MICROBIOLOGY

Systems Metabolic Engineering Strategies: Integrating Systems and Synthetic Biology with Metabolic Engineering

(2019) Kyeong Rok Choi et al.   TRENDS IN BIOTECHNOLOGY

Reply to Zhou and Li: Plasticity of the genomic haplotype ofSynechococcus elongatusleads to rapid strain adaptation under laboratory conditions

(2019) Justin Ungerer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

(2019) Chuankai Cheng et al.   PLoS Computational Biology

Metabolic flux responses to deletion of 20 core enzymes reveal flexibility and limits of E. coli metabolism

(2019) Christopher P. Long et al.   METABOLIC ENGINEERING

A concerted systems biology analysis of phenol metabolism in Rhodococcus opacus PD630

(2019) Garrett W. Roell et al.   METABOLIC ENGINEERING

Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution

(2019) Minjeong Kang et al.   Frontiers in Microbiology

Isolating live cells after high-throughput, long-term, time-lapse microscopy

(2019) Scott Luro et al.   NATURE METHODS

Real-time visualization of mutations and their fitness effects in single bacteria

(2019) Lydia Robert et al.   Nature Protocols

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

(2019) Troy E. Sandberg et al.   METABOLIC ENGINEERING

OUP accepted manuscript

(2018)   BIOINFORMATICS

Genomic Instability Promoted by Overexpression of Mismatch Repair Factors in Yeast: A Model for Understanding Cancer Progression

(2018) Ujani Chakraborty et al.   GENETICS

Burden-driven feedback control of gene expression

(2018) Francesca Ceroni et al.   NATURE METHODS

Using deep learning to model the hierarchical structure and function of a cell

(2018) Jianzhu Ma et al.   NATURE METHODS

Diverse genetic error modes constrain large-scale bio-based production

(2018) Peter Rugbjerg et al.   Nature Communications

Genomic Instability Promoted by Overexpression of Mismatch Repair Factors in Yeast: A Model for Understanding Cancer Progression

(2018) Ujani Chakraborty et al.   GENETICS

Inhibiting the Evolution of Antibiotic Resistance

(2018) Mark N. Ragheb et al.   MOLECULAR CELL

Heterogeneity in efflux pump expression predisposes antibiotic-resistant cells to mutation

(2018) Imane El Meouche et al.   SCIENCE

How adaptive evolution reshapes metabolism to improve fitness: recent advances and future outlook

(2018) Christopher P Long et al.   Current Opinion in Chemical Engineering

Purity by design: Reducing impurities in bioproduction by stimulus-controlled global translational downregulation of non-product proteins

(2018) Daniel Bojar et al.   METABOLIC ENGINEERING

Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

(2017) Christopher P. Long et al.   METABOLIC ENGINEERING

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme inEscherichia coli

(2017) Christopher P. Long et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploiting nongenetic cell-to-cell variation for enhanced biosynthesis

(2016) Yi Xiao et al.   Nature Chemical Biology

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals

(2015) Aindrila Mukhopadhyay   TRENDS IN MICROBIOLOGY

Adaptation to High Ethanol Reveals Complex Evolutionary Pathways

(2015) Karin Voordeckers et al.   PLoS Genetics

Phenotypic states become increasingly sensitive to perturbations near a bifurcation in a synthetic gene network

(2015) Kevin Axelrod et al.   eLife

A load driver device for engineering modularity in biological networks

(2014) Deepak Mishra et al.   NATURE BIOTECHNOLOGY

Precise estimates of mutation rate and spectrum in yeast

(2014) Y. O. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimizing Metabolite Production Using Periodic Oscillations

(2014) Steven W. Sowa et al.   PLoS Computational Biology

Adaptive laboratory evolution – principles and applications for biotechnology

(2013) Martin Dragosits et al.   Microbial Cell Factories

β-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity

(2013) A. Gutierrez et al.   Nature Communications

Low-mutation-rate, reduced-genome Escherichia coli: An improved host for faithful maintenance of engineered genetic constructs

(2012) Balint Csorgo et al.   Microbial Cell Factories

Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors

(2012) Felix Moser et al.   ACS Synthetic Biology

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

(2010) Y. Taniguchi et al.   SCIENCE

Invariability of central metabolic flux distribution in Shewanella oneidensis MR-1 under environmental or genetic perturbations

(2009) Yinjie J. Tang et al.   BIOTECHNOLOGY PROGRESS

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY