Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering

Total synthesis of Escherichia coli with a recoded genome

(2019) Julius Fredens et al.   NATURE

From Designing the Molecules of Life to Designing Life: Future Applications Derived from Advances in DNA Technologies

(2018) Richie E. Kohman et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Synthetic Genomics: From DNA Synthesis to Genome Design

(2018) Lianrong Wang et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Genome-scale biological models for industrial microbial systems

(2018) Nan Xu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Emerging whole-cell modeling principles and methods

(2018) Arthur P Goldberg et al.   CURRENT OPINION IN BIOTECHNOLOGY

Escherichia coli as a host for metabolic engineering

(2018) Sammy Pontrelli et al.   METABOLIC ENGINEERING

Advances and prospects of Bacillus subtilis cellular factories: From rational design to industrial applications

(2018) Yang Gu et al.   METABOLIC ENGINEERING

The challenges facing synthetic biology in eukaryotes

(2018) Francesca Ceroni et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

Genome modularity and synthetic biology: Engineering systems

(2018) Milsee Mol et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Cell-free prediction of protein expression costs for growing cells

(2018) Olivier Borkowski et al.   Nature Communications

MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes

(2018) Lin Wang et al.   ACS Synthetic Biology

Traceability, reproducibility and wiki-exploration for “à-la-carte” reconstructions of genome-scale metabolic models

(2018) Méziane Aite et al.   PLoS Computational Biology

COBRAme: A computational framework for genome-scale models of metabolism and gene expression

(2018) Colton J. Lloyd et al.   PLoS Computational Biology

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms

(2018) Patricia Calero et al.   Microbial Biotechnology

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

A Review of Dynamic Modeling Approaches and Their Application in Computational Strain Optimization for Metabolic Engineering

(2018) Osvaldo D. Kim et al.   Frontiers in Microbiology

Less Is More: Toward a Genome-Reduced Bacillus Cell Factory for “Difficult Proteins”

(2018) Rocío Aguilar Suárez et al.   ACS Synthetic Biology

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

(2018) Hao Wang et al.   PLoS Computational Biology

The Synthetic Microbiology Caucus : from abstract ideas to turning microbes into cellular machines and back

(2018) Wei E. Huang et al.   Microbial Biotechnology

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

(2018) Tuure Hameri et al.   METABOLIC ENGINEERING

Large scale validation of an efficient CRISPR/Cas-based multi gene editing protocol in Escherichia coli

(2017) Francesca Zerbini et al.   Microbial Cell Factories

FOCuS: a metaheuristic algorithm for computing knockouts from genome-scale models for strain optimization

(2017) Sarma Mutturi   Molecular BioSystems

Emerging and evolving concepts in gene essentiality

(2017) Giulia Rancati et al.   NATURE REVIEWS GENETICS

Design of a synthetic yeast genome

(2017) Sarah M. Richardson et al.   SCIENCE

Minimal Cells—Real and Imagined

(2017) John I. Glass et al.   Cold Spring Harbor Perspectives in Biology

Cloning and Transplantation of the Mesoplasma florum Genome

(2017) Vincent Baby et al.   ACS Synthetic Biology

Rewiring the Glucose Transportation and Central Metabolic Pathways for Overproduction of N -Acetylglucosamine in Bacillus subtilis

(2017) Yang Gu et al.   Biotechnology Journal

CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency

(2017) Dongdong Zhao et al.   Scientific Reports

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

The quest for the minimal bacterial genome

(2016) Esteban Martínez-García et al.   CURRENT OPINION IN BIOTECHNOLOGY

Large-scale reduction of theBacillus subtilisgenome: consequences for the transcriptional network, resource allocation, and metabolism

(2016) Daniel R. Reuß et al.   GENOME RESEARCH

Toward Community Standards and Software for Whole-Cell Modeling

(2016) Dagmar Waltemath et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

(2016) Dagmar Waltemath et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Defining synonymous codon compression schemes by genome recoding

(2016) Kaihang Wang et al.   NATURE

CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA

(2016) Jianting Zhou et al.   NUCLEIC ACIDS RESEARCH

Emergent rules for codon choice elucidated by editing rare arginine codons inEscherichia coli

(2016) Michael G. Napolitano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Design, synthesis, and testing toward a 57-codon genome

(2016) N. Ostrov et al.   SCIENCE

Design and synthesis of a minimal bacterial genome

(2016) C. A. Hutchison et al.   SCIENCE

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

(2016) Yanfeng Liu et al.   Nature Communications

The Next Generation of Synthetic Biology Chassis: Moving Synthetic Biology from the Laboratory to the Field

(2016) Bryn L. Adams   ACS Synthetic Biology

Microbial enzymes: industrial progress in 21st century

(2016) Rajendra Singh et al.   3 Biotech

Microbial enzymes: industrial progress in 21st century

(2016) Rajendra Singh et al.   3 Biotech

Gene knockout identification for metabolite production improvement using a hybrid of genetic ant colony optimization and flux balance analysis

(2015) Abdul Hakim Mohamed Salleh et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

(2015) Peter D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

Enhancing recombinant protein production with an Escherichia coli host strain lacking insertion sequences

(2014) Myung Keun Park et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Multivariate modular metabolic engineering for pathway and strain optimization

(2014) Bradley Walters Biggs et al.   CURRENT OPINION IN BIOTECHNOLOGY

Systems Biology Perspectives on Minimal and Simpler Cells

(2014) J. C. Xavier et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Programming biological operating systems: genome design, assembly and activation

(2014) Daniel G Gibson   NATURE METHODS

Principles of genetic circuit design

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

Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering

(2014) Natalie J Ma et al.   Nature Protocols

Engineering redox balance through cofactor systems

(2014) Xiulai Chen et al.   TRENDS IN BIOTECHNOLOGY

Elementary flux modes in a nutshell: Properties, calculation and applications

(2013) Jürgen Zanghellini et al.   Biotechnology Journal

Genetic manipulations restored the growth fitness of reduced-genome Escherichia coli

(2013) Yasutaka Hirokawa et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction

(2013) E. J. O{middle dot}Brien et al.   Molecular Systems Biology

High-level semi-synthetic production of the potent antimalarial artemisinin

(2013) C. J. Paddon et al.   NATURE

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

ReacKnock: Identifying Reaction Deletion Strategies for Microbial Strain Optimization Based on Genome-Scale Metabolic Network

(2013) Zixiang Xu et al.   PLoS One

Genomically Recoded Organisms Expand Biological Functions

(2013) M. J. Lajoie et al.   SCIENCE

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

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

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

GenBank

(2012) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome

(2012) Wei Liu et al.   PLoS One

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

From essential to persistent genes: a functional approach to constructing synthetic life

(2012) Carlos G. Acevedo-Rocha et al.   TRENDS IN GENETICS

RibM from Streptomyces davawensis is a riboflavin/roseoflavin transporter and may be useful for the optimization of riboflavin production strains

(2011) Sabrina Hemberger et al.   BMC BIOTECHNOLOGY

Designs for life: protocell models in the laboratory

(2011) Alicja J. Dzieciol et al.   CHEMICAL SOCIETY REVIEWS

Adaptive laboratory evolution—harnessing the power of biology for metabolic engineering

(2011) Vasiliy A Portnoy et al.   CURRENT OPINION IN BIOTECHNOLOGY

Recent advances in reconstruction and applications of genome-scale metabolic models

(2011) Tae Yong Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Oxidative stress sensitivity of engineered Escherichia coli cells with a reduced genome

(2011) Yumi Iwadate et al.   FEMS MICROBIOLOGY LETTERS

Batch and continuous culture-based selection strategies for acetic acid tolerance in xylose-fermenting Saccharomyces cerevisiae

(2011) Jeremiah Wright et al.   FEMS YEAST RESEARCH

From zero to hero—Design-based systems metabolic engineering of Corynebacterium glutamicum for l-lysine production

(2011) Judith Becker et al.   METABOLIC ENGINEERING

EMILiO: A fast algorithm for genome-scale strain design

(2011) Laurence Yang et al.   METABOLIC ENGINEERING

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency

(2011) Robert J. Conrado et al.   NUCLEIC ACIDS RESEARCH

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

Building the blueprint of life

(2010) Christopher Henry et al.   Biotechnology Journal

OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains

(2010) Joonhoon Kim et al.   BMC Systems Biology

Synthetic lethality: General principles, utility and detection using genetic screens in human cells

(2010) Sebastian M.B. Nijman   FEBS LETTERS

Genome update: the 1000th genome - a cautionary tale

(2010) K. Lagesen et al.   MICROBIOLOGY-SGM

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Grand Challenge Commentary: Chassis cells for industrial biochemical production

(2010) Claudia E Vickers et al.   Nature Chemical Biology

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

OptForce: An Optimization Procedure for Identifying All Genetic Manipulations Leading to Targeted Overproductions

(2010) Sridhar Ranganathan et al.   PLoS Computational Biology

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

(2009) N. Tepper et al.   BIOINFORMATICS

Considerations for the design and construction of a synthetic platform cell for biotechnological applications

(2009) P.L. Foley et al.   BIOTECHNOLOGY AND BIOENGINEERING

Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum

(2009) Yohei Shinfuku et al.   Microbial Cell Factories

Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production

(2009) Jun Lee et al.   Microbial Cell Factories

Large-scale identification of genetic design strategies using local search

(2009) Desmond S Lun et al.   Molecular Systems Biology

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Genome engineering

(2009) Peter A Carr et al.   NATURE BIOTECHNOLOGY

Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast

(2009) C. Lartigue et al.   SCIENCE

Are essential genes really essential?

(2009) Michael A. D’Elia et al.   TRENDS IN MICROBIOLOGY

Novel Evolutionary Engineering Approach for Accelerated Utilization of Glucose, Xylose, and Arabinose Mixtures by Engineered Saccharomyces cerevisiae Strains

(2008) H. W. Wisselink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis

(2008) T. Morimoto et al.   DNA RESEARCH

Superpositioning of Deletions Promotes Growth of Escherichia coli with a Reduced Genome

(2008) H. Mizoguchi et al.   DNA RESEARCH

Use of Randomized Sampling for Analysis of Metabolic Networks

(2008) Jan Schellenberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Predicting synthetic rescues in metabolic networks

(2008) Adilson E Motter et al.   Molecular Systems Biology

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

eSGA: E. coli synthetic genetic array analysis

(2008) Gareth Butland et al.   NATURE METHODS

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE

Knowledge-making distinctions in synthetic biology

(2007) Maureen A. O'Malley et al.   BIOESSAYS