Towards next-generation cell factories by rational genome-scale engineering

Modular (de)construction of complex bacterial phenotypes by CRISPR/nCas9-assisted, multiplex cytidine base-editing

(2022) Daniel C. Volke et al.   Nature Communications

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

(2022) Feiran Li et al.   Nature Catalysis

Characterizing the portability of phage-encoded homologous recombination proteins

(2021) Gabriel T. Filsinger et al.   Nature Chemical Biology

Systematic Quantification of Sequence and Structural Determinants Controlling mRNA stability in Bacterial Operons

(2021) Daniel P. Cetnar et al.   ACS Synthetic Biology

In-situ generation of large numbers of genetic combinations for metabolic reprogramming via CRISPR-guided base editing

(2021) Yu Wang et al.   Nature Communications

Recent advances in the application of multiplex genome editing in Saccharomyces cerevisiae

(2021) Zi-Xu Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Advanced strategies and tools to facilitate and streamline microbial adaptive laboratory evolution

(2021) Yinan Wu et al.   TRENDS IN BIOTECHNOLOGY

Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation

(2021) Nick Fackler et al.   Annual Review of Chemical and Biomolecular Engineering

Recent advances in tuning the expression and regulation of genes for constructing microbial cell factories

(2021) Seung-Woon Jung et al.   BIOTECHNOLOGY ADVANCES

Portable bacterial CRISPR transcriptional activation enables metabolic engineering in Pseudomonas putida

(2021) Cholpisit Kiattisewee et al.   METABOLIC ENGINEERING

Growth-coupled selection of synthetic modules to accelerate cell factory development

(2021) Enrico Orsi et al.   Nature Communications

A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing

(2021) Yaojun Tong et al.   Nature Communications

ReScribe: An Unrestrained Tool Combining Multiplex Recombineering and Minimal-PAM ScCas9 for Genome Recoding Pseudomonas putida

(2021) Enrique Asin-Garcia et al.   ACS Synthetic Biology

Streamlined CRISPR genome engineering in wild-type bacteria using SIBR-Cas

(2021) Constantinos Patinios et al.   NUCLEIC ACIDS RESEARCH

(R)evolution-on-a-chip

(2021) Evgenios Bouzetos et al.   TRENDS IN BIOTECHNOLOGY

Growth of E. coli on formate and methanol via the reductive glycine pathway

(2020) Seohyoung Kim et al.   Nature Chemical Biology

Improved bacterial recombineering by parallelized protein discovery

(2020) Timothy M. Wannier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Image-Based Single Cell Sorting Automation in Droplet Microfluidics

(2020) Muhsincan Sesen et al.   Scientific Reports

Comparative Life Cycle Assessment of Glucose Production from Maize Starch and Woody Biomass Residues as a Feedstock

(2020) Jorge Blanco et al.   Applied Sciences-Basel

Ultrahigh-Throughput ESI-MS: Sampling pushed to six Samples per Second by Acoustic Ejection Mass Spectrometry

(2020) Tim Häbe et al.   ANALYTICAL CHEMISTRY

Converting Escherichia coli to a Synthetic Methylotroph Growing Solely on Methanol

(2020) Frederic Y.-H. Chen et al.   CELL

High-throughput screening for efficient microbial biotechnology

(2020) Aditya Sarnaik et al.   CURRENT OPINION IN BIOTECHNOLOGY

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping

(2020) Simon Höllerer et al.   Nature Communications

Biosystems Design by Machine Learning

(2020) Michael Jeffrey Volk et al.   ACS Synthetic Biology

The Ongoing Quest to Crack the Genetic Code for Protein Production

(2020) Thijs Nieuwkoop et al.   MOLECULAR CELL

Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale

(2020) Deepanwita Banerjee 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

An Automated Model Test System for Systematic Development and Improvement of Gene Expression Models

(2020) Alexander C. Reis et al.   ACS Synthetic Biology

Synthetic small regulatory RNAs in microbial metabolic engineering

(2020) Wen-Hai Xie et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Fluorescence-activated droplet sorting for enhanced pyruvic acid accumulation by Candida glabrata

(2020) Likun Guo et al.   BIORESOURCE TECHNOLOGY

Machine learning for metabolic engineering: A review

(2020) Christopher E. Lawson et al.   METABOLIC ENGINEERING

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

Systems biology based metabolic engineering for non-natural chemicals

(2019) Alessandra Biz et al.   BIOTECHNOLOGY ADVANCES

Acoustic mist ionization mass spectrometry (AMI-MS) as a drug discovery platform

(2019) Ian Sinclair et al.   Expert Opinion on Drug Discovery

Enzyme promiscuity shapes adaptation to novel growth substrates

(2019) Gabriela I Guzmán et al.   Molecular Systems Biology

Rapid evolution of reduced susceptibility against a balanced dual-targeting antibiotic through stepping-stone mutations

(2019) Petra Szili et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Syntrophic co-culture amplification of production phenotype for high-throughput screening of microbial strain libraries

(2019) Tatyana E. Saleski et al.   METABOLIC ENGINEERING

Building a global alliance of biofoundries

(2019) Nathan Hillson et al.   Nature Communications

Genome engineering of E. coli for improved styrene production and polymerization

(2019) Liya Liang et al.   METABOLIC ENGINEERING

Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts

(2019) Carlo C. Campa et al.   NATURE METHODS

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Simultaneous repression of multiple bacterial genes using nonrepetitive extra-long sgRNA arrays

(2019) Alexander C. Reis et al.   NATURE BIOTECHNOLOGY

Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria

(2019) Yang Liu et al.   Nature Communications

5′ untranslated regions: the next regulatory sequence in yeast synthetic biology

(2019) Yatti De Nijs et al.   BIOLOGICAL REVIEWS

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

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

Multi-functional genome-wide CRISPR system for high throughput genotype–phenotype mapping

(2019) Jiazhang Lian et al.   Nature Communications

Multiple-Site Diversification of Regulatory Sequences Enables Interspecies Operability of Genetic Devices

(2019) Angeles Hueso-Gil et al.   ACS Synthetic Biology

mpCRISTAR: Multiple Plasmid Approach for CRISPR/Cas9 and TAR-Mediated Multiplexed Refactoring of Natural Product Biosynthetic Gene Clusters

(2019) Hiyoung Kim et al.   ACS Synthetic Biology

Renewable methanol and formate as microbial feedstocks

(2019) Charles AR Cotton et al.   CURRENT OPINION IN BIOTECHNOLOGY

High-throughput screening for improved microbial cell factories, perspective and promise

(2019) Michael D Leavell et al.   CURRENT OPINION IN BIOTECHNOLOGY

Machine learning applications in systems metabolic engineering

(2019) Gi Bae Kim et al.   CURRENT OPINION IN BIOTECHNOLOGY

Model-based metabolism design: constraints for kinetic and stoichiometric models

(2018) Egils Stalidzans et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Hijacking CRISPR-Cas for high-throughput bacterial metabolic engineering: advances and prospects

(2018) Ioannis Mougiakos et al.   CURRENT OPINION IN BIOTECHNOLOGY

Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production

(2018) Rongming Liu et al.   METABOLIC ENGINEERING

Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering

(2018) Rongming Liu et al.   METABOLIC ENGINEERING

Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast

(2018) Eric M. Young et al.   METABOLIC ENGINEERING

MiYA, an efficient machine-learning workflow in conjunction with the YeastFab assembly strategy for combinatorial optimization of heterologous metabolic pathways in Saccharomyces cerevisiae

(2018) Yikang Zhou et al.   METABOLIC ENGINEERING

Multiplexed precision genome editing with trackable genomic barcodes in yeast

(2018) Kevin R Roy et al.   NATURE BIOTECHNOLOGY

Genome editing by natural and engineered CRISPR-associated nucleases

(2018) Wen Y. Wu et al.   Nature Chemical Biology

Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance

(2018) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Random sequences rapidly evolve into de novo promoters

(2018) Avihu H. Yona et al.   Nature Communications

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

(2018) Lun Cui et al.   Nature Communications

TARSyn: Tunable Antibiotic Resistance Devices Enabling Bacterial Synthetic Evolution and Protein Production

(2018) Maja Rennig et al.   ACS Synthetic Biology

Deaminase-mediated multiplex genome editing in Escherichia coli

(2018) Satomi Banno et al.   Nature Microbiology

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

Machine Learning of Designed Translational Control Allows Predictive Pathway Optimization in Escherichia coli

(2018) Adrian J. Jervis et al.   ACS Synthetic Biology

High-throughput multiplexed fluorescence-activated droplet sorting

(2018) Ouriel Caen et al.   Microsystems & Nanoengineering

Improved protein production and codon optimization analyses in Escherichia coli by bicistronic design

(2018) Thijs Nieuwkoop et al.   Microbial Biotechnology

Biosensor-assisted transcriptional regulator engineering for Methylobacterium extorquens AM1 to improve mevalonate synthesis by increasing the acetyl-CoA supply

(2017) Wei-Fan Liang et al.   METABOLIC ENGINEERING

Engineering biological systems using automated biofoundries

(2017) Ran Chao et al.   METABOLIC ENGINEERING

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms

(2017) Axel von Kamp et al.   Nature Communications

Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli

(2017) Sabine Oesterle et al.   Scientific Reports

Sugar Synthesis from CO2 in Escherichia coli

(2016) Niv Antonovsky et al.   CELL

Biosensor-based engineering of biosynthetic pathways

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

Intermediate-sensor assisted push–pull strategy and its application in heterologous deoxyviolacein production in Escherichia coli

(2016) Mingyue Fang et al.   METABOLIC ENGINEERING

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering

(2016) Andrew D Garst et al.   NATURE BIOTECHNOLOGY

Predictable tuning of protein expression in bacteria

(2016) Mads T Bonde et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Harnessing the power of microbial autotrophy

(2016) Nico J. Claassens et al.   NATURE REVIEWS MICROBIOLOGY

Fuelling the future: microbial engineering for the production of sustainable biofuels

(2016) James C. Liao et al.   NATURE REVIEWS MICROBIOLOGY

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

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

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges 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

Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort

(2016) Markus Jeschek et al.   Nature Communications

Improving Metabolic Pathway Efficiency by Statistical Model-Based Multivariate Regulatory Metabolic Engineering

(2016) Peng Xu et al.   ACS Synthetic Biology

Rapid and Efficient One-Step Metabolic Pathway Integration in E. coli

(2016) Marcelo C. Bassalo et al.   ACS Synthetic Biology

CRMAGE: CRISPR Optimized MAGE Recombineering

(2016) Carlotta Ronda et al.   Scientific Reports

Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms

(2015) Emma Watson et al.   Annual Review of Genetics

Coupling the CRISPR/Cas9 System with Lambda Red Recombineering Enables Simplified Chromosomal Gene Replacement in Escherichia coli

(2015) Michael E. Pyne et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multigene Editing in the Escherichia coli Genome via the CRISPR-Cas9 System

(2015) Yu Jiang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Microfluidic cell sorting: a review of the advances in the separation of cells from debulking to rare cell isolation

(2015) C. Wyatt Shields IV et al.   LAB ON A CHIP

Systems strategies for developing industrial microbial strains

(2015) Sang Yup Lee et al.   NATURE BIOTECHNOLOGY

Bricks and blueprints: methods and standards for DNA assembly

(2015) Arturo Casini et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Ensemble Modeling for Robustness Analysis in engineering non-native metabolic pathways

(2014) Yun Lee et al.   METABOLIC ENGINEERING

Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria

(2014) I. Farasat et al.   Molecular Systems Biology

Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA

(2014) Ryan R Gallagher et al.   Nature Protocols

Evolution-guided optimization of biosynthetic pathways

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

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Direct Mutagenesis of Thousands of Genomic Targets Using Microarray-Derived Oligonucleotides

(2014) Mads T. Bonde et al.   ACS Synthetic Biology

RNAi-Assisted Genome Evolution in Saccharomyces cerevisiae for Complex Phenotype Engineering

(2014) Tong Si et al.   ACS Synthetic Biology

Design and Kinetic Analysis of a Hybrid Promoter–Regulator System for Malonyl-CoA Sensing in Escherichia coli

(2013) Peng Xu et al.   ACS Chemical Biology

Reporter-based screening and selection of enzymes

(2013) Teunke van Rossum et al.   FEBS Journal

Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs

(2013) Dokyun Na et al.   NATURE BIOTECHNOLOGY

Spanning high-dimensional expression space using ribosome-binding site combinatorics

(2013) Lior Zelcbuch et al.   NUCLEIC ACIDS RESEARCH

Yeast Oligo-Mediated Genome Engineering (YOGE)

(2013) James E. DiCarlo et al.   ACS Synthetic Biology

Systems metabolic engineering of microorganisms for natural and non-natural chemicals

(2012) Jeong Wook Lee et al.   Nature Chemical Biology

Genome-scale promoter engineering by coselection MAGE

(2012) Harris H Wang et al.   NATURE METHODS

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

(2012) M. Jinek et al.   SCIENCE

Programming cells by multiplex genome engineering and accelerated evolution

(2009) Harris H. Wang et al.   NATURE

Recombineering: a homologous recombination-based method of genetic engineering

(2009) Shyam K Sharan et al.   Nature Protocols