A Framework for the Systematic Selection of Biosensor Chassis for Environmental Synthetic Biology

Ecological modelling approaches for predicting emergent properties in microbial communities

(2022) Naomi Iris van den Berg et al.   Nature Ecology & Evolution

Approaches to genetic tool development for rapid domestication of non-model microorganisms

(2021) Lauren A. Riley et al.   Biotechnology for Biofuels

Rapid and simultaneous screening of pathway designs and chassis organisms, applied to engineered living materials

(2021) Dechuan Meng et al.   METABOLIC ENGINEERING

Applications, challenges, and needs for employing synthetic biology beyond the lab

(2021) Sierra M. Brooks et al.   Nature Communications

Automated Rational Strain Construction Based on High-Throughput Conjugation

(2021) Niklas Tenhaef et al.   ACS Synthetic Biology

Translating New Synthetic Biology Advances for Biosensing Into the Earth and Environmental Sciences

(2021) Ilenne Del Valle et al.   Frontiers in Microbiology

The Volatilome: A Vital Piece of the Complete Soil Metabolome

(2021) Linnea K. Honeker et al.   Frontiers in Environmental Science

A navigation guide of synthetic biology tools for Pseudomonas putida

(2021) Maria Martin-Pascual et al.   BIOTECHNOLOGY ADVANCES

Advances in Genome-Scale Metabolic Modeling toward Microbial Community Analysis of the Human Microbiome

(2021) Elif Esvap et al.   ACS Synthetic Biology

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

(2021) Junhyeong Kim et al.   Frontiers in Microbiology

Efficient retroelement-mediated DNA writing in bacteria

(2021) Fahim Farzadfard et al.   Cell Systems

Species- and site-specific genome editing in complex bacterial communities

(2021) Benjamin E. Rubin et al.   Nature Microbiology

Synthetic Cassettes for pH-Mediated Sensing, Counting, and Containment

(2020) Finn Stirling et al.   Cell Reports

Soil organic matter attenuates the efficacy of flavonoid-based plant-microbe communication

(2020) Ilenne Del Valle et al.   Science Advances

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota

(2020) Christian Diener et al.   mSystems

Recent advances in domesticating non‐model microorganisms

(2020) Zia Fatma et al.   BIOTECHNOLOGY PROGRESS

Controlling the Implementation of Transgenic Microbes: Are We Ready for What Synthetic Biology Has to Offer?

(2020) Finn Stirling et al.   MOLECULAR CELL

Genetic circuit design automation for the gut resident species Bacteroides thetaiotaomicron

(2020) Mao Taketani et al.   NATURE BIOTECHNOLOGY

Development of a genetic toolset for the highly engineerable and metabolically versatile Acinetobacter baylyi ADP1

(2020) Bradley W Biggs et al.   NUCLEIC ACIDS RESEARCH

MicrobioLink: An Integrated Computational Pipeline to Infer Functional Effects of Microbiome–Host Interactions

(2020) Tahila Andrighetti et al.   Cells

Microbes as Biosensors

(2020) Maria Eugenia Inda et al.   Annual Review of Microbiology

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

CRAGE-Duet Facilitates Modular Assembly of Biological Systems for Studying Plant–Microbe Interactions

(2020) Bing Wang et al.   ACS Synthetic Biology

A compact Cascade–Cas3 system for targeted genome engineering

(2020) Bálint Csörgő et al.   NATURE METHODS

Innovations to culturing the uncultured microbial majority

(2020) William H. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes

(2020) Samuel M D Seaver et al.   NUCLEIC ACIDS RESEARCH

The Most Frequently Used Sequencing Technologies and Assembly Methods in Different Time Segments of the Bacterial Surveillance and RefSeq Genome Databases

(2020) Bo Segerman   Frontiers in Cellular and Infection Microbiology

CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering

(2020) Phuc Leo H. Vo et al.   NATURE BIOTECHNOLOGY

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

A Comparison of Microbial Genome Web Portals

(2019) Peter D. Karp et al.   Frontiers in Microbiology

Transposon-encoded CRISPR–Cas systems direct RNA-guided DNA integration

(2019) Sanne E. Klompe et al.   NATURE

RNA-guided DNA insertion with CRISPR-associated transposases

(2019) Jonathan Strecker et al.   SCIENCE

Syntrophy emerges spontaneously in complex metabolic systems

(2019) Eric Libby et al.   PLoS Computational Biology

Modelling approaches for studying the microbiome

(2019) Manish Kumar et al.   Nature Microbiology

Targeted transposition with Tn7 elements: safe sites, mobile plasmids, CRISPR/Cas and beyond

(2019) Joseph E. Peters   MOLECULAR MICROBIOLOGY

Common principles and best practices for engineering microbiomes

(2019) Christopher E. Lawson et al.   NATURE REVIEWS MICROBIOLOGY

Synthetic sequence entanglement augments stability and containment of genetic information in cells

(2019) Tomasz Blazejewski et al.   SCIENCE

Synthetic Biology Tools for the Fast-Growing Marine Bacterium Vibrio natriegens

(2019) Tanya Tschirhart et al.   ACS Synthetic Biology

Development of a New Biocontainment Strategy in Model Cyanobacterium Synechococcus Strains

(2019) Yuqing Zhou et al.   ACS Synthetic Biology

CRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria

(2019) Gaoyan Wang et al.   Nature Microbiology

Building a genome engineering toolbox in nonmodel prokaryotic microbes

(2018) Emily Freed et al.   BIOTECHNOLOGY AND BIOENGINEERING

Rapidly moving new bacteria to model-organism status

(2018) Hualan Liu et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pseudomonas putida as a functional chassis for industrial biocatalysis: From native biochemistry to trans -metabolism

(2018) Pablo I. Nikel et al.   METABOLIC ENGINEERING

Next-generation biocontainment systems for engineered organisms

(2018) Jeong Wook Lee et al.   Nature Chemical Biology

Toward an orthogonal central dogma

(2018) Chang C Liu et al.   Nature Chemical Biology

Metagenomic mining of regulatory elements enables programmable species-selective gene expression

(2018) Nathan I Johns et al.   NATURE METHODS

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

(2018) Patricia Calero et al.   Microbial Biotechnology

Engineered integrative and conjugative elements for efficient and inducible DNA transfer to undomesticated bacteria

(2018) Jennifer A. N. Brophy et al.   Nature Microbiology

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

(2018) Federico Baldini et al.   BIOINFORMATICS

Synthetic Biology Toolbox and Chassis Development in Bacillus subtilis

(2018) Yanfeng Liu et al.   TRENDS IN BIOTECHNOLOGY

A Multiplex Genome Editing Method for Escherichia coli Based on CRISPR-Cas12a

(2018) Xiang Ao et al.   Frontiers in Microbiology

Rational Design of Evolutionarily Stable Microbial Kill Switches

(2017) Finn Stirling et al.   MOLECULAR CELL

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Multiplex Genome Editing by Natural Transformation (MuGENT) for Synthetic Biology in Vibrio natriegens

(2017) Triana N. Dalia et al.   ACS Synthetic Biology

Microbial interactions: ecology in a molecular perspective

(2016) Raíssa Mesquita Braga et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Natural competence for transformation

(2016) Melanie Blokesch   CURRENT BIOLOGY

Synthetic bugs on the loose: containment options for deeply engineered (micro)organisms

(2016) Markus Schmidt et al.   CURRENT OPINION IN BIOTECHNOLOGY

Properties of alternative microbial hosts used in synthetic biology: towards the design of a modular chassis

(2016) Juhyun Kim et al.   Essays in Biochemistry

Synthetic biology approaches to biological containment: pre-emptively tackling potential risks

(2016) Leticia Torres et al.   Essays in Biochemistry

Towards Engineering Biological Systems in a Broader Context

(2016) Ophelia S. Venturelli et al.   JOURNAL OF MOLECULAR BIOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Manipulating Bacterial Communities by in situ Microbiome Engineering

(2016) Ravi U. Sheth et al.   TRENDS IN GENETICS

The Geobacillus Plasmid Set: A Modular Toolkit for Thermophile Engineering

(2016) Benjamin Reeve et al.   ACS Synthetic Biology

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

(2016) Bryn L. Adams   ACS Synthetic Biology

Broad-Host-Range ProUSER Vectors Enable Fast Characterization of Inducible Promoters and Optimization of p-Coumaric Acid Production in Pseudomonas putida KT2440

(2016) Patricia Calero et al.   ACS Synthetic Biology

Bacterial Communities: Interactions to Scale

(2016) Reed M. Stubbendieck et al.   Frontiers in Microbiology

Using Genome-scale Models to Predict Biological Capabilities

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

'Deadman' and 'Passcode' microbial kill switches for bacterial containment

(2015) Clement T Y Chan et al.   Nature Chemical Biology

Multilayered genetic safeguards limit growth of microorganisms to defined environments

(2015) Ryan R. Gallagher et al.   NUCLEIC ACIDS RESEARCH

A portable expression resource for engineering cross-species genetic circuits and pathways

(2015) Manish Kushwaha et al.   Nature Communications

A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly

(2015) Michael E. Lee et al.   ACS Synthetic Biology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Engineering complex biological systems in bacteria through recombinase-assisted genome engineering

(2014) Christine Nicole S Santos et al.   Nature Protocols

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

GeneGuard: A Modular Plasmid System Designed for Biosafety

(2014) Oliver Wright et al.   ACS Synthetic Biology

Broad host range plasmids

(2013) Aayushi Jain et al.   FEMS MICROBIOLOGY LETTERS

Building-in biosafety for synthetic biology

(2013) O. Wright et al.   MICROBIOLOGY-SGM

Preparing synthetic biology for the world

(2013) Gerd H. G. Moe-Behrens et al.   Frontiers in Microbiology

Contextualizing context for synthetic biology - identifying causes of failure of synthetic biological systems

(2012) Stefano Cardinale et al.   Biotechnology Journal

The automatic annotation of bacterial genomes

(2012) E. J. Richardson et al.   BRIEFINGS IN BIOINFORMATICS

Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria

(2011) Oliver Hädicke et al.   BMC Systems Biology

Xenobiology: A new form of life as the ultimate biosafety tool

(2010) Markus Schmidt   BIOESSAYS

Microbial threat lists: obstacles in the quest for biosecurity?

(2010) Arturo Casadevall et al.   NATURE REVIEWS MICROBIOLOGY

Tracking, tuning, and terminating microbial physiology using synthetic riboregulators

(2010) J. M. Callura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Recombinant bacteria for environmental release: what went wrong and what we have learnt from it

(2009) V. de Lorenzo   CLINICAL MICROBIOLOGY AND INFECTION

Synthesis of orthogonal transcription-translation networks

(2009) W. An et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MicroScope: a platform for microbial genome annotation and comparative genomics

(2009) D. Vallenet et al.   Database-The Journal of Biological Databases and Curation

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS