Programmable bacterial catalysis - designing cells for biosynthesis of value-added compounds

Growth independent rhamnolipid production from glucose using the non-pathogenic Pseudomonas putida KT2440

(2012) Andreas Wittgens et al.   Microbial Cell Factories

Combined Effect of Improved Cell Yield and Increased Specific Productivity Enhances Recombinant Enzyme Production in Genome-Reduced Bacillus subtilis Strain MGB874

(2011) Kenji Manabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Redesigning Escherichia coli Metabolism for Anaerobic Production of Isobutanol

(2011) Cong T. Trinh et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial production of free fatty acids from freshwater macroalgal cellulose

(2011) Spencer W. Hoover et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Improving the prediction of Pseudomonas putida mt-2 growth kinetics with the use of a gene expression regulation model of the TOL plasmid

(2011) Michalis Koutinas et al.   BIOCHEMICAL ENGINEERING JOURNAL

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

(2011) G. Misirli et al.   BIOINFORMATICS

In silico analysis and experimental improvement of taxadiene heterologous biosynthesis in Escherichia coli

(2011) Hailin Meng et al.   BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

Flux coupling and transcriptional regulation within the metabolic network of the photosynthetic bacterium Synechocystis sp. PCC6803

(2011) Arnau Montagud et al.   Biotechnology Journal

The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene

(2011) Rafael Silva-Rocha et al.   BMC Systems Biology

A retrosynthetic biology approach to metabolic pathway design for therapeutic production

(2011) Pablo Carbonell et al.   BMC Systems Biology

The minimal genome--a metabolic and environmental comparison

(2011) M. T. DeWall et al.   Briefings in Functional Genomics

Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440

(2011) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Optimization of the In-Silico-Designed Kemp Eliminase KE70 by Computational Design and Directed Evolution

(2011) Olga Khersonsky et al.   JOURNAL OF MOLECULAR BIOLOGY

Linking genes to microbial growth kinetics—An integrated biochemical systems engineering approach

(2011) Michalis Koutinas et al.   METABOLIC ENGINEERING

An evolutionary strategy for isobutanol production strain development in Escherichia coli

(2011) Kevin M. Smith et al.   METABOLIC ENGINEERING

Modulating substrate specificity of histone acetyltransferase with unnatural amino acids

(2011) Kinjal Rajesh Mehta et al.   Molecular BioSystems

Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals

(2011) Clementina Dellomonaco et al.   NATURE

Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors

(2011) Guillermo Rodrigo et al.   NUCLEIC ACIDS RESEARCH

De novo Biosynthesis of Biodiesel by Escherichia coli in Optimized Fed-Batch Cultivation

(2011) Yangkai Duan et al.   PLoS One

Two Different Template Replicators Coexisting in the Same Protocell: Stochastic Simulation of an Extended Chemoton Model

(2011) István Zachar et al.   PLoS One

Minimization of the Legionella pneumophila genome reveals chromosomal regions involved in host range expansion

(2011) T. J. O'Connor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic Biology: Integrated Gene Circuits

(2011) N. Nandagopal et al.   SCIENCE

A bacterial platform for fermentative production of plant alkaloids

(2011) Akira Nakagawa et al.   Nature Communications

Automatic Design of Digital Synthetic Gene Circuits

(2011) Mario A. Marchisio et al.   PLoS Computational Biology

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

(2011) Matthew A. Oberhardt et al.   PLoS Computational Biology

Using Chemobiosynthesis and Synthetic Mini-Polyketide Synthases To Produce Pharmaceutical Intermediates in Escherichia coli

(2010) H. G. Menzella et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

(2010) Arnau Montagud et al.   BMC Systems Biology

Prediction of novel synthetic pathways for the production of desired chemicals

(2010) Ayoun Cho et al.   BMC Systems Biology

Engineering Enzyme Specificity Using Computational Design of a Defined-Sequence Library

(2010) Shaun M. Lippow et al.   CHEMISTRY & BIOLOGY

Improving a Natural Enzyme Activity through Incorporation of Unnatural Amino Acids

(2010) Isaac N. Ugwumba et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Autonomous induction of recombinant proteins by minimally rewiring native quorum sensing regulon of E. coli

(2010) Chen-Yu Tsao et al.   METABOLIC ENGINEERING

Quantification of the physiochemical constraints on the export of spider silk proteins by Salmonella type III secretion

(2010) Daniel M Widmaier et al.   Microbial Cell Factories

Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology

(2010) Philippe Marguet et al.   PLoS One

Expanding metabolism for total biosynthesis of the nonnatural amino acid L-homoalanine

(2010) K. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli

(2010) P. K. Ajikumar et al.   SCIENCE

Microbial Biosynthesis of Alkanes

(2010) A. Schirmer et al.   SCIENCE

Stochastic Simulation of the Chemoton

(2009) Sven Van Segbroeck et al.   ARTIFICIAL LIFE

Using multi-objective computational design to extend protein promiscuity

(2009) Maria Suarez et al.   BIOPHYSICAL CHEMISTRY

Frameworks for Programming Biological Function through RNA Parts and Devices

(2009) Maung Nyan Win et al.   CHEMISTRY & BIOLOGY

Responses of Pseudomonas to small toxic molecules by a mosaic of domains

(2009) Juan L Ramos et al.   CURRENT OPINION IN MICROBIOLOGY

Cell cycle-dependent variations in protein concentration

(2009) Natalie A. Cookson et al.   NUCLEIC ACIDS RESEARCH

FMM: a web server for metabolic pathway reconstruction and comparative analysis

(2009) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

(2009) E. Yus et al.   SCIENCE

Transcriptome Complexity in a Genome-Reduced Bacterium

(2009) M. Guell et al.   SCIENCE

TinkerCell: modular CAD tool for synthetic biology

(2009) Deepak Chandran et al.   Journal of Biological Engineering

Analyzing Protein Interaction Networks Using Structural Information

(2008) Christina Kiel et al.   Annual Review of Biochemistry

Production of Glucaric Acid from a Synthetic Pathway in Recombinant Escherichia coli

(2008) T. S. Moon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Optimization of Metabolic Capacity and Flux through Environmental Cues To Maximize Hydrogen Production by the Cyanobacterium "Arthrospira (Spirulina) maxima"

(2008) G. Ananyev et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Synthetic biology with RNA motifs

(2008) Hirohide Saito et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes

(2008) Jessica C Zweers et al.   Microbial Cell Factories

Bacterial Hosts for Natural Product Production

(2008) Haoran Zhang et al.   MOLECULAR PHARMACEUTICS

Strain Improvement of RecombinantEscherichia colifor Efficient Production of Plant Flavonoids

(2008) Effendi Leonard et al.   MOLECULAR PHARMACEUTICS

Template-directed synthesis of a genetic polymer in a model protocell

(2008) Sheref S. Mansy et al.   NATURE

Thermostability of model protocell membranes

(2008) S. S. Mansy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De Novo Computational Design of Retro-Aldol Enzymes

(2008) L. Jiang et al.   SCIENCE