High‐quality genome‐scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism

(2019) Morgan N. Price et al.   mSystems

Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism

(2019) Mitchell G. Thompson et al.   mBio

Engineering Pseudomonas putida KT2440 for efficient ethylene glycol utilization

(2018) Mary Ann Franden et al.   METABOLIC ENGINEERING

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

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

From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida

(2018) Michael Kohlstedt et al.   METABOLIC ENGINEERING

Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

(2018) Yara Seif et al.   Nature Communications

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models

(2017) Qianqian Yuan et al.   PLoS One

A metabolic pathway for catabolizing levulinic acid in bacteria

(2017) Jacqueline M. Rand et al.   Nature Microbiology

Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

(2017) Brian T. Burger et al.   mSystems

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis

(2016) Eugeni Belda et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative genome-scale modelling ofStaphylococcus aureusstrains identifies strain-specific metabolic capabilities linked to pathogenicity

(2016) Emanuele Bosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis

(2016) Jared T. Broddrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pseudomonas putida—a versatile host for the production of natural products

(2015) Anita Loeschcke et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Analysis of the core genome and pangenome of P seudomonas putida

(2015) Zulema Udaondo et al.   ENVIRONMENTAL MICROBIOLOGY

Optimizing genome-scale network reconstructions

(2014) Jonathan Monk et al.   NATURE BIOTECHNOLOGY

Biotechnological domestication of pseudomonads using synthetic biology

(2014) Pablo I. Nikel et al.   NATURE REVIEWS MICROBIOLOGY

Robustness and Plasticity of Metabolic Pathway Flux among Uropathogenic Isolates of Pseudomonas aeruginosa

(2014) Antje Berger et al.   PLoS One

Lignin valorization through integrated biological funneling and chemical catalysis

(2014) J. G. Linger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Iron-Regulated Expression of Alginate Production, Mucoid Phenotype, and Biofilm Formation by Pseudomonas aeruginosa

(2014) J. R. Wiens et al.   mBio

The Life History ofPseudomonas syringae: Linking Agriculture to Earth System Processes

(2013) Cindy E. Morris et al.   Annual Review of Phytopathology

Isolation and characterization of lignin-degrading bacteria from rainforest soils

(2013) Xing-Feng Huang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition

(2013) Jozef BJH van Duuren et al.   BMC BIOTECHNOLOGY

Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments

(2013) J. M. Monk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

Pseudomonas aeruginosa: new insights into pathogenesis and host defenses

(2013) Shaan L. Gellatly et al.   Pathogens and Disease

Analysis of the plant growth-promoting properties encoded by the genome of the rhizobacteriumPseudomonas putida BIRD-1

(2012) Amalia Roca et al.   ENVIRONMENTAL MICROBIOLOGY

The polyhydroxyalkanoate metabolism controls carbon and energy spillage in Pseudomonas putida

(2012) I. F. Escapa et al.   ENVIRONMENTAL MICROBIOLOGY

Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model

(2012) Kosei Tanaka et al.   NUCLEIC ACIDS RESEARCH

Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis

(2012) J. Nogales et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Regulatory Tasks of the Phosphoenolpyruvate-Phosphotransferase System of Pseudomonas putida in Central Carbon Metabolism

(2012) M. Chavarria et al.   mBio

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

(2012) Joyce E. Loper et al.   PLoS Genetics

Response of Pseudomonas putida KT2440 to Increased NADH and ATP Demand

(2011) Birgitta E. Ebert et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Pathways for degradation of lignin in bacteria and fungi

(2011) Timothy D. H. Bugg et al.   NATURAL PRODUCT REPORTS

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

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

The glycerophospholipid inventory of Pseudomonas putida is conserved between strains and enables growth condition-related alterations

(2011) Jana Rühl et al.   Microbial Biotechnology

Iron uptake and metabolism in pseudomonads

(2010) Pierre Cornelis   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

In silicogenome-scale metabolic analysis ofPseudomonas putidaKT2440 for polyhydroxyalkanoate synthesis, degradation of aromatics and anaerobic survival

(2010) Seung Bum Sohn et al.   Biotechnology Journal

Identification of conditionally essential genes for growth ofPseudomonas putidaKT2440 on minimal medium through the screening of a genome-wide mutant library

(2010) M. Antonia Molina-Henares et al.   ENVIRONMENTAL MICROBIOLOGY

The Pseudomonas Story

(2010) Norberto J. Palleroni   ENVIRONMENTAL MICROBIOLOGY

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Siderophore-mediated iron acquisition in the entomopathogenic bacterium Pseudomonas entomophila L48 and its close relative Pseudomonas putida KT2440

(2009) Sandra Matthijs et al.   BIOMETALS

Review: Lipopolysaccharide biosynthesis in Pseudomonas aeruginosa

(2009) Jerry D. King et al.   Innate Immunity

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory

(2008) Juan Nogales et al.   BMC Systems Biology

Metabolic response of Pseudomonas putida during redox biocatalysis in the presence of a second octanol phase

(2008) Lars M. Blank et al.   FEBS Journal

Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology

(2008) Jacek Puchałka et al.   PLoS Computational Biology