Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501

Next-generation genome-scale models for metabolic engineering

(2015) Zachary A King et al.   CURRENT OPINION IN BIOTECHNOLOGY

NAD-Independent l-Lactate Dehydrogenase Required for l-Lactate Utilization in Pseudomonas stutzeri A1501

(2015) Chao Gao et al.   JOURNAL OF BACTERIOLOGY

Construction of a genome-scale metabolic network of the plant pathogenPectobacterium carotovorumprovides new strategies for bactericide discovery

(2014) Cheng Wang et al.   FEBS LETTERS

Reconstruction of a generic metabolic network model of cancer cells

(2014) Mahdieh Hadi et al.   Molecular BioSystems

A genome-scale metabolic model of Methanococcus maripaludis S2 for CO2capture and conversion to methane

(2014) Nishu Goyal et al.   Molecular BioSystems

The Denitrification Characteristics of Pseudomonas stutzeri SC221-M and Its Application to Water Quality Control in Grass Carp Aquaculture

(2014) Bin Deng et al.   PLoS One

FCDECOMP: Decomposition of metabolic networks based on flux coupling relations

(2014) Abolfazl Rezvan et al.   Journal of Bioinformatics and Computational Biology

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

Software platforms to facilitate reconstructing genome-scale metabolic networks

(2013) Joshua J. Hamilton et al.   ENVIRONMENTAL MICROBIOLOGY

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

(2013) Henning Knoop et al.   PLoS Computational Biology

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

(2013) Jonathan M. Dreyfuss et al.   PLoS Computational Biology

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

(2013) Rasmus Agren et al.   PLoS Computational Biology

Analysis of Metabolic Subnetworks by Flux Cone Projection

(2012) Sayed-Amir Marashi et al.   Algorithms for Molecular Biology

Efficient bioconversion of l-threonine to 2-oxobutyrate using whole cells of Pseudomonas stutzeri SDM

(2012) Wen Zhang et al.   BIORESOURCE TECHNOLOGY

Mathematical optimization applications in metabolic networks

(2012) Ali R. Zomorrodi et al.   METABOLIC ENGINEERING

In Silico Insights into the Symbiotic Nitrogen Fixation in Sinorhizobium meliloti via Metabolic Reconstruction

(2012) Hansheng Zhao et al.   PLoS One

Efficient Production of Pyruvate from DL-Lactate by the Lactate-Utilizing Strain Pseudomonas stutzeri SDM

(2012) Chao Gao et al.   PLoS One

Involvement of the ammonium transporter AmtB in nitrogenase regulation and ammonium excretion in Pseudomonas stutzeri A1501

(2012) Tao Zhang et al.   RESEARCH IN MICROBIOLOGY

Metabolic network modeling and simulation for drug targeting and discovery

(2011) Hyun Uk Kim et al.   Biotechnology Journal

Reconstruction of a genome-scale metabolic network of Rhodococcus erythropolis for desulfurization studies

(2011) Shilpi Aggarwal et al.   Molecular BioSystems

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism

(2011) R. L. Chang et al.   Molecular Systems Biology

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

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

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

(2011) Jan Schellenberger et al.   Nature Protocols

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

(2011) S. Mintz-Oron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis

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

Efficient Production of 2-Oxobutyrate from 2-Hydroxybutyrate by Using Whole Cells of Pseudomonas stutzeri Strain SDM

(2010) C. Gao et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Global transcriptional analysis of nitrogen fixation and ammonium repression in root-associated Pseudomonas stutzeri A1501

(2010) Yongliang Yan et al.   BMC GENOMICS

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN 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

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

(2010) Ines Thiele et al.   Nature Protocols

Genome-scale modeling and in silico analysis of mouse cell metabolic network

(2009) Suresh Selvarasu et al.   Molecular BioSystems

Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001

(2009) Ali Navid et al.   Molecular BioSystems

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

(2008) Juan Nogales et al.   BMC Systems Biology

Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1

(2008) M. A. Oberhardt et al.   JOURNAL OF BACTERIOLOGY

metaTIGER: a metabolic evolution resource

(2008) John W. Whitaker et al.   NUCLEIC ACIDS RESEARCH

Nitrogen fixation island and rhizosphere competence traits in the genome of root-associated Pseudomonas stutzeri A1501

(2008) Y. Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Jacek Puchałka et al.   PLoS Computational Biology

Nitrate respiration in Pseudomonas stutzeri A15 and its involvement in rice and wheat root colonization

(2007) Hans Rediers et al.   MICROBIOLOGICAL RESEARCH

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism

(2007) Orland Gonzalez et al.   Molecular BioSystems