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

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Molecular Biosystems

• Publication date

  2008-01-22

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1039/b715203ePMID 18213408
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Survival of Halobacteria Within Fluid Inclusions in Salt Crystals

  2008cited by this paper
• Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis.

  2007cited by this paper
• Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli

  2007cited by this paper
• The Physiological Role of the Ribulose Monophosphate Pathway in Bacteria and Archaea

  2006cited by this paper
• Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

  2006cited by this paper
• Towards multidimensional genome annotation

  2006cited by this paper
• Metabolic networks in motion: 13C-based flux analysis

  2006cited by this paper
• The Ribulose Monophosphate Pathway Substitutes for the Missing Pentose Phosphate Pathway in the Archaeon Thermococcus kodakaraensis

  2006cited by this paper
• Analysis of Growth of Lactobacillus plantarum WCFS1 on a Complex Medium Using a Genome-scale Metabolic Model*

  2006cited by this paper
• The membrane proteome of Halobacterium salinarum

  2005cited by this paper
• Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation

  2005cited by this paper
• Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation

  2005cited by this paper
• Polarization multiplexed write-once-read-many optical data storage in bacteriorhodopsin films.

  2005cited by this paper
• Ribose-5-Phosphate Biosynthesis in Methanocaldococcus jannaschii Occurs in the Absence of a Pentose-Phosphate Pathway

  2005cited by this paper
• High resolution 13C-solid state NMR of bacteriorhodopsin: assignment of specific aspartic acids and structural implications of single site mutations

  2004cited by this paper
• Bow ties, metabolism and disease.

  2004cited by this paper
• Bacteriorhodopsin as a high-resolution, high-capacity buffer for digital holographic measurements

  2004cited by this paper
• Halobacterium noricense sp. nov., an archaeal isolate from a bore core of an alpine Permian salt deposit, classification of Halobacterium sp. NRC-1 as a strain of H. salinarum and emended description of H. salinarum

  2004cited by this paper
• L-Aspartate semialdehyde and a 6-deoxy-5-ketohexose 1-phosphate are the precursors to the aromatic amino acids in Methanocaldococcus jannaschii.

  2004cited by this paper
• An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

  2003cited by this paper
• Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms

  2003cited by this paper
• The effects of alternate optimal solutions in constraint-based genome-scale metabolic models.

  2003cited by this paper
• Genome-scale microbial in silico models: the constraints-based approach.

  2003cited by this paper
• Dynamic flux balance analysis of diauxic growth in Escherichia coli.

  2002cited by this paper
• Genome-Scale Metabolic Model of Helicobacter pylori 26695

  2002cited by this paper
• Energy balance for analysis of complex metabolic networks.

  2002cited by this paper
• The KEGG databases at GenomeNet

  2002cited by this paper
• Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.

  2001cited by this paper
• Regulation of gene expression in flux balance models of metabolism.

  2001cited by this paper
• Selection analyses of insertional mutants using subgenic-resolution arrays

  2001cited by this paper
• Metabolic modeling of microbial strains in silico.

  2001cited by this paper
• In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

  2001cited by this paper
• Enzyme data and metabolic information: BRENDA, a resource for research in biology, biochemistry, and medicine

  2000cited by this paper
• Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.

  2000cited by this paper
• Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal

  2000cited by this paper
• The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.

  2000cited by this paper
• Recursive MILP model for finding all the alternate optima in LP models for metabolic networks

  2000cited by this paper
• Genome sequence of Halobacterium species NRC-1.

  2000cited by this paper
• Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.

  2000cited by this paper
• Pathway alignment: application to the comparative analysis of glycolytic enzymes.

  1999cited by this paper
• Kinetic mechanism of glucose dehydrogenase from Halobacterium salinarum.

  1999cited by this paper
• Systems Properties of the Haemophilus influenzaeRd Metabolic Genotype*

  1999cited by this paper
• Halobacteria: the evidence for longevity

  1998cited by this paper
• The structure and mechanism of the family of retinal proteins from halophilic archaea.

  1998cited by this paper
• Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster

  1996cited by this paper
• Dynamics of a bloom of halophilic archaea in the Dead Sea

  1995cited by this paper
• Archaea : a laboratory manual

  1995cited by this paper
• ON ELEMENTARY FLUX MODES IN BIOCHEMICAL REACTION SYSTEMS AT STEADY STATE

  1994cited by this paper
• Ribose biosynthesis in methanogenic bacteria

  1994cited by this paper
• Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110

  1994cited by this paper
• Pathway of glycogen metabolism in Methanococcus maripaludis

  1994cited by this paper
• Halococcus salifodinae sp. nov., an Archaeal Isolate from an Austrian Salt Mine

  1994cited by this paper
• Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns

  1993cited by this paper
• Archaeal halophiles (halobacteria) from two British salt mines

  1993cited by this paper
• Glycolysis and Entner-Doudoroff pathways in Halobacterium halobium: some new observations based on 13C NMR spectroscopy.

  1990cited by this paper
• Mevalonic acid is partially synthesized from amino acids in Halobacterium cutirubrum: a 13C nuclear magnetic resonance study

  1986cited by this paper
• Population dynamics of halobacteria in the Dead Sea water column1

  1983cited by this paper
• Anaerobic growth of halobacteria.

  1980cited by this paper
• Potassium uniport and ATP synthesis in Halobacterium halobium.

  1978cited by this paper
• Growth and nutrition of extremely halophilic bacteria.

  1969cited by this paper
• Arginine Metabolism in Halobacterium salinarium, an Obligately Halophilic Bacterium

  1966cited by this paper
• Bow Ties, Metabolism and Disease

  year unknowncited by this paper

• Improving poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis with the construction of a genome-scale metabolic model for Haloferax mediterranei.

  2025cites this paper
• New Analytical Methodology to Reveal Biosignatures on Mars and Ocean Worlds.

  2025cites this paper
• Reconstruction and analyses of genome-scale halomonas metabolic network yield a highly efficient PHA production

  2024cites this paper
• Elucidating metabolic pathways through genomic analysis in highly heavy metal-resistant Halobacterium salinarum strains

  2024cites this paper
• Genome‐Scale Metabolic Modeling of Halomonas elongata 153B Explains Polyhydroxyalkanoate and Ectoine Biosynthesis in Hypersaline Environments

  2024cites this paper
• Unveiling the potential of systems biology in biotechnology and biomedical research

  2024cites this paper
• Metabolic Flux Modeling in Marine Ecosystems.

  2024cites this paper
• Application of coincidence index in the discovery of co-expressed metabolic pathways

  2023cites this paper
• Halomonas spp., as chassis for low-cost production of chemicals

  2022influential citation
• Biofilms of Halobacterium salinarum as a tool for phenanthrene bioremediation

  2020influential citation
• A genome-scale metabolic network reconstruction of extremely halophilic bacterium Salinibacter ruber

  2019cites this paper
• Whole‐genome comparison between the type strain of Halobacterium salinarum (DSM 3754T) and the laboratory strains R1 and NRC‐1

  2019cites this paper
• In a Quest for Engineering Acidophiles for Biomining Applications: Challenges and Opportunities

  2018cites this paper
• Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea

  2018cites this paper
• Fractionation of nitrogen isotopes during amino acid metabolism in heterotrophic and chemolithoautotrophic microbes across Eukarya, Bacteria, and Archaea: Effects of nitrogen sources and metabolic pathways

  2017cites this paper
• Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis

  2017cites this paper
• Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

  2017influential citation
• Constraint-based metabolic modelling of marine microbes and communities.

  2017cites this paper
• Growth and Metabolism of Extremophilic Microorganisms

  2016cites this paper
• Cheminformatics for genome-scale metabolic reconstructions

  2015cites this paper
• Genome-scale reconstruction of the metabolic network in Pseudomonas stutzeri A1501.

  2015cites this paper
• Novel expression and characterization of a light driven proton pump archaerhodopsin 4 in a Halobacterium salinarum strain.

  2015cites this paper
• Model organism databases

  2015cites this paper
• A Manual Curation Strategy to Improve Genome Annotation: Application to a Set of Haloarchael Genomes

  2015cites this paper
• Dynamic Metabolite Profiling in an Archaeon Connects Transcriptional Regulation to Metabolic Consequences

  2015cites this paper
• Dynamic Regulation of Metabolism in Archaea

  2015cites this paper
• ON THE USE AND FUTURE OF ALTERNATIVE TESTING STRATEGIES IN REGULATORY TOXICOLOGY

  2014cites this paper
• Carbohydrate Metabolism in Archaea: Current Insights into Unusual Enzymes and Pathways and Their Regulation

  2014cites this paper
• Network motifs that recur across species, including gene regulatory and protein–protein interaction networks

  2014cites this paper
• Plant genome-scale modeling and implementation.

  2014cites this paper
• The Family Halobacteriaceae

  2014cites this paper
• SYSTEMS BIOTECHNOLOGY FOR INDUSTRIAL MICROORGANISMS

  2014cites this paper
• Network motifs provide signatures that characterize metabolism.

  2013cites this paper
• Development of computational methods for the determination of biomass composition and evaluation of its impact in genome-scale models predictions

  2013cites this paper
• An Optimization Rule for In Silico Identification of Targeted Overproduction in Metabolic Pathways

  2013cites this paper
• Integration of Metabolic Knowledge for Genome‐Scale Metabolic Reconstruction

  2013cites this paper
• Simple topological properties predict functional misannotations in a metabolic network

  2013cites this paper
• Clonagem e expressão do gene da bacteriorodopsina em Cupriavidus necator.

  2012cites this paper
• A Systems Biology Approach to Drug Targets in Pseudomonas aeruginosa Biofilm

  2012cites this paper
• MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases

  2012cites this paper
• A model of energy limitation and population structuring to estimate phototrophic growth of industrially significant Halobacterium salinarum strains

  2012cites this paper
• Methods for the refinement of genome-scale metabolic networks

  2012cites this paper
• Mechanisms of Resistance to Ionizing Radiation in Extremophiles

  2012cites this paper
• Network Motifs Provide Signatures That Characterize Metabolism and Produce Novel Insights into the Evolutionary History of the Eukaryotic Cell.

  2012influential citation
• Supplementary Information : Network motifs provide signatures that characterize metabolism

  2012cites this paper
• Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico

  2012cites this paper
• Ecological Aspects of the Distribution of Different Autotrophic CO2 Fixation Pathways

  2011cites this paper
• Metabolic reconstruction of the archaeon methanogen Methanosarcina Acetivorans

  2011cites this paper
• Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis.

  2011cites this paper
• Genome-scale reconstruction of metabolic network for a halophilic extremophile, Chromohalobacter salexigens DSM 3043

  2011influential citation
• Of fish and men: a comparative study for genome-scale metabolic networks.

  2011cites this paper
• From Communicational to Computational: Systems Modeling Approaches for Psychiatric Research

  2010cites this paper
• The structure and function of complex Halobacterium salinarum metabolic network

  2010cites this paper
• The structure and function of complex Halobacterium salinarum metabolic network

  2010cites this paper
• Large scale physiological readjustment during growth enables rapid, comprehensive and inexpensive systems analysis

  2010cites this paper
• Characterization of Growth and Metabolism of the Haloalkaliphile Natronomonas pharaonis

  2010cites this paper
• The self-similarity of trunk metabolism.

  2010cites this paper
• BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

  2010cites this paper
• Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1

  2010cites this paper
• A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

  2009cites this paper
• Applications of genome-scale metabolic reconstructions

  2009cites this paper
• Systems Analysis of Bioenergetics and Growth of the Extreme Halophile Halobacterium salinarum

  2009influential citation
• Phosphate-Dependent Behavior of the Archaeon Halobacterium salinarum Strain R1

  2009cites this paper
• Accomplishments in genome‐scale in silico modeling for industrial and medical biotechnology

  2009cites this paper
• Genome-Scale Reconstruction, Modeling, and Simulation of E. coli℉s Metabolic Network

  2009cites this paper
• Systems Biology: Its Past, Present and Potential

  2009cites this paper
• Life‐style changes of a halophilic archaeon analyzed by quantitative proteomics

  2009cites this paper
• Metabolic network discovery through reverse engineering of metabolome data

  2009cites this paper
• Review Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology

  2009cites this paper
• Genome-Wide Proteomics and Quantitative Analyses on Halophilic Archaea

  2008influential citation
• Metabolism of halophilic archaea

  2008cites this paper
• Identification of the arginine/ornithine antiporter ArcD from Halobacterium salinarum

  2008cites this paper
• Hybrid Modeling in Computational Neuropsychiatry

  2008cites this paper
• Genomics and functional genomics with haloarchaea

  2008cites this paper
• Genome information management and integrated data analysis with HaloLex

  2008cites this paper
• Determination of optimal metabolic pathways through a new learning algorithm

  2008cites this paper
• Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

  2007cites this paper