In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling (Q37816217)

23 August 2017

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title

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling (English)

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23 August 2017

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Geobacter

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3

Derek R Lovley

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23 August 2017

2

Bernhard Ø Palsson

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23 August 2017

Radhakrishnan Mahadevan

series ordinal

1

object named as

Radhakrishnan Mahadevan

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23 August 2017

language of work or name

English

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publication date

6 December 2010

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Nature Reviews Microbiology

23 August 2017

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23 August 2017

9

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23 August 2017

39-50

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23 August 2017

1

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maintained by WikiProject

23 August 2017

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https://scigraph.springernature.com/pub.10.1038/nrmicro2456

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cites work

Reconstruction of biochemical networks in microorganisms

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Applications of genome-scale metabolic reconstructions

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Towards multidimensional genome annotation

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

What is flux balance analysis?

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Understanding human metabolic physiology: a genome-to-systems approach

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Global reconstruction of the human metabolic network based on genomic and bibliomic data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

High-throughput methods for culturing microorganisms in very-low-nutrient media yield diverse new marine isolates

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Dissimilatory Fe(III) and Mn(IV) reduction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Oxidation of aromatic contaminants coupled to microbial iron reduction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Geobacter lovleyi sp. nov. strain SZ, a novel metal-reducing and tetrachloroethene-dechlorinating bacterium.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Geobacter bemidjiensis sp. nov. and Geobacter psychrophilus sp. nov., two novel Fe(III)-reducing subsurface isolates

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Microbial reduction of uranium

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Vanadium respiration by Geobacter metallireducens: novel strategy for in situ removal of vanadium from groundwater

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Humic substances as electron acceptors for microbial respiration

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Dissimilatory metal reduction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Stimulating the In Situ Activity of Geobacter Species To Remove Uranium from the Groundwater of a Uranium-Contaminated Aquifer

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Sustained removal of uranium from contaminated groundwater following stimulation of dissimilatory metal reduction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Relationships between microbial community structure and hydrochemistry in a landfill leachate-polluted aquifer.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Dominance of Geobacteraceae in BTX-degrading enrichments from an iron-reducing aquifer

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Power output and columbic efficiencies from biofilms of Geobacter sulfurreducens comparable to mixed community microbial fuel cells

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Graphite electrodes as electron donors for anaerobic respiration

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Graphite electrode as a sole electron donor for reductive dechlorination of tetrachlorethene by Geobacter lovleyi.

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Geobacter sulfurreducens strain engineered for increased rates of respiration

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Genomic and microarray analysis of aromatics degradation in Geobacter metallireducens and comparison to a Geobacter isolate from a contaminated field site

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Genome-scale constraint-based modeling of Geobacter metallireducens

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Elucidation of an alternate isoleucine biosynthesis pathway in Geobacter sulfurreducens

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Properties of metabolic networks: structure versus function

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Characterizing regulation of metabolism in Geobacter sulfurreducens through genome-wide expression data and sequence analysis

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Global organization of metabolic fluxes in the bacterium Escherichia coli

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

The large-scale organization of metabolic networks

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast.

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

The degree of redundancy in metabolic genes is linked to mode of metabolism

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

Extracellular electron transfer via microbial nanowires

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

https://api.crossref.org/works/10.1038%2FNRMICRO2456

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1 reference

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12 December 2020

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Identifiers

DOI

10.1038/NRMICRO2456

1 reference

23 August 2017

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