Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments (Q42743118)

6 November 2017

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments (English)

1 reference

6 November 2017

7

Derek R Lovley

1 reference

6 November 2017

Kai Zhuang

1

1 reference

6 November 2017

Mounir Izallalen

2

1 reference

6 November 2017

Paula Mouser

3

1 reference

6 November 2017

Hanno Richter

4

1 reference

6 November 2017

Carla Risso

5

1 reference

6 November 2017

Radhakrishnan Mahadevan

6

1 reference

6 November 2017

29 July 2010

1 reference

6 November 2017

1 reference

6 November 2017

5

1 reference

6 November 2017

2

1 reference

6 November 2017

305-316

1 reference

Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation.

6 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Applications of genome-scale metabolic reconstructions

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Genome-scale comparison and constraint-based metabolic reconstruction of the facultative anaerobic Fe(III)-reducer Rhodoferax ferrireducens

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Genome-scale constraint-based modeling of Geobacter metallireducens

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Subsurface clade of Geobacteraceae that predominates in a diversity of Fe(III)-reducing subsurface environments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Metabolic modeling of a mutualistic microbial community.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Microbial incorporation of 13C-labeled acetate at the field scale: detection of microbes responsible for reduction of U(VI).

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Rates of microbial metabolism in deep coastal plain aquifers

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Requirement for a Microbial Consortium To Completely Oxidize Glucose in Fe(III)-Reducing Sediments.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Sulfate reducers can outcompete methanogens at freshwater sulfate concentrations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

DNA microarray analysis of nitrogen fixation and Fe(III) reduction in Geobacter sulfurreducens

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Game-theoretical approaches to studying the evolution of biochemical systems

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

OptStrain: a computational framework for redesign of microbial production systems.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Dissimilatory Fe(III) and Mn(IV) reduction

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Evolution of cross-feeding in microbial populations

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Cleaning up with genomics: applying molecular biology to bioremediation

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Genome of Geobacter sulfurreducens: Metal Reduction in Subsurface Environments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Enumeration and characterization of iron(III)-reducing microbial communities from acidic subsurface sediments contaminated with uranium(VI)

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Rhodoferax ferrireducens sp. nov., a psychrotolerant, facultatively anaerobic bacterium that oxidizes acetate with the reduction of Fe(III).

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Thirteen years of building constraint-based in silico models of Escherichia coli

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

An evolutionary scenario for the transition to undifferentiated multicellularity

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Dynamic flux balance analysis of diauxic growth in Escherichia coli

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Enrichment of members of the family Geobacteraceae associated with stimulation of dissimilatory metal reduction in uranium-contaminated aquifer sediments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

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

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Fat synthesis in adipose tissue. An examination of stoichiometric constraints

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Dissimilatory Fe(III) and Mn(IV) reduction

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Transcriptome of Geobacter uraniireducens growing in uranium-contaminated subsurface sediments

27 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Geobacter sulfurreducens strain engineered for increased rates of respiration

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Dynamic metabolic engineering for increasing bioprocess productivity

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Uranium removal from groundwater via in situ biostimulation: Field-scale modeling of transport and biological processes

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Cooperation and competition in the evolution of ATP-producing pathways

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3105697

Is maximization of molar yield in metabolic networks favoured by evolution?

16 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FISMEJ.2010.117

Methane production from bicarbonate and acetate in an anoxic marine sediment

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FISMEJ.2010.117

A discrete model of bacterial metabolism

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20668487

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Bioremediation. Anaerobes to the rescue

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20668487

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Methane production, sulfate reduction and competition for substrates in the sediments of Lake Washington

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FISMEJ.2010.117

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/ISMEJ.2010.117

1 reference

6 November 2017

1 reference

6 November 2017

PubMed publication ID

20668487

1 reference