Metabolic network modeling of microbial communities (Q30279122)

12 August 2017

1 reference

title

Metabolic network modeling of microbial communities (English)

1 reference

12 August 2017

Matthew B Biggs

1

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Gregory L Medlock

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Gregory L Medlock

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2

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Glynis L Kolling

object named as

Glynis L Kolling

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3

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Jason A. Papin

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4

object named as

Jason A Papin

1 reference

12 August 2017

24 June 2015

1 reference

Wiley interdisciplinary reviews. Systems biology and medicine

12 August 2017

1 reference

12 August 2017

7

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12 August 2017

317-334

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12 August 2017

5

1 reference

Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Where next for microbiome research?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Biological insights through nontargeted metabolomics.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Inter- and intraspecies metabolite exchange promotes virulence of antibiotic-resistant Staphylococcus aureus

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Binning metagenomic contigs by coverage and composition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

A peptide-based method for 13C Metabolic Flux Analysis in microbial communities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Functional implications of the microbial community structure of undefined mesophilic starter cultures

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Staphylococcus aureus alters growth activity, autolysis, and antibiotic tolerance in a human host-adapted Pseudomonas aeruginosa lineage

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Recent advances in genomic DNA sequencing of microbial species from single cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Nutrient cross-feeding in the microbial world

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Emergent biosynthetic capacity in simple microbial communities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Distinct signatures of host-microbial meta-metabolome and gut microbiome in two C57BL/6 strains under high-fat diet

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Elucidating the interactions between the human gut microbiota and its host through metabolic modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Towards predictive models of the human gut microbiome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Microbial regulation of global biogeochemical cycles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Recent advances in the reconstruction of metabolic models and integration of omics data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

EBI metagenomics--a new resource for the analysis and archiving of metagenomic data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Comparative metabolic systems analysis of pathogenic Burkholderia

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Software platforms to facilitate reconstructing genome-scale metabolic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Novel multiscale modeling tool applied to Pseudomonas aeruginosa biofilm formation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Understanding the interactions between bacteria in the human gut through metabolic modeling

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Interspecies interactions stimulate diversification of the Streptomyces coelicolor secreted metabolome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Community flux balance analysis for microbial consortia at balanced growth

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Microbial syntrophy: interaction for the common good

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Redirector: designing cell factories by reconstructing the metabolic objective

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Integrating cellular metabolism into a multiscale whole-body model

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

A systems biology approach to studying the role of microbes in human health.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

A statistical framework for accurate taxonomic assignment of metagenomic sequencing reads

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Integration of expression data in genome-scale metabolic network reconstructions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Critical review of activated sludge modeling: state of process knowledge, modeling concepts, and limitations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Imaging secondary metabolism of Streptomyces sp. Mg1 during cellular lysis and colony degradation of competing Bacillus subtilis.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Engineering microbial consortia to enhance biomining and bioremediation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Computational systems biology and in silico modeling of the human microbiome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Rapid identification of high-confidence taxonomic assignments for metagenomic data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Towards synthetic microbial consortia for bioprocessing.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Thermophilic anaerobic oxidation of methane by marine microbial consortia

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Ecosystems biology of microbial metabolism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Prospects for systems biology and modeling of the gut microbiome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Gut microbiome-host interactions in health and disease

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Taxonomic metagenome sequence assignment with structured output models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Functional integration of a metabolic network model and expression data without arbitrary thresholding.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Direct coupling of a genome-scale microbial in silico model and a groundwater reactive transport model.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Environments that induce synthetic microbial ecosystems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Clustering metagenomic sequences with interpolated Markov models

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

The application of flux balance analysis in systems biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Incorporating microbial ecology into the metabolic modelling of polyphosphate accumulating organisms and glycogen accumulating organisms.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Systems approaches to microbial communities and their functioning.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

A catalog of reference genomes from the human microbiome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Applications of genome-scale metabolic reconstructions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Assembling the marine metagenome, one cell at a time

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

GrowMatch: an automated method for reconciling in silico/in vivo growth predictions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Stress- and growth rate-related differences between plate count and real-time PCR data during growth of Listeria monocytogenes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Large-scale reconstruction and phylogenetic analysis of metabolic environments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Engineering microbial consortia: a new frontier in synthetic biology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Context-specific metabolic networks are consistent with experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

The unseen majority: soil microbes as drivers of plant diversity and productivity in terrestrial ecosystems

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Metabolic modeling of a mutualistic microbial community.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Evolutionary programming as a platform for in silico metabolic engineering

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Hydrogen production by Rhodobacter sphaeroides strain O.U.001 using spent media of Enterobacter cloacae strain DM11

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Metagenomics: application of genomics to uncultured microorganisms

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Application of tetranucleotide frequencies for the assignment of genomic fragments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Analysis of optimality in natural and perturbed metabolic networks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Dynamic flux balance analysis of diauxic growth in Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Constraint-based modeling analysis of the metabolism of two Pelobacter species

3 June 2018

1 reference

Competitive and cooperative metabolic interactions in bacterial communities.

21 January 2018

1 reference

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures.

21 January 2018

1 reference

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

21 January 2018

1 reference

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

21 January 2018

1 reference

Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut

21 January 2018

1 reference

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association

21 January 2018

1 reference

Dynamic model-based analysis of furfural and HMF detoxification by pure and mixed batch cultures of S. cerevisiae and S. stipitis.

21 January 2018

1 reference

Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production.

21 January 2018

1 reference

Expanding metabolic networks: scopes of compounds, robustness, and evolution

21 January 2018

1 reference

Panorganismal gut microbiome-host metabolic crosstalk

21 January 2018

1 reference

Dynamic flux balance modeling of S. cerevisiae and E. coli co-cultures for efficient consumption of glucose/xylose mixtures

21 January 2018

1 reference

Hydrophilic interaction chromatography-mass spectrometry for anionic metabolic profiling of urine from antibiotic-treated rats

21 January 2018

1 reference

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

21 January 2018

1 reference

Comparative genome-scale metabolic modeling of actinomycetes: The topology of essential core metabolism

21 January 2018

1 reference

Optimization based automated curation of metabolic reconstructions

21 January 2018

1 reference

Long-term phenotypic evolution of bacteria.

21 January 2018

1 reference

Emergent cooperation in microbial metabolism

21 January 2018

1 reference

A road map for the development of community systems (CoSy) biology

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4575871

Probiotic Administration Attenuates Myocardial Hypertrophy and Heart Failure After Myocardial Infarction in the Rat

26 November 2018

1 reference

The importance of compartmentalization in metabolic flux models: yeast as an ecosystem of organelles

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26109480

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Metabolic synergy: increasing biosynthetic capabilities by network cooperation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26109480

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/WSBM.1308

1 reference

12 August 2017

1 reference

12 August 2017

1 reference

PMCID

4575871