Computational systems biology and in silico modeling of the human microbiome (Q38010422)

26 August 2017

Computational systems biology and in silico modeling of the human microbiome (English)

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26 August 2017

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1

Elhanan Borenstein

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26 August 2017

15 May 2012

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Briefings in Bioinformatics

26 August 2017

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26 August 2017

13

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26 August 2017

6

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26 August 2017

769-780

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Succession of microbial consortia in the developing infant gut microbiome

26 August 2017

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Topographical and temporal diversity of the human skin microbiome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Bacterial community variation in human body habitats across space and time

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The human microbiome project

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Diversity of the human intestinal microbial flora

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

A core gut microbiome in obese and lean twins

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Obesity and the human microbiome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The evolution of molecular biology into systems biology.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Systems biology: a brief overview

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Mathematical models in microbial systems biology

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Molecular eco-systems biology: towards an understanding of community function

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Systems approaches to microbial communities and their functioning.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Genome-scale models of bacterial metabolism: reconstruction and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Applications of genome-scale metabolic reconstructions

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Biological networks: the tinkerer as an engineer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

From genomics to chemical genomics: new developments in KEGG

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

An overview of data models for the analysis of biochemical pathways

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The large-scale organization of metabolic networks

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Metabolic network structure determines key aspects of functionality and regulation

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The evolution of modularity in bacterial metabolic networks.

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Using the topology of metabolic networks to predict viability of mutant strains

21 January 2018

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https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Comparison of network-based pathway analysis methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

What is flux balance analysis?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Environmental variability and modularity of bacterial metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Large-scale reconstruction and phylogenetic analysis of metabolic environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Network-based approaches for linking metabolism with environment

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Topological signatures of species interactions in metabolic networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Metabolic-network-driven analysis of bacterial ecological strategies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

A catalog of reference genomes from the human microbiome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Rules of engagement: interspecies interactions that regulate microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Syntrophy in anaerobic global carbon cycles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Network structure and biodiversity loss in food webs: robustness increases with connectance

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Food-web structure and network theory: The role of connectance and size

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Synthetic cooperation in engineered yeast populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Multispecies communities: interspecies interactions influence growth on saliva as sole nutritional source

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Enterotypes of the human gut microbiome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

A global network of coexisting microbes from environmental and whole-genome sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Using network analysis to explore co-occurrence patterns in soil microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

A comparison of taxon co-occurrence patterns for macro- and microorganisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The large-scale organization of the bacterial network of ecological co-occurrence interactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Metabolic modeling of a mutualistic microbial community.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Emergent cooperation in microbial metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Ecosystems biology of microbial metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

A rendezvous with our microbes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Comparative metagenomics of microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

A method for identifying keystone species in food web models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The NIH Human Microbiome Project

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

MicrobesOnline: an integrated portal for comparative and functional genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

The RAST Server: rapid annotations using subsystems technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

IMG/M: a data management and analysis system for metagenomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Reconstruction of biochemical networks in microorganisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

iPath: interactive exploration of biochemical pathways and networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Cytoscape 2.8: new features for data integration and network visualization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Durable alteration of the colonic microbiota by the administration of donor fecal flora

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Creating and characterizing communities of human gut microbes in gnotobiotic mice

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Targeting the human microbiome with antibiotics, probiotics, and prebiotics: gastroenterology enters the metagenomics era

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

Therapeutic transplantation of the distal gut microbiota

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBS022

21 January 2018

Identifiers

DOI

10.1093/BIB/BBS022

1 reference

journals/bib/Borenstein12

26 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PubMed ID

22589385