标题
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
作者
关键词
-
出版物
mSystems
Volume 3, Issue 3, Pages e00209-17
出版商
American Society for Microbiology
发表日期
2018-04-25
DOI
10.1128/msystems.00209-17
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis
- (2017) Jennifer A. Bartell et al. Nature Communications
- Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis
- (2017) Jaeyun Sung et al. Nature Communications
- SteadyCom: Predicting microbial abundances while ensuring community stability
- (2017) Siu Hung Joshua Chan et al. PLoS Computational Biology
- BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
- (2017) Eugen Bauer et al. PLoS Computational Biology
- MMinte: an application for predicting metabolic interactions among the microbial species in a community
- (2016) Helena Mendes-Soares et al. BMC BIOINFORMATICS
- Mobile genes in the human microbiome are structured from global to individual scales
- (2016) I. L. Brito et al. NATURE
- Measurement of bacterial replication rates in microbial communities
- (2016) Christopher T Brown et al. NATURE BIOTECHNOLOGY
- Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
- (2016) Stefanía Magnúsdóttir et al. NATURE BIOTECHNOLOGY
- A microfluidics-based in vitro model of the gastrointestinal human–microbe interface
- (2016) Pranjul Shah et al. Nature Communications
- Adaptive evolution of complex innovations through stepwise metabolic niche expansion
- (2016) Balázs Szappanos et al. Nature Communications
- Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0
- (2016) Brian R. Granger et al. PLoS Computational Biology
- Recovering complete and draft population genomes from metagenome datasets
- (2016) Naseer Sangwan et al. Microbiome
- Metabolic Network Prediction of Drug Side Effects
- (2016) Itay Shaked et al. Cell Systems
- Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes
- (2016) Anna Heintz-Buschart et al. Nature Microbiology
- Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations
- (2016) Tatiana Shashkova et al. PLoS One
- Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico
- (2015) Almut Heinken et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Quantitative Imaging of Gut Microbiota Spatial Organization
- (2015) Kristen A. Earle et al. Cell Host & Microbe
- Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
- (2015) Saeed Shoaie et al. Cell Metabolism
- BiGG Models: A platform for integrating, standardizing and sharing genome-scale models
- (2015) Zachary A. King et al. NUCLEIC ACIDS RESEARCH
- The ecology of the microbiome: Networks, competition, and stability
- (2015) K. Z. Coyte et al. SCIENCE
- Metabolic network modeling of microbial communities
- (2015) Matthew B. Biggs et al. Wiley Interdisciplinary Reviews-Systems Biology and Medicine
- Systems biology of host-microbe metabolomics
- (2015) Almut Heinken et al. Wiley Interdisciplinary Reviews-Systems Biology and Medicine
- Human metabolic atlas: an online resource for human metabolism
- (2015) Natapol Pornputtapong et al. Database-The Journal of Biological Databases and Curation
- Calibration and analysis of genome-based models for microbial ecology
- (2015) Stilianos Louca et al. eLife
- Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires
- (2015) Eugen Bauer et al. Microbiome
- Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes
- (2015) Stefanía Magnúsdóttir et al. Frontiers in Genetics
- Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction
- (2014) Ibrahim E El-Semman et al. BMC Systems Biology
- Recent advances in the reconstruction of metabolic models and integration of omics data
- (2014) Rajib Saha et al. CURRENT OPINION IN BIOTECHNOLOGY
- Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe
- (2014) A. Heinken et al. JOURNAL OF BACTERIOLOGY
- Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host
- (2014) H. Salem et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
- (2014) William R. Harcombe et al. Cell Reports
- Why model?
- (2014) Olaf Wolkenhauer Frontiers in Physiology
- Gut-derived short-chain fatty acids are vividly assimilated into host carbohydrates and lipids
- (2013) Gijs den Besten et al. AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
- The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism
- (2013) Gijs den Besten et al. JOURNAL OF LIPID RESEARCH
- Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells
- (2013) Yukihiro Furusawa et al. NATURE
- Diet rapidly and reproducibly alters the human gut microbiome
- (2013) Lawrence A. David et al. NATURE
- Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation
- (2013) Matthew B. Biggs et al. PLoS One
- Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
- (2013) J. M. Monk et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Understanding the interactions between bacteria in the human gut through metabolic modeling
- (2013) Saeed Shoaie et al. Scientific Reports
- Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction
- (2012) H.S. Haraldsdóttir et al. BIOPHYSICAL JOURNAL
- The Impact of the Gut Microbiota on Human Health: An Integrative View
- (2012) Jose C. Clemente et al. CELL
- A systems biology approach to studying the role of microbes in human health
- (2012) Ines Thiele et al. CURRENT OPINION IN BIOTECHNOLOGY
- The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
- (2012) Erwin G Zoetendal et al. ISME Journal
- A metagenome-wide association study of gut microbiota in type 2 diabetes
- (2012) Junjie Qin et al. NATURE
- Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods
- (2012) Nathan E. Lewis et al. NATURE REVIEWS MICROBIOLOGY
- OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities
- (2012) Ali R. Zomorrodi et al. PLoS Computational Biology
- Microbial Co-occurrence Relationships in the Human Microbiome
- (2012) Karoline Faust et al. PLoS Computational Biology
- rBioNet: A COBRA toolbox extension for reconstructing high-quality biochemical networks
- (2011) S. G. Thorleifsson et al. BIOINFORMATICS
- Lessons from Studying Insect Symbioses
- (2011) Angela E. Douglas Cell Host & Microbe
- Treating Clostridium difficile Infection With Fecal Microbiota Transplantation
- (2011) Johan S. Bakken et al. Clinical Gastroenterology and Hepatology
- A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011
- (2011) J. D. Orth et al. Molecular Systems Biology
- Ecology drives a global network of gene exchange connecting the human microbiome
- (2011) Chris S. Smillie et al. NATURE
- The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes
- (2011) Mark W. J. van Passel et al. PLoS One
- Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
- (2011) S. Greenblum et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models
- (2010) R. M. T. Fleming et al. BIOINFORMATICS
- Computationally efficient flux variability analysis
- (2010) Steinn Gudmundsson et al. BMC BIOINFORMATICS
- Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments
- (2010) Kai Zhuang et al. ISME Journal
- High-throughput generation, optimization and analysis of genome-scale metabolic models
- (2010) Christopher S Henry et al. NATURE BIOTECHNOLOGY
- What is flux balance analysis?
- (2010) Jeffrey D Orth et al. NATURE BIOTECHNOLOGY
- A protocol for generating a high-quality genome-scale metabolic reconstruction
- (2010) Ines Thiele et al. Nature Protocols
- Probiotics and the gut microbiota in intestinal health and disease
- (2010) Mélanie G. Gareau et al. Nature Reviews Gastroenterology & Hepatology
- Environments that Induce Synthetic Microbial Ecosystems
- (2010) Niels Klitgord et al. PLoS Computational Biology
- Gut microbiota fermentation of prebiotics increases satietogenic and incretin gut peptide production with consequences for appetite sensation and glucose response after a meal
- (2009) Patrice D Cani et al. AMERICAN JOURNAL OF CLINICAL NUTRITION
- The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
- (2009) Ron Caspi et al. NUCLEIC ACIDS RESEARCH
- Human gut microbiota in obesity and after gastric bypass
- (2009) H. Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice
- (2009) P. J. Turnbaugh et al. Science Translational Medicine
- High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota
- (2008) E G Zoetendal et al. GUT
- The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
- (2008) Adam M Feist et al. NATURE BIOTECHNOLOGY
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