More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes
出版年份 2017 全文链接
标题
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes
作者
关键词
Microbiome, Microbiota, Genome-scale metabolic model, Culturing, Minimal media, Phenotype prediction, Interspecies interactions
出版物
Microbiome
Volume 5, Issue 1, Pages -
出版商
Springer Nature
发表日期
2017-07-14
DOI
10.1186/s40168-017-0299-x
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes
- (2017) Joana C. Xavier et al. METABOLIC ENGINEERING
- Prediction of metabolic fluxes from gene expression data with Huber penalty convex optimization function
- (2017) Shao-Wu Zhang et al. Molecular BioSystems
- BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
- (2017) Eugen Bauer et al. PLoS Computational Biology
- Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease
- (2016) Robert Häsler et al. GUT
- Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
- (2016) Hilary P. Browne et al. NATURE
- Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
- (2016) Stefanía Magnúsdóttir et al. NATURE BIOTECHNOLOGY
- A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice
- (2016) Hubert Plovier et al. NATURE MEDICINE
- Oscillospira : a Central, Enigmatic Component of the Human Gut Microbiota
- (2016) Tom Konikoff et al. TRENDS IN MICROBIOLOGY
- Culture of previously uncultured members of the human gut microbiota by culturomics
- (2016) Jean-Christophe Lagier et al. Nature Microbiology
- Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database
- (2015) Jarmo Ritari et al. BMC GENOMICS
- Using Genome-scale Models to Predict Biological Capabilities
- (2015) Edward J. O’Brien et al. CELL
- Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome
- (2015) Saeed Shoaie et al. Cell Metabolism
- Single-cell genomics of uncultivated deep-branching magnetotactic bacteria reveals a conserved set of magnetosome genes
- (2015) Sebastian Kolinko et al. ENVIRONMENTAL MICROBIOLOGY
- Identification of an anti-inflammatory protein fromFaecalibacterium prausnitzii, a commensal bacterium deficient in Crohn’s disease
- (2015) E Quévrain et al. GUT
- Metabolic dependencies drive species co-occurrence in diverse microbial communities
- (2015) Aleksej Zelezniak et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal
- (2015) Thi Phuong Nam Bui et al. Nature Communications
- Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating
- (2015) Páraic Ó Cuív et al. Scientific Reports
- Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways
- (2015) Zachary A. King et al. PLoS Computational Biology
- Species interactions differ in their genetic robustness
- (2015) Lon M. Chubiz et al. Frontiers in Microbiology
- Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires
- (2015) Eugen Bauer et al. Microbiome
- Fecal Microbiota Transplant for Treatment of Clostridium difficile Infection in Immunocompromised Patients
- (2014) Colleen R Kelly et al. AMERICAN JOURNAL OF GASTROENTEROLOGY
- Microbial genomics, transcriptomics and proteomics: new discoveries in decomposition research using complementary methods
- (2014) Petr Baldrian et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- Nutritional requirements and media development for Lactococcus lactis IL1403
- (2014) Kadri Aller et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database
- (2014) Daniel S Weaver et al. BMC Systems Biology
- 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
- Refining metabolic models and accounting for regulatory effects
- (2014) Joonhoon Kim et al. CURRENT OPINION IN BIOTECHNOLOGY
- Effect of diet on the intestinal microbiota and its activity
- (2014) Erwin G. Zoetendal et al. CURRENT OPINION IN GASTROENTEROLOGY
- Bile acids and the gut microbiome
- (2014) Jason M. Ridlon et al. CURRENT OPINION IN GASTROENTEROLOGY
- Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed
- (2014) Jennifer D Rocca et al. ISME Journal
- Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe
- (2014) A. Heinken et al. JOURNAL OF BACTERIOLOGY
- An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli
- (2014) J. Carrera et al. Molecular Systems Biology
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics
- (2014) William R. Harcombe et al. Cell Reports
- Systematic Evaluation of Methods for Integration of Transcriptomic Data into Constraint-Based Models of Metabolism
- (2014) Daniel Machado et al. PLoS Computational Biology
- A Novel Nutritional Predictor Links Microbial Fastidiousness with Lowered Ubiquity, Growth Rate, and Cooperativeness
- (2014) Raphy Zarecki et al. PLoS Computational Biology
- Methods for integration of transcriptomic data in genome-scale metabolic models
- (2014) Min Kyung Kim et al. Computational and Structural Biotechnology Journal
- RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria
- (2013) Pavel S Novichkov et al. BMC GENOMICS
- Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models
- (2013) J. P. Faria et al. BRIEFINGS IN BIOINFORMATICS
- Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome
- (2013) Corinne Ferrier Maurice et al. CELL
- Comparative Metabolic Systems Analysis of Pathogenic Burkholderia
- (2013) J. A. Bartell et al. JOURNAL OF BACTERIOLOGY
- Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli
- (2013) D. McCloskey et al. Molecular Systems Biology
- A community-driven global reconstruction of human metabolism
- (2013) Ines Thiele et al. NATURE BIOTECHNOLOGY
- Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile
- (2013) Els van Nood et al. NEW ENGLAND JOURNAL OF MEDICINE
- The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
- (2013) Ron Caspi et al. NUCLEIC ACIDS RESEARCH
- Data, information, knowledge and principle: back to metabolism in KEGG
- (2013) Minoru Kanehisa et al. NUCLEIC ACIDS RESEARCH
- Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules
- (2013) R. Levy et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis
- (2013) P. M. Smith et al. SCIENCE
- Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks
- (2013) Sriram Chandrasekaran et al. PLoS Computational Biology
- The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum
- (2013) Rasmus Agren et al. PLoS Computational Biology
- Parallel Exploitation of Diverse Host Nutrients Enhances Salmonella Virulence
- (2013) Benjamin Steeb et al. PLoS Pathogens
- Molecular Analysis of Model Gut Microbiotas by Imaging Mass Spectrometry and Nanodesorption Electrospray Ionization Reveals Dietary Metabolite Transformations
- (2012) Christopher M. Rath et al. ANALYTICAL CHEMISTRY
- Modeling of leishmaniasis infection dynamics: novel application to the design of effective therapies
- (2012) Bettina M Länger et al. BMC Systems Biology
- MicrobesFlux: a web platform for drafting metabolic models from the KEGG database
- (2012) Xueyang Feng et al. BMC Systems Biology
- Computational systems biology and in silico modeling of the human microbiome
- (2012) E. Borenstein BRIEFINGS IN BIOINFORMATICS
- A Whole-Cell Computational Model Predicts Phenotype from Genotype
- (2012) Jonathan R. Karr et al. CELL
- Towards metagenome-scale models for industrial applications—the case of Lactic Acid Bacteria
- (2012) Filipe Branco dos Santos et al. CURRENT OPINION IN BIOTECHNOLOGY
- Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota
- (2012) Michael Graham Espey FREE RADICAL BIOLOGY AND MEDICINE
- The role of the gut microbiota in nutrition and health
- (2012) Harry J. Flint et al. Nature Reviews Gastroenterology & Hepatology
- Genomic sequencing of uncultured microorganisms from single cells
- (2012) Roger S. Lasken NATURE REVIEWS MICROBIOLOGY
- The “Most Wanted” Taxa from the Human Microbiome for Whole Genome Sequencing
- (2012) Anthony A. Fodor et al. PLoS One
- Constraint-based modeling analysis of the metabolism of two Pelobacter species
- (2011) Jun Sun et al. BMC Systems Biology
- A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities
- (2011) Eleftheria Tzamali et al. BMC Systems Biology
- Exploring Metabolic Pathway Reconstruction and Genome-Wide Expression Profiling in Lactobacillus reuteri to Define Functional Probiotic Features
- (2011) Delphine M. Saulnier 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
- Competitive and cooperative metabolic interactions in bacterial communities
- (2011) Shiri Freilich et al. Nature Communications
- Systematizing the generation of missing metabolic knowledge
- (2010) Jeffrey D. Orth et al. BIOTECHNOLOGY AND BIOENGINEERING
- Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing
- (2010) Fahimeh Salimi et al. Biotechnology Journal
- A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1
- (2010) Martin I Sigurdsson et al. BMC Systems Biology
- Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models
- (2010) Nathan E Lewis et al. Molecular Systems Biology
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- 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
- Probabilistic integrative modeling of genome-scale metabolic and regulatory networks inEscherichia coliandMycobacterium tuberculosis
- (2010) Sriram Chandrasekaran et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Environments that Induce Synthetic Microbial Ecosystems
- (2010) Niels Klitgord et al. PLoS Computational Biology
- The NIH Human Microbiome Project
- (2009) et al. GENOME RESEARCH
- Applications of genome-scale metabolic reconstructions
- (2009) Matthew A Oberhardt et al. Molecular Systems Biology
- GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions
- (2009) Vinay Satish Kumar et al. PLoS Computational Biology
- Genome-Scale Metabolic Network Analysis of the Opportunistic Pathogen Pseudomonas aeruginosa PAO1
- (2008) M. A. Oberhardt et al. JOURNAL OF BACTERIOLOGY
- The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
- (2008) Adam M Feist et al. NATURE BIOTECHNOLOGY
- Genome-scale analyses of health-promoting bacteria: probiogenomics
- (2008) Marco Ventura et al. NATURE REVIEWS MICROBIOLOGY
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now