| scholarly article | Q13442814 |
| P50 | author | Roie Levy | Q83769861 |
| Elhanan Borenstein | Q107185090 | ||
| P2093 | author name string | Ohad Manor | |
| P2860 | cites work | Whole genome amplification and de novo assembly of single bacterial cells | Q21142771 |
| Environments that induce synthetic microbial ecosystems | Q21563487 | ||
| The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome | Q42648414 | ||
| Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments | Q42743118 | ||
| Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life | Q42918686 | ||
| Genovo: de novo assembly for metagenomes | Q46842122 | ||
| The microbiome as a human organ. | Q55056198 | ||
| A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis | Q22065827 | ||
| Insights into the phylogeny and coding potential of microbial dark matter | Q24490632 | ||
| Obesity alters gut microbial ecology | Q24531503 | ||
| The gut flora as a forgotten organ | Q24550824 | ||
| Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice | Q24568168 | ||
| A human gut microbial gene catalogue established by metagenomic sequencing | Q24618931 | ||
| A whole-cell computational model predicts phenotype from genotype | Q24622101 | ||
| Metagenomic analysis of the human distal gut microbiome | Q24633486 | ||
| Microbial community gene expression in ocean surface waters | Q24651959 | ||
| Identifying bacterial genes and endosymbiont DNA with Glimmer | Q24653724 | ||
| Global reconstruction of the human metabolic network based on genomic and bibliomic data | Q24677060 | ||
| Metagenomics for studying unculturable microorganisms: cutting the Gordian knot | Q24811165 | ||
| Computational meta'omics for microbial community studies | Q26825114 | ||
| An obesity-associated gut microbiome with increased capacity for energy harvest | Q27860515 | ||
| Microbial ecology: human gut microbes associated with obesity | Q27861004 | ||
| The gut microbiota as an environmental factor that regulates fat storage | Q28131676 | ||
| Metabolic network structure determines key aspects of functionality and regulation | Q28214885 | ||
| Programmable bacteria detect and record an environmental signal in the mammalian gut | Q28236112 | ||
| Using the topology of metabolic networks to predict viability of mutant strains | Q28246806 | ||
| What is flux balance analysis? | Q28275348 | ||
| Microbial co-occurrence relationships in the human microbiome | Q28481283 | ||
| Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment | Q28710518 | ||
| Microdroplet-enabled highly parallel co-cultivation of microbial communities | Q28742380 | ||
| Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation | Q28757646 | ||
| APE: Analyses of Phylogenetics and Evolution in R language | Q29546513 | ||
| KEGG for integration and interpretation of large-scale molecular data sets | Q29547277 | ||
| Diet rapidly and reproducibly alters the human gut microbiome | Q29547454 | ||
| The large-scale organization of metabolic networks | Q29547498 | ||
| Community structure and metabolism through reconstruction of microbial genomes from the environment | Q29547528 | ||
| Prodigal: prokaryotic gene recognition and translation initiation site identification | Q29547611 | ||
| A metagenome-wide association study of gut microbiota in type 2 diabetes | Q29547726 | ||
| Comparative metagenomics of microbial communities | Q29555844 | ||
| Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans | Q29614455 | ||
| Gut microbiota from twins discordant for obesity modulate metabolism in mice | Q29614796 | ||
| Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences | Q29615050 | ||
| The vaginal microbiome in health and disease | Q35243537 | ||
| Metabolic modeling of a mutualistic microbial community. | Q35742362 | ||
| Predicting a human gut microbiota's response to diet in gnotobiotic mice | Q35829905 | ||
| Soil metaproteomics - Comparative evaluation of protein extraction protocols. | Q36147433 | ||
| MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads | Q36368703 | ||
| Xenobiotics shape the physiology and gene expression of the active human gut microbiome | Q36554412 | ||
| Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut | Q36564712 | ||
| The evolution of modularity in bacterial metabolic networks. | Q36657624 | ||
| Large-scale reconstruction and phylogenetic analysis of metabolic environments | Q36936268 | ||
| Defined spatial structure stabilizes a synthetic multispecies bacterial community | Q36984976 | ||
| Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla | Q37138595 | ||
| Rules of engagement: interspecies interactions that regulate microbial communities | Q37187806 | ||
| The gastrointestinal microbiota as a site for the biotransformation of drugs | Q37235756 | ||
| Metabolic-network-driven analysis of bacterial ecological strategies | Q37282861 | ||
| Spatial self-organization favors heterotypic cooperation over cheating | Q37295444 | ||
| Mighty small: Observing and modeling individual microbes becomes big science. | Q37318089 | ||
| Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism | Q37318311 | ||
| Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut. | Q37406127 | ||
| Computational deconvolution: extracting cell type-specific information from heterogeneous samples | Q37417280 | ||
| Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage | Q37425722 | ||
| Bacterial colonization factors control specificity and stability of the gut microbiota | Q37483694 | ||
| Sense from sequence reads: methods for alignment and assembly | Q37618545 | ||
| Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis | Q37627585 | ||
| Web of ecological interactions in an experimental gut microbiota | Q37756238 | ||
| Strategies for culture of 'unculturable' bacteria | Q37757054 | ||
| The oral microbiome in health and disease and the potential impact on personalized dental medicine | Q37929297 | ||
| Computational systems biology and in silico modeling of the human microbiome | Q38010422 | ||
| A systems biology approach to studying the role of microbes in human health. | Q38055938 | ||
| Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships | Q38578618 | ||
| Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products | Q39177394 | ||
| Competitive and cooperative metabolic interactions in bacterial communities. | Q39676882 | ||
| Xenobiotics and the human gut microbiome: metatranscriptomics reveal the active players | Q40300533 | ||
| New approaches for isolation of previously uncultivated oral bacteria | Q40311047 | ||
| Computational reconstruction of tissue‐specific metabolic models: application to human liver metabolism | Q41846171 | ||
| An ecological network of polysaccharide utilization among human intestinal symbionts | Q41955485 | ||
| Emergent cooperation in microbial metabolism | Q42397954 | ||
| Topological signatures of species interactions in metabolic networks | Q42592490 | ||
| A de novo metagenomic assembly program for shotgun DNA reads. | Q42643842 | ||
| Strong inter-population cooperation leads to partner intermixing in microbial communities | Q34566652 | ||
| Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities | Q34691436 | ||
| Metaproteomics of our microbiome - developing insight in function and activity in man and model systems | Q34740353 | ||
| Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice | Q34794391 | ||
| Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules | Q34822704 | ||
| Human colonic microbiota associated with diet, obesity and weight loss | Q34823807 | ||
| Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants | Q34830182 | ||
| Science and complexity. | Q34854677 | ||
| Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults | Q34936050 | ||
| Understanding the interactions between bacteria in the human gut through metabolic modeling | Q34975280 | ||
| Genome assembly reborn: recent computational challenges | Q34984047 | ||
| Human gut microbiome adopts an alternative state following small bowel transplantation | Q35006562 | ||
| Synergistic interactions in the microbial world | Q35007709 | ||
| Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution | Q35022283 | ||
| Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota | Q35069150 | ||
| Mathematical modeling of primary succession of murine intestinal microbiota. | Q35075057 | ||
| Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans | Q35080321 | ||
| Environmental and gut bacteroidetes: the food connection. | Q35084646 | ||
| Genome-scale microbial in silico models: the constraints-based approach. | Q35101082 | ||
| Thirteen years of building constraint-based in silico models of Escherichia coli | Q35109629 | ||
| Metatranscriptomics of the human oral microbiome during health and disease | Q35137846 | ||
| Emergent biosynthetic capacity in simple microbial communities | Q35200847 | ||
| Evidence for a core gut microbiota in the zebrafish. | Q35222659 | ||
| Microbiota and SCFA in lean and overweight healthy subjects | Q29615812 | ||
| A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea | Q29616591 | ||
| Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome | Q29617424 | ||
| The impact of the gut microbiota on human health: an integrative view | Q29617446 | ||
| Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation | Q29617796 | ||
| In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data | Q29618471 | ||
| Antibiotic-induced shifts in the mouse gut microbiome and metabolome increase susceptibility to Clostridium difficile infection | Q30066419 | ||
| Evaluation of microbial community reproducibility, stability and composition in a human distal gut chemostat model. | Q31135273 | ||
| Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract | Q33266094 | ||
| Simultaneous assessment of soil microbial community structure and function through analysis of the meta-transcriptome | Q33346229 | ||
| In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. | Q33517877 | ||
| Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood | Q33605558 | ||
| Graph-based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata | Q33691388 | ||
| MetAMOS: a modular and open source metagenomic assembly and analysis pipeline | Q33741975 | ||
| Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules | Q33779279 | ||
| Multispecies communities: interspecies interactions influence growth on saliva as sole nutritional source | Q33870205 | ||
| Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics | Q33900751 | ||
| Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives | Q33959353 | ||
| The large-scale organization of the bacterial network of ecological co-occurrence interactions. | Q33959392 | ||
| Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps | Q34041056 | ||
| A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities | Q34050854 | ||
| Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota | Q34149345 | ||
| OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities | Q34154442 | ||
| IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth | Q34229322 | ||
| Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease | Q34241773 | ||
| Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing | Q34257026 | ||
| Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill | Q34283016 | ||
| Growing unculturable bacteria | Q34290686 | ||
| Lymphotoxin regulates commensal responses to enable diet-induced obesity | Q34295896 | ||
| Reverse Ecology: from systems to environments and back | Q34347514 | ||
| The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria | Q34378530 | ||
| Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization | Q34398619 | ||
| The evolution of mutualism in gut microbiota via host epithelial selection | Q34489494 | ||
| Temporal expression-based analysis of metabolism | Q34499316 | ||
| Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease | Q34499601 | ||
| Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE | Q34509501 | ||
| P433 | issue | 5 | |
| P921 | main subject | metagenomics | Q903778 |
| microbiome | Q1330402 | ||
| P304 | page(s) | 742-752 | |
| P577 | publication date | 2014-08-28 | |
| P1433 | published in | Cell Metabolism | Q1254684 |
| P1476 | title | Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome | |
| P478 | volume | 20 |
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| Q28610549 | Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes |
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