A framework for human microbiome research (scientific article)

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Q93164952	Gut microbes modulate host response to immune checkpoint inhibitor cancer immunotherapy
Q89999726	Gut microbial diversity and genus-level differences identified in cervical cancer patients versus healthy controls
Q35544903	Gut microbial metabolism and colon cancer: can manipulations of the microbiota be useful in the management of gastrointestinal health?
Q37251311	Gut microbiome alterations in patients with stage 4 hepatitis C.
Q64903198	Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study.
Q34826566	Gut microbiome and liver diseases
Q38836354	Gut microbiome in chronic kidney disease: challenges and opportunities
Q47447695	Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients.
Q54942694	Gut microbiomes of wild great apes fluctuate seasonally in response to diet.
Q104466010	Gut microbiota alteration in adolescent anorexia nervosa does not normalize with short-term weight restoration
Q46629674	Gut microbiota analysis reveals a marked shift to bifidobacteria by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446.
Q55428575	Gut microbiota components are associated with fixed airway obstruction in asthmatic patients living in the tropics.
Q35441677	Gut microbiota of humans, dogs and cats: current knowledge and future opportunities and challenges
Q92495254	Gutted! Unraveling the Role of the Microbiome in Major Depressive Disorder
Q39021192	H-BLAST: a fast protein sequence alignment toolkit on heterogeneous computers with GPUs
Q100737106	HLA-A alleles including HLA-A29 affect the composition of the gut microbiome: a potential clue to the pathogenesis of birdshot retinochoroidopathy
Q62732816	HMP16SData: Efficient Access to the Human Microbiome Project Through Bioconductor
Q35844611	HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes
Q33650329	Helminth colonization is associated with increased diversity of the gut microbiota.
Q35597586	Helminths and the microbiota: parts of the hygiene hypothesis.
Q26795715	Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design
Q38031314	High throughput sequencing methods for microbiome profiling: application to food animal systems
Q33835890	High-fat maternal diet during pregnancy persistently alters the offspring microbiome in a primate model
Q47552742	High-resolution microbiome profiling uncovers Fusobacterium nucleatum, Lactobacillus gasseri/johnsonii, and Lactobacillus vaginalis associated to oral and oropharyngeal cancer in saliva from HPV positive and HPV negative patients treated with surger
Q26824148	High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats
Q36671075	Highlights of the 2012 Research Workshop: Using nutrigenomics and metabolomics in clinical nutrition research
Q64057209	Horizontal gene transfer in human-associated microorganisms inferred by phylogenetic reconstruction and reconciliation
Q47706517	Host genetic variation and its microbiome interactions within the Human Microbiome Project
Q28607663	Host genetic variation impacts microbiome composition across human body sites
Q28069401	Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Q34318941	Host-associated bacterial taxa from Chlorobi, Chloroflexi, GN02, Synergistetes, SR1, TM7, and WPS-2 Phyla/candidate divisions
Q26829479	Host-microbe interactions shaping the gastrointestinal environment
Q55081938	Household siblings and nasal and fecal microbiota in infants.
Q41024163	Human Gut Microbiota: Toward an Ecology of Disease
Q57816760	Human Microbe-Disease Association Prediction Based on Adaptive Boosting
Q28085629	Human Microbiome: When a Friend Becomes an Enemy
Q36523766	Human Microbiota of the Argentine Population- A Pilot Study
Q37093117	Human Thanatomicrobiome Succession and Time Since Death
Q35936314	Human colorectal mucosal microbiota correlates with its host niche physiology revealed by endomicroscopy
Q40988509	Human genome-microbiome interaction: metagenomics frontiers for the aetiopathology of autoimmune diseases
Q37582015	Human gut microbes use multiple transporters to distinguish vitamin B₁₂ analogs and compete in the gut.
Q28655573	Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013
Q26779242	Human microbiomes and their roles in dysbiosis, common diseases, and novel therapeutic approaches
Q47874427	Human microbiota, blood group antigens, and disease
Q34423484	ICON: chronic rhinosinusitis
Q58793405	IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
Q37661739	IMG/M 4 version of the integrated metagenome comparative analysis system
Q89763236	IPCO: Inference of Pathways from Co-variance analysis
Q35136984	Identification and characterization of alternative splicing in parasitic nematode transcriptomes
Q31048577	Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers
Q64093410	Identification of Pathogenic Bacteria from Public Libraries via Proteomics Analysis
Q92316643	Identification of Patulin from Penicillium coprobium as a Toxin for Enteric Neurons
Q63383919	Identification of bioactive metabolites using activity metabolomics
Q34158577	Identification of diversity-generating retroelements in human microbiomes
Q34762294	Identification of household bacterial community and analysis of species shared with human microbiome
Q30684641	Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data
Q35854627	Identification of low abundance microbiome in clinical samples using whole genome sequencing
Q37022862	Identification, Recovery, and Refinement of Hitherto Undescribed Population-Level Genomes from the Human Gastrointestinal Tract.
Q35627668	Identifying personal microbiomes using metagenomic codes
Q36306640	Immune disorders and its correlation with gut microbiome
Q37424494	Immunologic Factors in Human Milk and Disease Prevention in the Preterm Infant
Q90812878	Impact of Early Life Antibiotic Exposure and Neonatal Hyperoxia on the Murine Microbiome and Lung Injury
Q64911807	Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis.
Q37123686	Impact of manure fertilization on the abundance of antibiotic-resistant bacteria and frequency of detection of antibiotic resistance genes in soil and on vegetables at harvest
Q38968015	Impact of maternal nutrition in pregnancy and lactation on offspring gut microbial composition and function
Q27025506	Impact of the gut microbiota on the development of obesity and type 2 diabetes mellitus
Q35837709	Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis
Q34538581	Implications of the human microbiome project for epidemiology
Q33594425	Importance of Diversity in the Oral Microbiota including Candida Species Revealed by High-Throughput Technologies
Q35798523	Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering
Q89881666	Improving Characterization of Understudied Human Microbiomes Using Targeted Phylogenetics
Q39385024	Increasing the reach of forensic genetics with massively parallel sequencing
Q36824179	Individuality, Stability, and Variability of the Plaque Microbiome
Q26999090	Individualized medicine and the microbiome in reproductive tract
Q48350060	Indole production provides limited benefit to Escherichia coli during co-culture with Enterococcus faecalis.
Q31149548	Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota
Q30571637	Inferring correlation networks from genomic survey data
Q31150385	Inferring human microbial dynamics from temporal metagenomics data: Pitfalls and lessons
Q35807983	Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease
Q57117487	Inflammation-Related Mechanisms in Chronic Kidney Disease Prediction, Progression, and Outcome
Q63483854	Influence of 4-week multi-strain probiotic administration on resting-state functional connectivity in healthy volunteers
Q35816819	Influence of H7N9 virus infection and associated treatment on human gut microbiota
Q54257322	Influence of fecal collection conditions and 16S rRNA gene sequencing at two centers on human gut microbiota analysis.
Q35956380	Influences of Plant Species, Season and Location on Leaf Endophytic Bacterial Communities of Non-Cultivated Plants
Q47668620	Informatics for Nutritional Genetics and Genomics
Q51391353	Initial insights into bacterial succession during human decomposition.
Q35182581	Insights from 20 years of bacterial genome sequencing
Q37076557	Integrated network-diversity analyses suggest suppressive effect of Hodgkin's lymphoma and slightly relieving effect of chemotherapy on human milk microbiome
Q36449342	Integrating next-generation sequencing and traditional tongue diagnosis to determine tongue coating microbiome
Q38578618	Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships
Q35677348	Inter-Individual Differences in the Oral Bacteriome Are Greater than Intra-Day Fluctuations in Individuals
Q35596087	Inter-individual differences in the gene content of human gut bacterial species
Q55224612	Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples.
Q38709535	Inter-personal diversity and temporal dynamics of dental, tongue, and salivary microbiota in the healthy oral cavity
Q26778722	Interactions Between the Gastrointestinal Microbiome and Clostridium difficile
Q90115049	Intestinal flora imbalance affects bile acid metabolism and is associated with gallstone formation
Q54220496	Intestinal microbial-derived sphingolipids are inversely associated with childhood food allergy.
Q35202957	Intestinal microbiota in metabolic diseases: from bacterial community structure and functions to species of pathophysiological relevance
Q34686359	Investigators' perspectives on translating human microbiome research into clinical practice
Q35599821	Is there interaction between gut microbial profile and cardiovascular risk in chronic kidney disease patients?
Q36764435	Ketone body metabolism and cardiovascular disease
Q36170879	Key Microbiota Identification Using Functional Gene Analysis during Pepper (Piper nigrum L.) Peeling
Q38645220	LRLSHMDA: Laplacian Regularized Least Squares for Human Microbe-Disease Association prediction
Q49994906	La peau : un écosystème microbien: The skin: a microbial ecosystem.
Q52757658	Lactobacillus plantarum LP‑Onlly alters the gut flora and attenuates colitis by inducing microbiome alteration in interleukin‑10 knockout mice.
Q90064938	Large scale microbiome profiling in the cloud
Q38980699	Large-scale 16S gene assembly using metagenomics shotgun sequences
Q45658610	Learned and unlearned concepts in periodontal diagnostics: a 50-year perspective
Q35825456	Library preparation methodology can influence genomic and functional predictions in human microbiome research
Q35231650	Limits to robustness and reproducibility in the demarcation of operational taxonomic units
Q54974865	Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks.
Q35803008	Linking Biosynthetic Gene Clusters to their Metabolites via Pathway- Targeted Molecular Networking
Q49894760	Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats.
Q35151847	Longitudinal analysis of the premature infant intestinal microbiome prior to necrotizing enterocolitis: a case-control study
Q92972311	Longitudinal changes in the gut microbiome of infants on total parenteral nutrition
Q30655697	Looking at microbial metabolism by high-resolution (2)H-NMR spectroscopy
Q38739840	Lung-gut cross-talk: evidence, mechanisms and implications for the mucosal inflammatory diseases.
Q30954158	MICCA: a complete and accurate software for taxonomic profiling of metagenomic data.
Q37228280	MMinte: an application for predicting metabolic interactions among the microbial species in a community.
Q92396954	Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors
Q92348691	Massive metagenomic data analysis using abundance-based machine learning
Q39870861	Maternal Antibiotic Treatment Impacts Development of the Neonatal Intestinal Microbiome and Antiviral Immunity.
Q28085574	Maternal Microbiome and Pregnancy Outcomes That Impact Infant Health: A Review
Q38617172	Maternal microbiomes in preterm birth: Recent progress and analytical pipelines
Q40078675	Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy.
Q34030850	MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm
Q64081328	Measuring sequencer size bias using REcount: a novel method for highly accurate Illumina sequencing-based quantification
Q39056719	Measuring the diversity of the human microbiota with targeted next-generation sequencing
Q35944302	Mechanisms Linking the Gut Microbiome and Glucose Metabolism
Q38875058	Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology
Q35682348	Mechanotransduction: use the force(s).
Q33741975	MetAMOS: a modular and open source metagenomic assembly and analysis pipeline
Q55443060	Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative.
Q35646018	Meta-omics uncover temporal regulation of pathways across oral microbiome genera during in vitro sugar metabolism
Q37678008	MetaDP: a comprehensive web server for disease prediction of 16S rRNA metagenomic datasets
Q38625472	MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling
Q90821363	MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities
Q35033956	MetaRef: a pan-genomic database for comparative and community microbial genomics
Q41052834	Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules
Q35816663	Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment
Q38280837	Metabolic engineering to enhance the value of plants as green factories
Q34003241	Metabolic modeling of common Escherichia coli strains in human gut microbiome
Q21092513	Metabolic reconstruction for metagenomic data and its application to the human microbiome
Q38800832	Metabolite and Microbiome Interplay in Cancer Immunotherapy
Q38197830	Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery
Q35793358	Metabolome progression during early gut microbial colonization of gnotobiotic mice
Q38160492	Metabolomics as a diagnostic tool in gastroenterology
Q47128650	Metagenome Analysis of Bodily Microbiota in a Mouse Model of Alzheimer Disease Using Bacteria-derived Membrane Vesicles in Blood
Q36072273	Metagenome-wide association studies: fine-mining the microbiome
Q35861348	Metagenomic Approach for Identification of the Pathogens Associated with Diarrhea in Stool Specimens
Q30588275	Metagenomic analysis of double-stranded DNA viruses in healthy adults
Q33641834	Metagenomic analysis of the medicinal leech gut microbiota
Q35644620	Metagenomic insights into the bioaerosols in the indoor and outdoor environments of childcare facilities
Q24599864	Metagenomic microbial community profiling using unique clade-specific marker genes
Q35039243	Metagenomic profiling of known and unknown microbes with microbeGPS.
Q35857415	Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria
Q63437587	Metagenomic sequencing of “HPV-negative” condylomas detects novel putative HPV types
Q35179505	Metagenomic sequencing reveals altered metabolic pathways in the oral microbiota of sailors during a long sea voyage
Q36845498	Metagenomic sequencing reveals microbiota and its functional potential associated with periodontal disease
Q35021237	Metagenomic species profiling using universal phylogenetic marker genes
Q33779279	Metagenomic systems biology and metabolic modeling of the human microbiome: from species composition to community assembly rules
Q31140588	Metagenomics and Single-Cell Omics Data Analysis for Human Microbiome Research
Q24288894	Metagenomics for pathogen detection in public health
Q66679812	Metagenomics in ophthalmology: current findings and future prospectives
Q37593138	Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods
Q26747593	Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis
Q26779142	Metagenomics: A New Way to Illustrate the Crosstalk between Infectious Diseases and Host Microbiome
Q35658689	Metaproteomic analysis using the Galaxy framework.
Q55311014	Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis.
Q48239720	Metatranscriptome of human faecal microbial communities in a cohort of adult men.
Q30985772	Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool
Q91662790	Methods for Studying Gut Microbiota: A Primer for Physicians
Q64082276	Michigan cohorts to determine associations of maternal pre-pregnancy body mass index with pregnancy and infant gastrointestinal microbial communities: Late pregnancy and early infancy
Q26749155	Microbes Drive Evolution of Animals and Plants: the Hologenome Concept
Q90114640	Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome
Q34531231	Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring
Q39397814	Microbial biofilms and the human skin microbiome
Q89931322	Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists
Q28679293	Microbial genomics: an increasingly revealing interface in human health and disease
Q34337828	Microbial interactions: from networks to models
Q47192317	Microbial profiling: extend ethnicity of human microbiome
Q28484111	Microbial regulation of glucose metabolism and cell-cycle progression in mammalian colonocytes
Q50801598	Microbiology: Learning about who we are.
Q64085609	Microbiome Learning Repo (ML Repo): A public repository of microbiome regression and classification tasks
Q35077495	Microbiome analysis of stool samples from African Americans with colon polyps.
Q92686610	Microbiome applications for pathology: challenges of low microbial biomass samples during diagnostic testing
Q35105814	Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase
Q35230090	Microbiome diversity and asthma and allergy risk
Q64095720	Microbiome diversity in carriers of fluoroquinolone resistant
Q34478193	Microbiome dynamics of human epidermis following skin barrier disruption.
Q37406119	Microbiome, demystifying the role of microbial communities in the biosphere
Q48030065	Microbiome-health interactions in older people
Q38100615	Microbiomes
Q58572768	Microbiomes Associated With Foods From Plant and Animal Sources
Q46386341	Microbiomes of the normal middle ear and ears with chronic otitis media
Q26781408	Microbiomes: unifying animal and plant systems through the lens of community ecology theory
Q34982363	Microbiomic signatures of psoriasis: feasibility and methodology comparison.
Q92408920	Microbiota and Its Role on Viral Evasion: Is It With Us or Against Us?
Q53688571	Microbiota and metabolic diseases.
Q34525116	Microbiota diversity and gene expression dynamics in human oral biofilms
Q55423917	Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes.
Q35801931	Microbiota in Inflammatory Bowel Disease Pathogenesis and Therapy: Is It All About Diet?
Q29617115	Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour
Q35343786	Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
Q28241240	Minireview: Gut microbiota: the neglected endocrine organ
Q91933893	Minor compositional alterations in faecal microbiota after five weeks and five months storage at room temperature on filter papers
Q35287649	Mitochondrial DNA sequence variation is largely conserved at birth with rare de novo mutations in neonates
Q36101216	MixMC: A Multivariate Statistical Framework to Gain Insight into Microbial Communities
Q55384385	Modulation of Active Gut Microbiota by Lactobacillus rhamnosus GG in a Diet Induced Obesity Murine Model.
Q37280636	Molecular Microbiological Profile of Chronic Suppurative Otitis Media
Q30838403	Molecular Taxonomic Profiling of Bacterial Communities in a Gilthead Seabream (Sparus aurata) Hatchery
Q35599906	Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome.
Q35182493	Molecular ecological tools to decipher the role of our microbial mass in obesity
Q37621335	Molecular pathways: gene-environment interactions regulating dietary fiber induction of proliferation and apoptosis via butyrate for cancer prevention
Q62731347	Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome
Q31157021	Motivations of participants in the citizen science of microbiomics: data from the British Gut Project
Q92383004	Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
Q38793931	Multidrug Efflux Systems in Helicobacter cinaedi
Q35362706	Multiorganismal insects: diversity and function of resident microorganisms
Q110949519	Multiple comparative metagenomics using multisetk-mer counting
Q91719572	MyDGR: a server for identification and characterization of diversity-generating retroelements
Q28069635	Nanosized Drug Delivery Systems in Gastrointestinal Targeting: Interactions with Microbiota
Q40411790	Nasal Airway Microbiota Profile and Severe Bronchiolitis in Infants: A Case-Control Study
Q36340566	Natural product discovery from the human microbiome.
Q89668935	Network analyses in microbiome based on high-throughput multi-omics data
Q59794105	New Insights into Human Nostril Microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a Resource for the Microbiome of the Human Aerodigestive Tract
Q28314889	New classes of self-cleaving ribozymes revealed by comparative genomics analysis
Q27309229	Next generation sequencing data of a defined microbial mock community
Q38061737	Next-generation sequencing in the clinic: promises and challenges
Q38073562	Next-generation sequencing technologies and their impact on microbial genomics.
Q41877598	Niches, population structure and genome reduction in Ochrobactrum intermedium: clues to technology-driven emergence of pathogens
Q34600094	No evidence of harms of probiotic Lactobacillus rhamnosus GG ATCC 53103 in healthy elderly-a phase I open label study to assess safety, tolerability and cytokine responses
Q64067971	Non-host class II ribonucleotide reductase in Thermus viruses: sequence adaptation and host interaction
Q52587021	Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity.
Q35329631	Not all biofluids are created equal: chewing over salivary diagnostics and the epigenome
Q47203079	Novel human microbe-disease association prediction using network consistency projection
Q35585761	Novel systems modeling methodology in comparative microbial metabolomics: identifying key enzymes and metabolites implicated in autism spectrum disorders
Q35665589	Obesity and the microbiome
Q33925806	Oligotyping analysis of the human oral microbiome
Q38750137	Omics for Understanding the Gut-Liver-Microbiome Axis and Precision Medicine
Q35920767	On the Origins and Control of Community Types in the Human Microbiome
Q38898139	On the pathogenesis of insulin-dependent diabetes mellitus: the role of microbiota
Q35966819	One step closer to understanding the role of bacteria in diabetic foot ulcers: characterising the microbiome of ulcers.
Q34952830	Ontogenetic variation in epibiont community structure in the deep-sea yeti crab, Kiwa puravida: convergence among crustaceans
Q36185149	Open-Source Sequence Clustering Methods Improve the State Of the Art.
Q36256376	Optimisation of methods for bacterial skin microbiome investigation: primer selection and comparison of the 454 versus MiSeq platform.
Q29994526	Optimizing methods and dodging pitfalls in microbiome research
Q55339477	Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin.
Q89554883	Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy
Q35163557	Oral cavity contains distinct niches with dynamic microbial communities
Q98952709	Oral microbiome and onset of oral mucositis in patients with squamous cell carcinoma of the head and neck
Q36064426	Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma
Q34769990	Oral microbiome of deep and shallow dental pockets in chronic periodontitis
Q35981566	Oral microbiota: a promising predictor of human oral and systemic diseases
Q39821051	Osmoregulation and the human mycobiome
Q36332158	PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive
Q37657003	PBHMDA: Path-Based Human Microbe-Disease Association Prediction
Q89149012	PERFect: PERmutation Filtering test for microbiome data
Q55513273	PRWHMDA: Human Microbe-Disease Association Prediction by Random Walk on the Heterogeneous Network with PSO.
Q30833683	PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data
Q36872690	Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome
Q57817540	PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features
Q37581528	Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities
Q43422693	Pathology and viral metagenomics, a recent history
Q37417363	Patient-Specific Bacteroides Genome Variants in Pouchitis
Q33551636	Pediatric Obesity and Cardiometabolic Disorders: Risk Factors and Biomarkers
Q33791192	Performing Skin Microbiome Research: A Method to the Madness
Q55257306	Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses.
Q40876404	Phage-bacteria interaction network in human oral microbiome.
Q38124254	Pharmacometabonomics and personalized medicine
Q90596621	Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota
Q34692435	Phylogenetics and the human microbiome
Q91709676	Plasmid detection and assembly in genomic and metagenomic data sets
Q89544426	Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens
Q35589413	Power and sample-size estimation for microbiome studies using pairwise distances and PERMANOVA
Q35788482	Power law analysis of the human microbiome
Q46464238	Prebiotic potential of L-sorbose and xylitol in promoting the growth and metabolic activity of specific butyrate-producing bacteria in human fecal culture
Q42350237	Precision Medicine
Q55040682	Precision medicine: the foundation of future cancer therapeutics.
Q94464342	Predicting Microbe-Disease Association by Learning Graph Representations and Rule-Based Inference on the Heterogeneous Network
Q89965298	Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa
Q42656052	Prediction of microbe-disease association from the integration of neighbor and graph with collaborative recommendation model
Q36329323	Prediction of virus-host infectious association by supervised learning methods.
Q38667894	Preliminary Evidence for an Association Between the Composition of the Gut Microbiome and Cognitive Function in Neurologically Healthy Older Adults
Q35886804	Presence of mycobacterial L-forms in human blood: Challenge of BCG vaccination
Q40614261	Primer and platform effects on 16S rRNA tag sequencing
Q36151837	Probing the diversity of healthy oral microbiome with bioinformatics approaches
Q64910852	Probiotics in Extraintestinal Diseases: Current Trends and New Directions.
Q38921638	Probiotics, gut microbiota, and their influence on host health and disease.
Q37684976	Problems and prospects of current studies on the microecology of tongue coating
Q33611925	Processing faecal samples: a step forward for standards in microbial community analysis
Q46251646	Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing
Q35540747	Progress and challenges in developing metabolic footprints from diet in human gut microbial cometabolism
Q57142155	Progress of analytical tools and techniques for human gut microbiome research
Q37717517	Proteobacteria explain significant functional variability in the human gut microbiome.
Q90641992	Protocol for a Longitudinal Analysis of the Vaginal Microbiome from a Pregnant Cohort of African Women in Nigeria
Q34768472	Pyrosequencing analysis of the human microbiota of healthy Chinese undergraduates
Q52613233	Quantification of Human Microbiome Stability Over Six Months: Implications for Epidemiologic Studies.
Q28272991	Quantifying your body: a how-to guide from a systems biology perspective
Q36641649	Quantitation and composition of cutaneous microbiota in diabetic and nondiabetic men.
Q35182932	Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments
Q30941690	RVD2: an ultra-sensitive variant detection model for low-depth heterogeneous next-generation sequencing data.
Q34768924	Random sampling process leads to overestimation of β-diversity of microbial communities
Q40324507	Randomised clinical trial: faecal microbiota transplantation for recurrent Clostridum difficile infection - fresh, or frozen, or lyophilised microbiota from a small pool of healthy donors delivered by colonoscopy.
Q34499358	Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology
Q39153870	Rapid replacement by non-vaccine pneumococcal serotypes may mitigate the impact of the pneumococcal conjugate vaccine on nasopharyngeal bacterial ecology
Q90396533	Recent Advancements in Intestinal Microbiota Analyses: A Review for Non-Microbiologists
Q34431538	Reconceptualizing major depressive disorder as an infectious disease
Q35022283	Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution
Q35085994	Recruiting human microbiome shotgun data to site-specific reference genomes
Q38669617	Reference standards for next-generation sequencing
Q39443984	Regulation of inflammation by microbiota interactions with the host.
Q36685310	Regulation of intestinal microbiota by the NLR protein family
Q33730723	Relating the metatranscriptome and metagenome of the human gut.
Q47559233	ReprDB and panDB: minimalist databases with maximal microbial representation
Q39189413	Reproductive Microbiomes
Q38417651	Reprogramming of human somatic cells by bacteria.
Q35032072	Research on neonatal microbiomes: what neonatologists need to know
Q36397518	Reshaping Darwin's Tree: Impact of the Symbiome
Q28081298	Resistance and tolerance to foreign elements by prokaryotic immune systems - curating the genome
Q46251995	Resources and tools for the high-throughput, multi-omic study of intestinal microbiota
Q36984593	Respiratory syncytial virus and rhinovirus severe bronchiolitis are associated with distinct nasopharyngeal microbiota
Q43750030	Response to the commentaries on the paper: Propionibacterium acnes strain populations in the human skin microbiome associated with acne
Q90950487	Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels
Q57231381	Rhizosphere bacteria and fungi associated with plant growth in soils of three replanted apple orchards
Q36392081	Rodent models to study the relationships between mammals and their bacterial inhabitants
Q35801939	Role of the Gut Microbiome in Obesity and Diabetes Mellitus
Q33613115	Role of the Gut Microbiome in Uremia: A Potential Therapeutic Target
Q36886503	Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ
Q34407175	Role of the gut microbiota in inflammatory bowel disease pathogenesis: what have we learnt in the past 10 years?
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P6179	Dimensions Publication ID	1027248000
P356	DOI	10.1038/NATURE11209
P3181	OpenCitations bibliographic resource ID	92274
P932	PMC publication ID	3377744
P698	PubMed publication ID	22699610
P5875	ResearchGate publication ID	225308981

P50	author	George Weinstock	Q5546130
		Jeroen Raes	Q50285889
		Jacques Izard	Q50286720
		Curtis Huttenhower	Q19397499
		Rob Knight	Q20657126
		Makedonka Mitreva	Q28805278
		Lynn Schriml	Q28913673
		Jacques Ravel	Q30093147
		Janet K Jansson	Q52358628
		Ruth Ley	Q52672991
		Mircea Podar	Q54114979
		Kathie A Mihindukulasuriya	Q55474161
		Nicholas B King	Q56550545
		Vivien R. Bonazzi	Q56875421
		Tatyana Vishnivetskaya	Q57002985
		Jeffery A Schloss	Q57011035
		Matthew C. Ross	Q59539083
		Shibu Yooseph	Q60639037
		Fah J. Sathirapongsasuti	Q60668552
		Konstantinos Mavrommatis	Q64362448
		M. Nathalia Garcia	Q64786831
		Mihai Pop	Q102229170
		Jennifer R Wortman	Q30347966
		Nicola Segata	Q30348945
		Nikos C. Kyrpides	Q30348949
		Jeremy Zucker	Q30513835
		Sean Conlan	Q32640745
		Patrick D. Schloss	Q37391412
		Omry Koren	Q41048834
		Heidi H. Kong	Q42556182
		Ashlee Earl	Q43144023
		Gary L Andersen	Q44016653
		Thomas M. Schmidt	Q46832703
		Sergey Koren	Q47451219
P2860	cites work	Metabolic reconstruction for metagenomic data and its application to the human microbiome	Q21092513
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		QIIME allows analysis of high-throughput community sequencing data	Q24616873
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		Structure, function and diversity of the healthy human microbiome	Q24626370
		The NIH Human Microbiome Project	Q24642619
		eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations	Q24644077
		Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities	Q24647611
		Search and clustering orders of magnitude faster than BLAST	Q29547431
		Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates	Q29616592
		Accuracy and quality of massively parallel DNA pyrosequencing	Q29622857
		Hypothesis testing and power calculations for taxonomic-based human microbiome data	Q30584286
		A catalog of reference genomes from the human microbiome	Q33583040
		Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies	Q34109852
		Microbial metagenomics: beyond the genome	Q34165228
		Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem	Q34298942
		A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP)	Q34311659
		Optimizing read mapping to reference genomes to determine composition and species prevalence in microbial communities	Q34311700
		Evaluation of 16S rDNA-based community profiling for human microbiome research	Q34312366
P275	copyright license	Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported	Q15643954
P6216	copyright status	copyrighted	Q50423863
P433	issue	7402
P407	language of work or name	English	Q1860
P921	main subject	microbiome	Q1330402
P304	page(s)	215-21
P577	publication date	2012-06-14
P1433	published in	Nature	Q180445
P1476	title	A framework for human microbiome research
P478	volume	486

A framework for human microbiome research

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