| scholarly article | Q13442814 |
| P8978 | DBLP publication ID | journals/ploscb/FriedmanA12 |
| P356 | DOI | 10.1371/JOURNAL.PCBI.1002687 |
| P932 | PMC publication ID | 3447976 |
| P698 | PubMed publication ID | 23028285 |
| P5875 | ResearchGate publication ID | 231742899 |
| P50 | author | Eric J. Alm | Q88440801 |
| P2093 | author name string | Jonathan Friedman | |
| P2860 | cites work | A framework for human microbiome research | Q24602401 |
| Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons | Q29614292 | ||
| The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity | Q33332445 | ||
| Ironing out the wrinkles in the rare biosphere through improved OTU clustering | Q33541671 | ||
| Illumina-based analysis of microbial community diversity | Q33934016 | ||
| Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies | Q34109852 | ||
| Microbial community resemblance methods differ in their ability to detect biologically relevant patterns | Q34168516 | ||
| Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata | Q34700457 | ||
| Microbiology in the post-genomic era. | Q37162151 | ||
| P275 | copyright license | Creative Commons Attribution 4.0 International | Q20007257 |
| P6216 | copyright status | copyrighted | Q50423863 |
| P433 | issue | 9 | |
| P304 | page(s) | e1002687 | |
| P577 | publication date | 2012-09-20 | |
| P1433 | published in | PLOS Computational Biology | Q2635829 |
| P1476 | title | Inferring correlation networks from genomic survey data | |
| P478 | volume | 8 |
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| Q92890552 | A Microbiome Study Reveals Seasonal Variation in Endophytic Bacteria Among different Mulberry Cultivars |
| Q64070036 | A New Method to Correct for Habitat Filtering in Microbial Correlation Networks |
| Q36010465 | A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments |
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| Q90207879 | A field guide for the compositional analysis of any-omics data |
| Q48121310 | A human gut phage catalog correlates the gut phageome with type 2 diabetes. |
| Q58800559 | A metagenomic study of the gut microbiome in Behcet's disease |
| Q49843935 | A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera. |
| Q21559533 | A modular organization of the human intestinal mucosal microbiota and its association with inflammatory bowel disease |
| Q35781450 | A multi-platform metabolomics approach identifies highly specific biomarkers of bacterial diversity in the vagina of pregnant and non-pregnant women |
| Q42687933 | A multivariate distance-based analytic framework for microbial interdependence association test in longitudinal study. |
| Q99608541 | A network approach to elucidate and prioritize microbial dark matter in microbial communities |
| Q28084823 | A network-based approach to disturbance transmission through microbial interactions |
| Q35648525 | A null model for Pearson coexpression networks |
| Q36280857 | A phylogenetic transform enhances analysis of compositional microbiota data |
| Q57459082 | A primer on investigating the role of the microbiome in brain and cognitive development |
| Q95660240 | A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities |
| Q91808470 | A sparse covarying unit that describes healthy and impaired human gut microbiota development |
| Q64064286 | A theoretical framework for controlling complex microbial communities |
| Q34812367 | ANOVA-like differential expression (ALDEx) analysis for mixed population RNA-Seq |
| Q48102092 | Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome |
| Q36970731 | Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium |
| Q57492086 | Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future |
| Q64284339 | Age-based dynamic changes of phylogenetic composition and interaction networks of health pig gut microbiome feeding in a uniformed condition |
| Q64124389 | Airway Microbiota Is Associated with Upregulation of the PI3K Pathway in Lung Cancer |
| Q90347606 | Alterations in Gut Microbiota of Gestational Diabetes Patients During the First Trimester of Pregnancy |
| Q90744374 | Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer |
| Q96685651 | Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms |
| Q90754502 | Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men |
| Q90189684 | An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome |
| Q92787893 | An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data |
| Q58611298 | An exploration of Prevotella-rich microbiomes in HIV and men who have sex with men |
| Q35002637 | An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile |
| Q41474970 | Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing |
| Q58605400 | Analysis and correction of compositional bias in sparse sequencing count data |
| Q34916610 | Analysis of changes in diversity and abundance of the microbial community in a cystic fibrosis patient over a multiyear period |
| Q35668886 | Analysis of composition of microbiomes: a novel method for studying microbial composition |
| Q103836644 | Analysis of microbial compositions: a review of normalization and differential abundance analysis |
| Q46798481 | Application of a single-colony coculture technique to the isolation of hitherto unculturable gut bacteria |
| Q36625923 | Application of multivariate statistical techniques in microbial ecology |
| Q35648753 | Aquarium microbiome response to ninety-percent system water change: Clues to microbiome management |
| Q64076189 | Archaeorhizomycetes Spatial Distribution in Soils Along Wide Elevational and Environmental Gradients Reveal Co-abundance Patterns With Other Fungal Saprobes and Potential Weathering Capacities |
| Q39520053 | Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children |
| Q35622649 | Atmospheric N deposition alters connectance, but not functional potential among saprotrophic bacterial communities. |
| Q97883401 | BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment |
| Q39739252 | BMPOS: a Flexible and User-Friendly Tool Sets for Microbiome Studies |
| Q47115071 | Bacterial alterations in salivary microbiota and their association in oral cancer |
| Q60644957 | Bacterial community activity and dynamics in the biofilm of an experimental hybrid wetland system treating greywater |
| Q60046532 | Bacterial diversity and community in Qula from the Qinghai-Tibetan Plateau in China |
| Q37604562 | Balance Trees Reveal Microbial Niche Differentiation. |
| Q46237897 | Balanced Fertilization Decreases Environmental Filtering on Soil Bacterial Community Assemblage in North China |
| Q58002986 | Bayesian-multiplicative treatment of count zeros in compositional data sets |
| Q60547176 | Best practices for analysing microbiomes |
| Q55397115 | Bioactive polyamine production by a novel hybrid system comprising multiple indigenous gut bacterial strategies. |
| Q42662790 | Biogeographic variation in the microbiome of the ecologically important sponge, Carteriospongia foliascens. |
| Q38655478 | Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities. |
| Q33744957 | Biogeography of the ecosystems of the healthy human body |
| Q33682296 | Bioinformatic Approaches Including Predictive Metagenomic Profiling Reveal Characteristics of Bacterial Response to Petroleum Hydrocarbon Contamination in Diverse Environments. |
| Q28072941 | Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System |
| Q46260772 | Body size phenotypes comprehensively assess cardiometabolic risk and refine the association between obesity and gut microbiota |
| Q94570343 | Body-size Scaling is Related to Gut Microbial Diversity, Metabolism and Dietary Niche of Arboreal Folivorous Flying Squirrels |
| Q30966997 | CCLasso: correlation inference for compositional data through Lasso |
| Q92668185 | Campylobacter Abundance in Breastfed Infants and Identification of a New Species in the Global Enterics Multicenter Study |
| Q34594904 | Can you sequence ecology? Metagenomics of adaptive diversification |
| Q38376483 | Challenges in microbial ecology: building predictive understanding of community function and dynamics |
| Q57110689 | Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection |
| Q28828954 | Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds |
| Q92925864 | Characteristic dysbiosis of gut microbiota of Chinese patients with diarrhea-predominant irritable bowel syndrome by an insight into the pan-microbiome |
| Q92058227 | Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust |
| Q57099069 | Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions |
| Q35999188 | Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments |
| Q45210170 | Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee. |
| Q36968301 | Characterization of the gut microbiome in epidemiologic studies: the multiethnic cohort experience |
| Q96608935 | Characterizing dysbiosis of gut microbiome in PD: evidence for overabundance of opportunistic pathogens |
| Q92130881 | Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic Ocean |
| Q30699134 | Climate change alters ecological strategies of soil bacteria. |
| Q87898051 | Clustering network layers with the strata multilayer stochastic block model |
| Q60045830 | Co-existence of multiple bacterivorous clevelandellid ciliate species in hindgut of wood-feeding cockroaches in light of their prokaryotic consortium |
| Q36875170 | Co-occurrence Analysis of Microbial Taxa in the Atlantic Ocean Reveals High Connectivity in the Free-Living Bacterioplankton |
| Q37384237 | CoNet app: inference of biological association networks using Cytoscape. |
| Q38668200 | Cohesion: a method for quantifying the connectivity of microbial communities |
| Q89889603 | Coinfinder: detecting significant associations and dissociations in pangenomes |
| Q34714359 | Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle. |
| Q62802243 | Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment |
| Q64226670 | Combined Metabarcoding and Co-occurrence Network Analysis to Profile the Bacterial, Fungal and Communities and Their Interactions in Maize Stalks |
| Q94671805 | Combining whole-genome shotgun sequencing and rRNA gene amplicon analyses to improve detection of microbe-microbe interaction networks in plant leaves |
| Q58695409 | Community Structure, Dynamics and Interactions of Bacteria, Archaea and Fungi in Subtropical Coastal Wetland Sediments |
| Q38914938 | Community dynamics drive punctuated engraftment of the fecal microbiome following transplantation using freeze-dried, encapsulated fecal microbiota. |
| Q94671416 | Community-level signatures of ecological succession in natural bacterial communities |
| Q47249231 | Comparative Metagenomics |
| Q90048032 | Comparative Study on Different Remediation Strategies Applied in Petroleum-Contaminated Soils |
| Q39544929 | Comparative assessment of differential network analysis methods |
| Q89561592 | Comparing Analytical Methods for the Gut Microbiome and Aging: Gut Microbial Communities and Body Weight in the Osteoporotic Fractures in Men (MrOS) Study |
| Q57810831 | Competitive lottery-based assembly of selected clades in the human gut microbiome |
| Q47158099 | Composition of Micro-eukaryotes on the Skin of the Cascades Frog (Rana cascadae) and Patterns of Correlation between Skin Microbes and Batrachochytrium dendrobatidis |
| Q31108768 | Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data |
| Q26825114 | Computational meta'omics for microbial community studies |
| Q35208886 | Conducting a microbiome study |
| Q91071918 | Consecutive lactate formation and chain elongation to reduce exogenous chemicals input in repeated-batch food waste fermentation |
| Q38604864 | Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly |
| Q52607020 | Constructing Lightweight And Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA). |
| Q60916326 | Copper Affects Composition and Functioning of Microbial Communities in Marine Biofilms at Environmentally Relevant Concentrations |
| Q33743142 | Correlating microbial diversity patterns with geochemistry in an extreme and heterogeneous environment of mine tailings. |
| Q31048490 | Correlation detection strategies in microbial data sets vary widely in sensitivity and precision. |
| Q94545232 | Correlations Between Prokaryotic Microbes and Stress-Resistant Algae in Different Corals Subjected to Environmental Stress in Hong Kong |
| Q36209280 | Cross-biome comparison of microbial association networks |
| Q33849220 | Deciphering biodiversity and interactions between bacteria and microeukaryotes within epilithic biofilms from the Loue River, France. |
| Q39923601 | Deciphering microbial interactions and detecting keystone species with co-occurrence networks |
| Q92621834 | Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia |
| Q40486127 | Deciphering the Pathobiome: Intra- and Interkingdom Interactions Involving the Pathogen Erysiphe alphitoides |
| Q59329004 | Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women |
| Q92097882 | Defining microbial biomarkers for risk of preterm labor |
| Q33917852 | Demonstrating microbial co-occurrence pattern analyses within and between ecosystems |
| Q35902683 | Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota |
| Q92156775 | Detecting interaction networks in the human microbiome with conditional Granger causality |
| Q49445263 | Detection of stable community structures within gut microbiota co-occurrence networks from different human populations. |
| Q30412052 | Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition |
| Q29547454 | Diet rapidly and reproducibly alters the human gut microbiome |
| Q37629945 | Differences in Gut Metabolites and Microbial Composition and Functions between Egyptian and U.S. Children Are Consistent with Their Diets |
| Q36794186 | Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms. |
| Q33566352 | Differential abundance analysis for microbial marker-gene surveys |
| Q31155436 | Differential correlation for sequencing data. |
| Q52372053 | Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia. |
| Q92726018 | Difficulty in inferring microbial community structure based on co-occurrence network approaches |
| Q35023834 | Diffuse symbioses: roles of plant-plant, plant-microbe and microbe-microbe interactions in structuring the soil microbiome. |
| Q92146713 | Direct interaction network and differential network inference from compositional data via lasso penalized D-trace loss |
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| Q46253067 | Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes |
| Q39028873 | Disentangling Interactions in the Microbiome: A Network Perspective |
| Q37504387 | Disentangling the influence of earthworms in sugarcane rhizosphere. |
| Q92088273 | Disentangling the mechanisms shaping the surface ocean microbiota |
| Q60949727 | Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study |
| Q37157483 | Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms. |
| Q92765247 | Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma |
| Q37190070 | Distinctly altered gut microbiota in the progression of liver disease |
| Q37287119 | Distinguishing the Signals of Gingivitis and Periodontitis in Supragingival Plaque: a Cross-Sectional Cohort Study in Malawi. |
| Q46250587 | Diversity and Cyclical Seasonal Transitions in the Bacterial Community in a Large and Deep Perialpine Lake |
| Q35826608 | Diversity of key players in the microbial ecosystems of the human body |
| Q89720792 | Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed |
| Q92686073 | Dynamic and Asymmetric Changes of the Microbial Communities after Cohousing in Laboratory Mice |
| Q59136262 | Dynamic linear models guide design and analysis of microbiota studies within artificial human guts |
| Q33917859 | Dynamic models of the complex microbial metapopulation of lake mendota |
| Q64056791 | Dynamics of archaeal community in soil with application of composted tannery sludge |
| Q34284501 | Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning |
| Q51093231 | Dysbiosis is not an answer. |
| Q37670397 | Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome |
| Q59360929 | Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus |
| Q46256745 | Dysbiosis of the microbiome in gastric carcinogenesis |
| Q46267301 | Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake |
| Q35069150 | Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota |
| Q33767505 | Ecological networking of cystic fibrosis lung infections |
| Q96127845 | Ecological succession in the vaginal microbiota during pregnancy and birth |
| Q57046504 | Effects of Phytoremediation Treatment on Bacterial Community Structure and Diversity in Different Petroleum-Contaminated Soils |
| Q37257667 | Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis) |
| Q35609377 | Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism |
| Q99207553 | Effects of environmental factors on microbiota of fruits and soil of Coffea arabica in Brazil |
| Q91615778 | Effects of protease and phytase supplements on small intestinal microbiota and amino acid digestibility in broiler chickens |
| Q35023973 | Emergence shapes the structure of the seed microbiota |
| Q37229478 | Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. |
| Q93347337 | Enteric fungal microbiota dysbiosis and ecological alterations in colorectal cancer |
| Q46458655 | Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans |
| Q64890630 | Establishing microbial composition measurement standards with reference frames. |
| Q99234004 | Ethnic variation of oral microbiota in children |
| Q60044669 | Evaluating the profound effect of gut microbiome on host appetite in pigs |
| Q37676116 | Evidence for greater production of colonic short-chain fatty acids in overweight than lean humans. |
| Q46891920 | Evidence of global-scale aeolian dispersal and endemism in isolated geothermal microbial communities of Antarctica |
| Q57735585 | Evolutionary trends in host physiology outweigh dietary niche in structuring primate gut microbiomes |
| Q36012672 | Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR. |
| Q36134469 | Expanding the UniFrac Toolbox |
| Q47168166 | Experimental design and quantitative analysis of microbial community multiomics |
| Q100635895 | Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy |
| Q64075214 | Explore mediated co-varying dynamics in microbial community using integrated local similarity and liquid association analysis |
| Q89494720 | Exploring Soil Factors Determining Composition and Structure of the Bacterial Communities in Saline-Alkali Soils of Songnen Plain |
| Q93048639 | Exploring the Hospital Microbiome by High-Resolution 16S rRNA Profiling |
| Q27318788 | Expression of the Blood-Group-Related Gene B4galnt2 Alters Susceptibility to Salmonella Infection |
| Q37223239 | Extreme Dysbiosis of the Microbiome in Critical Illness |
| Q90395020 | Faecal microbiota and functional capacity associated with weaning weight in meat rabbits |
| Q90629044 | Framework for rational donor selection in fecal microbiota transplant clinical trials |
| Q57295505 | Functional shifts in microbial mats recapitulate early Earth metabolic transitions |
| Q46507362 | Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere |
| Q39366659 | Fungal dysbiosis: immunity and interactions at mucosal barriers. |
| Q48241173 | Fungi stabilize connectivity in the lung and skin microbial ecosystems |
| Q92379790 | GenePiper, a Graphical User Interface Tool for Microbiome Sequence Data Mining |
| Q56536590 | Generalized Hotelling's test for paired compositional data with application to human microbiome studies |
| Q57281301 | Geospatial variation in co-occurrence networks of nitrifying microbial guilds |
| Q91583846 | Glacial Runoff Promotes Deep Burial of Sulfur Cycling-Associated Microorganisms in Marine Sediments |
| Q36875942 | Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups |
| Q33786338 | Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. |
| Q91869147 | Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification |
| Q93086302 | Gut Microbiota Has a Widespread and Modifiable Effect on Host Gene Regulation |
| Q46274080 | Gut Microbiota Perturbations in Reactive Arthritis and Post-Infectious Spondyloarthritis. |
| Q98386045 | Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity |
| Q35635816 | Gut microbial succession follows acute secretory diarrhea in humans |
| Q92358237 | Gut microbiome associated with APC gene mutation in patients with intestinal adenomatous polyps |
| Q59803911 | Gut microbiome transition across a lifestyle gradient in Himalaya |
| Q60384919 | Gut microbiota is associated with obesity and cardiometabolic disease in a population in the midst of Westernization |
| Q35826754 | Gut mucosal microbiome across stages of colorectal carcinogenesis. |
| Q89494763 | High Diversity and Functional Complementation of Alimentary Canal Microbiota Ensure Small Brown Planthopper to Adapt Different Biogeographic Environments |
| Q43033147 | High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs |
| Q38924657 | High-resolution characterization of the human microbiome |
| Q46306996 | Host Genetic Control of the Oral Microbiome in Health and Disease |
| Q27341819 | Host Gut Motility Promotes Competitive Exclusion within a Model Intestinal Microbiota |
| Q37618401 | Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. |
| Q92727691 | Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle |
| Q35229455 | Host lifestyle affects human microbiota on daily timescales |
| Q31036697 | How should we measure proportionality on relative gene expression data? |
| Q36314112 | How to make more out of community data? A conceptual framework and its implementation as models and software |
| Q30756107 | Human papillomavirus community in healthy persons, defined by metagenomics analysis of human microbiome project shotgun sequencing data sets |
| Q42654482 | IL-17 signalling restructures the nasal microbiome and drives dynamic changes following Streptococcus pneumoniae colonization |
| Q98568275 | IMPARO: inferring microbial interactions through parameter optimisation |
| Q94502711 | Identification of Complex Rumen Microbiome Interaction Within Diverse Functional Niches as Mechanisms Affecting the Variation of Methane Emissions in Bovine |
| Q45070013 | Identification of microbiota dynamics using robust parameter estimation methods |
| Q64109752 | Identification of the Bacterial Biosynthetic Gene Clusters of the Oral Microbiome Illuminates the Unexplored Social Language of Bacteria during Health and Disease |
| Q33939979 | Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression |
| Q60920960 | Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children |
| Q43363370 | Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater |
| Q93163472 | Implication of gut microbiota in the association between infant antibiotic exposure and childhood obesity and adiposity accumulation |
| Q52619003 | In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis. |
| Q58553925 | Inference of Significant Microbial Interactions From Longitudinal Metagenomics Data |
| Q36188744 | Inferring Weighted Directed Association Network from Multivariate Time Series with a Synthetic Method of Partial Symbolic Transfer Entropy Spectrum and Granger Causality |
| Q36306297 | Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters |
| Q28651833 | Inferring meaningful communities from topology-constrained correlation networks |
| Q35345453 | Inferring microbial interaction networks based on consensus similarity network fusion |
| Q36329384 | Inferring microbial interaction networks from metagenomic data using SgLV-EKF algorithm |
| Q47658309 | Influence of resistance breeding in common bean on rhizosphere microbiome composition and function |
| Q92302733 | Inhibition of urinary stone disease by a multi-species bacterial network ensures healthy oxalate homeostasis |
| Q35840705 | Inhibitory bacteria reduce fungi on early life stages of endangered Colorado boreal toads (Anaxyrus boreas). |
| Q92921919 | Insight Into the Microbial Co-occurrence and Diversity of 73 Grapevine (Vitis vinifera) Crown Galls Collected Across the Northern Hemisphere |
| Q35692860 | Insights into the pan-microbiome: skin microbial communities of Chinese individuals differ from other racial groups |
| Q89495343 | Integrating Computational Methods to Investigate the Macroecology of Microbiomes |
| Q36409064 | Integrating Microbiome and Metabolome Data to Understand Infectious Airway Disease |
| 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 |
| Q55364506 | Interaction between Host MicroRNAs and the Gut Microbiota in Colorectal Cancer. |
| Q47862341 | Interactions between species introduce spurious associations in microbiome studies. |
| Q93010095 | Interactions between the gut microbiome and host gene regulation in cystic fibrosis |
| Q34889744 | Interactions in the microbiome: communities of organisms and communities of genes |
| Q58038972 | Interplay between gut microbiota metabolism and inflammation in HIV infection |
| Q35986664 | Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle |
| Q38863317 | Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies |
| Q30972903 | Investigating microbial co-occurrence patterns based on metagenomic compositional data. |
| Q90009717 | Japanese subgingival microbiota in health vs disease and their roles in predicted functions associated with periodontitis |
| Q92163369 | Jatrorrhizine Balances the Gut Microbiota and Reverses Learning and Memory Deficits in APP/PS1 transgenic mice |
| Q88778845 | Keystone taxa as drivers of microbiome structure and functioning |
| Q59137004 | Lactobacillus elicits a 'Marmite effect' on the chicken cecal microbiome |
| Q40464293 | Land scale biogeography of arsenic biotransformation genes in estuarine wetland. |
| Q50420625 | Large Blooms of Bacillales (Firmicutes) Underlie the Response to Wetting of Cyanobacterial Biocrusts at Various Stages of Maturity. |
| Q51801750 | Large pseudocounts and L2-norm penalties are necessary for the mean-field inference of Ising and Potts models. |
| Q35980546 | Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community |
| Q90065032 | Learning a mixture of microbial networks using minorization-maximization |
| Q91106801 | Learning representations of microbe-metabolite interactions |
| Q57003547 | Limitations of Correlation-Based Inference in Complex Virus-Microbe Communities |
| Q35770107 | Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota |
| Q54974865 | Linking Associations of Rare Low-Abundance Species to Their Environments by Association Networks. |
| Q41623323 | Linking Spatial Structure and Community-Level Biotic Interactions through Cooccurrence and Time Series Modeling of the Human Intestinal Microbiota. |
| Q46245573 | Location, Root Proximity, and Glyphosate-Use History Modulate the Effects of Glyphosate on Fungal Community Networks of Wheat |
| Q89820550 | Long-Term Effects of Multi-Drug-Resistant Tuberculosis Treatment on Gut Microbiota and Its Health Consequences |
| Q92383029 | Longitudinal multi-omics of host-microbe dynamics in prediabetes |
| Q91283730 | Loss of function dysbiosis associated with antibiotics and high fat, high sugar diet |
| Q45895724 | Loss of microbial diversity in soils is coincident with reductions in some specialized functions. |
| Q90597054 | Lotus japonicus Symbiosis Genes Impact Microbial Interactions between Symbionts and Multikingdom Commensal Communities |
| Q44995961 | Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants. |
| Q36040381 | MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses. |
| Q47215897 | MPLasso: Inferring microbial association networks using prior microbial knowledge |
| Q35337210 | MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome |
| Q37549123 | Machine learning techniques accurately classify microbial communities by bacterial vaginosis characteristics. |
| Q46243438 | Mapping the ecological networks of microbial communities. |
| Q92423134 | Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference |
| Q33891018 | Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans |
| Q35075057 | Mathematical modeling of primary succession of murine intestinal microbiota. |
| Q101166847 | Maturation of the gut microbiome during the first year of life contributes to the protective farm effect on childhood asthma |
| Q28822085 | Membrane filter method to study the effects of Lactobacillus acidophilus and Bifidobacterium longum on fecal microbiota |
| Q91933613 | Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue |
| Q30829857 | MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles |
| Q26799830 | Metabolic interactions in microbial communities: untangling the Gordian knot |
| Q83231503 | Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome |
| Q55242479 | Metagenomic Insights Into the Microbial Community and Nutrient Cycling in the Western Subarctic Pacific Ocean. |
| Q26747593 | Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis |
| Q34142801 | Metagenomics, paratransgenesis and the Anopheles microbiome: a portrait of the geographical distribution of the anopheline microbiota based on a meta-analysis of reported taxa. |
| Q90754117 | Microbe-host interplay in atopic dermatitis and psoriasis |
| Q35844002 | Microbial "social networks". |
| Q91740124 | Microbial Co-Occurrence Patterns and Keystone Species in the Gut Microbial Community of Mice in Response to Stress and Chondroitin Sulfate Disaccharide |
| Q58547081 | Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival |
| Q93062859 | Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data |
| Q64109958 | Microbial and metabolic succession on common building materials under high humidity conditions |
| Q31030229 | Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake |
| Q46357278 | Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient |
| Q35676513 | Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers |
| Q47149781 | Microbiome Datasets Are Compositional: And This Is Not Optional. |
| Q36069076 | Microbiome-wide association studies link dynamic microbial consortia to disease |
| Q47096559 | Microbiota Diversification and Crash Induced by Dietary Oxalate in the Mammalian Herbivore Neotoma albigula |
| Q93166938 | Microbiotyping the Sinonasal Microbiome |
| Q36064477 | Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes |
| Q89686266 | Model-based Comparisons of the Abundance Dynamics of Bacterial Communities in Two Lakes |
| Q92134921 | Modelling approaches for studying the microbiome |
| Q38647960 | Mucosal microbiome dysbiosis in gastric carcinogenesis. |
| Q55243928 | Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers. |
| Q33775089 | Multigenerational Influences of the Fut2 Gene on the Dynamics of the Gut Microbiota in Mice |
| Q30871031 | Multilevel regularized regression for simultaneous taxa selection and network construction with metagenomic count data |
| Q89668935 | Network analyses in microbiome based on high-throughput multi-omics data |
| Q35875133 | Network construction and structure detection with metagenomic count data |
| Q36832044 | Network modules and hubs in plant-root fungal biomes |
| Q35692548 | Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation |
| Q57897827 | Network topology reveals high connectance levels and few key microbial genera within soils |
| Q54974948 | Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo. |
| Q36197011 | Networks Depicting the Fine-Scale Co-Occurrences of Fungi in Soil Horizons |
| Q93141110 | New and Preliminary Evidence on Altered Oral and Gut Microbiota in Individuals with Autism Spectrum Disorder (ASD): Implications for ASD Diagnosis and Subtyping Based on Microbial Biomarkers |
| Q38866650 | Next-Generation Global Biomonitoring: Large-scale, Automated Reconstruction of Ecological Networks. |
| Q52325738 | Niche Separation Increases With Genetic Distance Among Bloom-Forming Cyanobacteria. |
| Q35765047 | Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review |
| Q31169829 | Normalization and microbial differential abundance strategies depend upon data characteristics |
| Q35792490 | Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut |
| Q27318164 | Oral Samples as Non-Invasive Proxies for Assessing the Composition of the Rumen Microbial Community |
| Q93135579 | Oral microbiome and obesity in a large study of low-income and African-American populations |
| Q54964104 | Oral microbiota reveals signs of acculturation in Mexican American women. |
| Q92783846 | Oropharyngeal microbiome of a college population following a meningococcal disease outbreak |
| Q50177789 | Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder. |
| Q47726452 | Oxygenation of Hypoxic Coastal Baltic Sea Sediments Impacts on Chemistry, Microbial Community Composition, and Metabolism |
| Q28552559 | Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli |
| Q90138643 | Penicillin Trunk Injection Affects Bacterial Community Structure in Citrus Trees |
| Q36306938 | Phylogenetic factorization of compositional data yields lineage-level associations in microbiome datasets. |
| Q46548670 | Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits |
| Q58794476 | Phylogeny-corrected identification of microbial gene families relevant to human gut colonization |
| Q55284749 | Predicted Bacterial Interactions Affect in Vivo Microbial Colonization Dynamics in Nematostella. |
| Q97587586 | Predicting disease occurrence with high accuracy based on soil macroecological patterns of Fusarium wilt |
| Q38792983 | Predicting microbial interactions through computational approaches |
| Q90887545 | Prokaryotic taxa play keystone roles in the soil microbiome associated with woody perennial plants in the genus Buxus |
| Q21145290 | Proportionality: a valid alternative to correlation for relative data |
| Q57117386 | Protist species richness and soil microbiome complexity increase towards climax vegetation in the Brazilian Cerrado |
| Q93162272 | Pseudomonas spp. are key players in agricultural biogas substrate degradation |
| Q91905094 | Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling |
| Q64090222 | Rarity of microbial species: In search of reliable associations |
| Q92759641 | Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities |
| Q47110624 | Recurrent patterns of microdiversity in a temperate coastal marine environment. |
| Q60644960 | Reduction of antibiotic resistome and integron-integrase genes in laboratory-scale photobioreactors treating municipal wastewater |
| Q40085659 | Regulation of life span by the gut microbiota in the short-lived African turquoise killifish |
| Q60307180 | Relationship between Gut Microbiota and Phosphorus Metabolism in Hemodialysis Patients: A Preliminary Exploration |
| Q35159836 | Reprograming of gut microbiome energy metabolism by the FUT2 Crohn's disease risk polymorphism |
| Q34973400 | Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis |
| Q35541062 | Resistant microbial cooccurrence patterns inferred by network topology |
| Q91752659 | Response of the eukaryotic plankton community to the cyanobacterial biomass cycle over 6 years in two subtropical reservoirs |
| Q37122169 | Restructuring of the Aquatic Bacterial Community by Hydric Dynamics Associated with Superstorm Sandy |
| Q28606606 | Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range |
| Q46248684 | SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing |
| Q92524315 | Selected Immunological Mediators and Cervical Microbial Signatures in Women with Chlamydia trachomatis Infection |
| Q40045674 | Shotgun metagenomics, from sampling to analysis |
| Q60044490 | Signatures within the esophageal microbiome are associated with host genetics, age, and disease |
| Q52579922 | Similarity of the dog and human gut microbiomes in gene content and response to diet. |
| Q28829035 | Skin fungal community and its correlation with bacterial community of urban Chinese individuals |
| Q50090945 | Small eukaryotic phytoplankton communities in tropical waters off Brazil are dominated by symbioses between Haptophyta and nitrogen-fixing cyanobacteria. |
| Q93059843 | Soil indigenous microbiome and plant genotypes cooperatively modify soybean rhizosphere microbiome assembly |
| Q35581990 | Sparse and compositionally robust inference of microbial ecological networks |
| Q50277213 | Spatial Heterogeneity and Co-occurrence of Mucosal and Luminal Microbiome across Swine Intestinal Tract. |
| Q37033758 | Spatial scale drives patterns in soil bacterial diversity. |
| Q46270552 | Specific eukaryotic plankton are good predictors of net community production in the Western Antarctic Peninsula. |
| Q64252151 | Sperm Microbiota and Its Impact on Semen Parameters |
| Q55400264 | Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial. |
| Q24658549 | Structural robustness of the gut mucosal microbiota is associated with Crohn's disease remission after surgery |
| Q39106010 | Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types. |
| Q64915998 | System for Quality-Assured Data Analysis: Flexible, reproducible scientific workflows. |
| Q31113719 | TMAinspiration: Decode Interdependencies in Multifactorial Tissue Microarray Data |
| Q55472574 | Taxonomy-aware feature engineering for microbiome classification. |
| Q90315546 | Temperature and nutrient levels correspond with lineage-specific microdiversification in the ubiquitous and abundant Limnohabitans freshwater genus |
| Q46701184 | Terroir is a key driver of seed-associated microbial assemblages. |
| Q92132530 | The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health |
| Q58566820 | The Endophytic Mycobiome of European Ash and Sycamore Maple Leaves - Geographic Patterns, Host Specificity and Influence of Ash Dieback |
| Q41676491 | The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young |
| Q92890526 | The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks |
| Q34384120 | The Human Microbiome Project: a community resource for the healthy human microbiome |
| Q41689731 | The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species |
| Q41473503 | The Maturing Development of Gut Microbiota in Commercial Piglets during the Weaning Transition |
| Q91933307 | The association between pneumococcal vaccination, ethnicity, and the nasopharyngeal microbiota of children in Fiji |
| Q42735071 | The ecological controls on the prevalence of candidate division TM7 in polar regions |
| Q46253527 | The gut mycobiome of the Human Microbiome Project healthy cohort. |
| Q33915560 | The intestinal metabolome: an intersection between microbiota and host |
| Q90170560 | The mycobiome of Australian tree hollows in relation to the Cryptococcus gattii and C. neoformans species complexes |
| Q55344452 | The queen's gut refines with age: longevity phenotypes in a social insect model. |
| Q35875882 | The role of tissue-specific microbiota in initial establishment success of Pacific oysters |
| Q89984790 | The structure of microbial populations in Nelore GIT reveals inter-dependency of methanogens in feces and rumen |
| Q64133058 | The use of next generation sequencing for improving food safety: Translation into practice |
| Q57160985 | The use of random forests modelling to detect yeast-mannan sensitive bacterial changes in the broiler cecum |
| Q90028283 | Thinking Outside the Cereal Box: Noncarbohydrate Routes for Dietary Manipulation of the Gut Microbiota |
| Q47423525 | Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung |
| Q46265911 | Time-resolved analysis of a denitrifying bacterial community revealed a core microbiome responsible for the anaerobic degradation of quinoline. |
| Q58778239 | Tongue Microbiota and Oral Health Status in Community-Dwelling Elderly Adults |
| Q89460004 | Tools for Analysis of the Microbiome |
| Q100559140 | Topological analysis reveals state transitions in human gut and marine bacterial communities |
| Q26998253 | Towards predictive models of the human gut microbiome |
| Q53073440 | Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment. |
| Q26744668 | Tracking Strains in the Microbiome: Insights from Metagenomics and Models |
| Q38706536 | Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients |
| Q36286224 | Two dynamic regimes in the human gut microbiome |
| Q58089433 | Uncertainty quantification of the effects of biotic interactions on community dynamics from nonlinear time-series data |
| Q55407903 | Uncovering the drivers of host-associated microbiota with joint species distribution modelling. |
| Q52613219 | Understanding sequencing data as compositions: an outlook and review. |
| Q30829889 | Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis |
| Q92483924 | Unique bacterial assembly, composition, and interactions in a parasitic plant and its host |
| Q36045881 | Universality of human microbial dynamics |
| Q35869866 | Unveiling Bacterial Interactions through Multidimensional Scaling and Dynamics Modeling. |
| Q38794392 | Unveiling microbial interactions in stratified mat communities from a warm saline shallow pond. |
| Q93116664 | Use and abuse of correlation analyses in microbial ecology |
| Q26766432 | Using "Omics" and Integrated Multi-Omics Approaches to Guide Probiotic Selection to Mitigate Chytridiomycosis and Other Emerging Infectious Diseases |
| Q92669580 | Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data |
| Q36369015 | Using null models to infer microbial co-occurrence networks. |
| Q60923488 | Vaginal microbiome variances in sample groups categorized by clinical criteria of bacterial vaginosis |
| Q36064244 | Variable responses of human microbiomes to dietary supplementation with resistant starch |
| Q91711655 | Variations in Fungal Community and Diversity in Doushen With Different Flavors |
| Q95660705 | Viral control of biomass and diversity of bacterioplankton in the deep sea |
| Q35844779 | Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment |
| Q58780011 | Visualizing balances of compositional data: A new alternative to balance dendrograms |
| Q93039935 | Wheat dwarfing influences selection of the rhizosphere microbiome |
| Q35661318 | Wine microbiome: A dynamic world of microbial interactions |
| Q36367832 | gCoda: Conditional Dependence Network Inference for Compositional Data |
| Q47136142 | propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis |
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