| scholarly article | Q13442814 |
| P50 | author | Levi Waldron | Q41044211 |
| Olivier Jousson | Q50016771 | ||
| Vagheesh Narasimhan | Q55182033 | ||
| Annalisa Ballarini | Q107596136 | ||
| Curtis Huttenhower | Q19397499 | ||
| Nicola Segata | Q30348945 | ||
| P2860 | cites work | Bifidobacterium animalis subsp. lactis fermented milk product reduces inflammation by altering a niche for colitogenic microbes | Q34241570 |
| NBC: the Naïve Bayes Classification tool webserver for taxonomic classification of metagenomic reads | Q34433963 | ||
| Accurate phylogenetic classification of variable-length DNA fragments | Q34593023 | ||
| Taxonomic classification of metagenomic shotgun sequences with CARMA3. | Q35153529 | ||
| Microbial community genomics in the ocean | Q36123645 | ||
| Metagenome fragment classification using N-mer frequency profiles | Q41947344 | ||
| Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models | Q42584806 | ||
| Taxonomic metagenome sequence assignment with structured output models | Q42790557 | ||
| Aligning short reads to reference alignments and trees | Q48132558 | ||
| A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio | Q48142160 | ||
| A simple, fast, and accurate method of phylogenomic inference | Q21184110 | ||
| Toward Automatic Reconstruction of a Highly Resolved Tree of Life | Q22065877 | ||
| Enterotypes of the human gut microbiome | Q24489818 | ||
| A framework for human microbiome research | Q24602401 | ||
| Integrative analysis of environmental sequences using MEGAN4 | Q24604814 | ||
| A human gut microbial gene catalogue established by metagenomic sequencing | Q24618931 | ||
| KEGG for representation and analysis of molecular networks involving diseases and drugs | Q24644514 | ||
| Mapping short DNA sequencing reads and calling variants using mapping quality scores | Q24644612 | ||
| Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities | Q24647611 | ||
| A core gut microbiome in obese and lean twins | Q24649648 | ||
| MEGAN analysis of metagenomic data | Q24673516 | ||
| Basic local alignment search tool | Q25938991 | ||
| The integrated microbial genomes system: an expanding comparative analysis resource | Q28262793 | ||
| Vaginal microbiome of reproductive-age women | Q28284755 | ||
| PhymmBL expanded: confidence scores, custom databases, parallelization and more | Q28730759 | ||
| Search and clustering orders of magnitude faster than BLAST | Q29547431 | ||
| The Ribosomal Database Project: improved alignments and new tools for rRNA analysis | Q29547434 | ||
| NCBI Reference Sequences: current status, policy and new initiatives | Q29614453 | ||
| The metagenomics of soil | Q33216317 | ||
| Molecular identification of bacteria associated with bacterial vaginosis. | Q33226498 | ||
| Use of simulated data sets to evaluate the fidelity of metagenomic processing methods | Q33283189 | ||
| Genomic comparisons of Brucella spp. and closely related bacteria using base compositional and proteome based methods | Q33657435 | ||
| MTR: taxonomic annotation of short metagenomic reads using clustering at multiple taxonomic ranks. | Q33761996 | ||
| Microbial metatranscriptomics in a permanent marine oxygen minimum zone. | Q33787220 | ||
| RAIphy: phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles | Q33807870 | ||
| Classifying short genomic fragments from novel lineages using composition and homology. | Q33986676 | ||
| Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies | Q34023960 | ||
| P433 | issue | 8 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | cell biology | Q7141 |
| metagenomics | Q903778 | ||
| P304 | page(s) | 811-4 | |
| P577 | publication date | 2012-08-01 | |
| P1433 | published in | Nature Methods | Q680640 |
| P1476 | title | Metagenomic microbial community profiling using unique clade-specific marker genes | |
| P478 | volume | 9 |
| Q94553773 | A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle |
| Q98158322 | A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes |
| Q61449824 | A Fungal World: Could the Gut Mycobiome Be Involved in Neurological Disease? |
| Q47656915 | A GLM-based latent variable ordination method for microbiome samples |
| Q36378923 | A Metagenomic Approach to Cyanobacterial Genomics. |
| Q46299278 | A Model-Based Approach For Species Abundance Quantification Based On Shotgun Metagenomic Data |
| Q37627113 | A Perspective Study of Koumiss Microbiome by Metagenomics Analysis Based on Single-Cell Amplification Technique |
| Q36359875 | A Robust Framework for Microbial Archaeology |
| Q38673187 | A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation |
| Q34154852 | A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes |
| Q47137286 | A comprehensive analysis of breast cancer microbiota and host gene expression. |
| Q89900155 | A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina |
| Q58052580 | A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links |
| Q28817498 | A conserved bacterial protein induces pancreatic beta cell expansion during zebrafish development |
| Q36254616 | A fast and robust protocol for metataxonomic analysis using RNAseq data |
| Q92287328 | A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota |
| Q34550721 | A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets |
| Q48121310 | A human gut phage catalog correlates the gut phageome with type 2 diabetes. |
| Q56557225 | A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers |
| Q97533331 | A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting |
| Q35034558 | A method for selectively enriching microbial DNA from contaminating vertebrate host DNA. |
| Q26851665 | A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome |
| Q42697171 | A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures |
| Q41158757 | A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis. |
| Q101574551 | A reference map of potential determinants for the human serum metabolome |
| Q34181822 | A systematic analysis of biosynthetic gene clusters in the human microbiome reveals a common family of antibiotics. |
| Q41860585 | A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter |
| Q31096681 | A two-part mixed-effects model for analyzing longitudinal microbiome compositional data |
| Q42688869 | Abundance estimation and differential testing on strain level in metagenomics data. |
| Q36045875 | Accounting for reciprocal host-microbiome interactions in experimental science |
| Q92800045 | Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data |
| Q35656712 | Accurate read-based metagenome characterization using a hierarchical suite of unique signatures |
| Q48171092 | Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities. |
| Q98197834 | Age- and duration-dependent effects of whey protein on high-fat diet-induced changes in body weight, lipid metabolism, and gut microbiota in mice |
| Q55224856 | Algorithms and strategies in short-read shotgun metagenomic reconstruction of plant communities. |
| Q37431258 | Alignment-free Transcriptomic and Metatranscriptomic Comparison Using Sequencing Signatures with Variable Length Markov Chains |
| Q34037715 | All-Food-Seq (AFS): a quantifiable screen for species in biological samples by deep DNA sequencing |
| Q95629921 | Alterations in Gut Microbiota of Patients With COVID-19 During Time of Hospitalization |
| Q96685651 | Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms |
| Q90189684 | An Integrated Multi-Disciplinary Perspectivefor Addressing Challenges of the Human Gut Microbiome |
| Q38874672 | An accurate and fast alignment-free method for profiling microbial communities |
| Q35896599 | An evaluation of the accuracy and speed of metagenome analysis tools |
| Q37677369 | An in vitro biofilm model system maintaining a highly reproducible species and metabolic diversity approaching that of the human oral microbiome |
| Q27028042 | An introduction to the analysis of shotgun metagenomic data |
| Q37223525 | Analytical tools and databases for metagenomics in the next-generation sequencing era |
| Q38370830 | Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past |
| Q27005869 | Ancient and modern environmental DNA |
| Q92887090 | Ancient pathogen genomics as an emerging tool for infectious disease research |
| Q36332375 | Ancient plant DNA in lake sediments. |
| Q38836453 | Antibiotic perturbation of the preterm infant gut microbiome and resistome |
| Q40831278 | Antibiotic resistance genes and human bacterial pathogens: Co-occurrence, removal, and enrichment in municipal sewage sludge digesters. |
| Q46250127 | Antibiotic resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses |
| Q28829366 | Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome |
| Q47820236 | Antimicrobial Resistance Gene Acquisition and Depletion Following Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection |
| Q60954922 | Antimicrobial Susceptibility and Genomic Structure of Isolates |
| Q30994632 | Application of metagenomic sequencing to food safety: detection of Shiga Toxin-producing Escherichia coli on fresh bagged spinach |
| Q31120665 | Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents |
| Q35624883 | Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes |
| Q64067943 | Assessing taxonomic metagenome profilers with OPAL |
| Q26860785 | Assessing the human gut microbiota in metabolic diseases |
| Q37717864 | Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications |
| Q35895903 | Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis |
| Q46297294 | Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. |
| Q37588925 | Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration. |
| Q99406108 | Associations of the intestinal microbiome with the complement system in neovascular age-related macular degeneration |
| Q35317726 | Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome |
| Q64269069 | Bacterial Community 16S rRNA Gene Sequencing Characterizes Riverine Microbial Impact on Lake Michigan |
| Q60954905 | Bacterial and Archaeal Viruses of Himalayan Hot Springs at Manikaran Modulate Host Genomes |
| Q35218567 | Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer |
| Q34557144 | Bacterial colonization and succession in a newly opened hospital. |
| Q35621482 | Bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing |
| Q35219172 | Bacterial rose garden for metagenomic SNP-based phylogeny visualization. |
| Q36324821 | Bayesian identification of bacterial strains from sequencing data |
| Q55240269 | Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity. |
| Q28069618 | Beyond 16S rRNA Community Profiling: Intra-Species Diversity in the Gut Microbiota |
| Q36216244 | Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut |
| Q31106599 | Biodiversity and functional genomics in the human microbiome |
| Q34290130 | Biogeography and individuality shape function in the human skin metagenome |
| Q33744957 | Biogeography of the ecosystems of the healthy human body |
| Q35137569 | Bioinformatic approaches reveal metagenomic characterization of soil microbial community |
| Q56785192 | Bioinformatics for Microbiome Research: Concepts, Strategies, and Advances |
| Q34499309 | Bioinformatics for the Human Microbiome Project |
| Q92602908 | Bogotá River anthropogenic contamination alters microbial communities and promotes spread of antibiotic resistance genes |
| Q55201689 | Bracken: estimating species abundance in metagenomics data |
| Q33647129 | Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation |
| Q94450938 | CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data |
| Q34471973 | CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. |
| Q37712615 | Carbohydrate staple food modulates gut microbiota of Mongolians in China |
| Q30390347 | Census-based rapid and accurate metagenome taxonomic profiling |
| Q35674518 | Center Variation in Intestinal Microbiota Prior to Late-Onset Sepsis in Preterm Infants |
| Q35636288 | Cervicovaginal bacteria are a major modulator of host inflammatory responses in the female genital tract |
| Q26798590 | Challenges and opportunities in understanding microbial communities with metagenome assembly (accompanied by IPython Notebook tutorial) |
| Q36096284 | Challenges of the Unknown: Clinical Application of Microbial Metagenomics |
| Q35962892 | Changes in the Functional Potential of the Gut Microbiome Following Probiotic Supplementation during Helicobacter Pylori Treatment. |
| Q35947349 | Changes in the Intestinal Microbiome and Alcoholic and Nonalcoholic Liver Diseases: Causes or Effects? |
| Q35145330 | Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX. |
| Q92782632 | Characterization of key bacterial species in the Daphnia magna microbiota using shotgun metagenomics |
| Q34525149 | Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics |
| Q30411884 | Characterization of the nasopharyngeal microbiota in health and during rhinovirus challenge |
| Q52593572 | Characterizing Phage Genomes for Therapeutic Applications. |
| Q30660828 | Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing |
| Q30840603 | Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data |
| Q30490594 | Clinical and Fecal Microbial Changes With Diet Therapy in Active Inflammatory Bowel Disease |
| Q40097858 | Clinical metagenomics of bone and joint infections: a proof of concept study. |
| Q36176879 | Combining bleach and mild predigestion improves ancient DNA recovery from bones |
| Q35794069 | Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome |
| Q34677641 | Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage |
| Q34078749 | Comparative analysis of functional metagenomic annotation and the mappability of short reads |
| Q64914632 | Comparative genomics and genome biology of Campylobacter showae. |
| Q35915768 | Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis. |
| Q104616962 | Comparing Circadian Rhythmicity in the Human Gut Microbiome |
| Q36232883 | Comparing genome versus proteome-based identification of clinical bacterial isolates |
| Q90128284 | Complex interactions between the microbiome and cancer immune therapy |
| Q54217774 | Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi. |
| Q38997181 | Computational Methods in Mass Spectrometry-Based Proteomics |
| Q26825114 | Computational meta'omics for microbial community studies |
| Q46251992 | Computational profiling of the gut-brain axis: microflora dysbiosis insights to neurological disorders |
| Q36364571 | ConStrains identifies microbial strains in metagenomic datasets |
| Q64112342 | Conditional Regression Based on a Multivariate Zero-Inflated Logistic-Normal Model for Microbiome Relative Abundance Data |
| Q58575614 | Considerations When Designing a Microbiome Study: Implications for Nursing Science |
| Q55664853 | CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads. |
| Q41926823 | Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software. |
| Q58454509 | Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens |
| Q50332885 | Current Bioinformatics resources in combating infectious diseases |
| Q26851992 | Current status and prospects of intestinal microbiome studies |
| Q41696192 | DESMAN: a new tool for de novo extraction of strains from metagenomes. |
| Q36207485 | DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms. |
| Q39788463 | DUDes: a top-down taxonomic profiler for metagenomics. |
| Q89620805 | Degradation of Recalcitrant Polyurethane and Xenobiotic Additives by a Selected Landfill Microbial Community and Its Biodegradative Potential Revealed by Proximity Ligation-Based Metagenomic Analysis |
| Q33917852 | Demonstrating microbial co-occurrence pattern analyses within and between ecosystems |
| Q47661889 | Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions. |
| Q41660282 | Detection of Bacterial Pathogens from Broncho-Alveolar Lavage by Next-Generation Sequencing |
| Q36772744 | Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing |
| Q28829489 | Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome |
| Q34629327 | Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections |
| Q90119176 | Diet influences the functions of the human intestinal microbiome |
| Q93032563 | Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids |
| Q37349241 | Differential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations |
| Q37430905 | Differential fecal microbiota are retained in broiler chicken lines divergently selected for fatness traits |
| Q92646127 | Draft Genome Sequence of Raoultella ornithinolytica P079F W, Isolated from the Feces of a Preterm Infant |
| Q92646135 | Draft Genome Sequences of Citrobacter freundii and Citrobacter murliniae Strains Isolated from the Feces of Preterm Infants |
| Q46251480 | Draft genomes of two Australian strains of the plant pathogen, Phytophthora cinnamomi |
| Q92601400 | Dual RNA-seq in Streptococcus pneumoniae Infection Reveals Compartmentalized Neutrophil Responses in Lung and Pleural Space |
| Q35758361 | Effects of dietary fiber on cecal short-chain fatty acid and cecal microbiota of broiler and laying-hen chicks |
| Q49912962 | Effects of timber harvesting on the genetic potential for carbon and nitrogen cycling in five North American forest ecozones. |
| Q90814981 | Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans |
| Q36014809 | Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization. |
| Q90093092 | Emerging Priorities for Microbiome Research |
| Q38900127 | Emerging Technologies for Gut Microbiome Research. |
| Q64069293 | Employing toxin-antitoxin genome markers for identification of and strains in human metagenomes |
| Q37577371 | Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform |
| Q47140369 | Enhancing the Resolution of Rumen Microbial Classification from Metatranscriptomic Data Using Kraken and Mothur. |
| Q47236614 | Enterotypes in the landscape of gut microbial community composition. |
| Q30379921 | Entropy-scaling search of massive biological data |
| Q59069853 | Environment dominates over host genetics in shaping human gut microbiota |
| Q36060603 | Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses |
| Q37473036 | Escherichia coli dysbiosis correlates with gastrointestinal dysfunction in children with cystic fibrosis |
| Q64075188 | Estimating the total genome length of a metagenomic sample using k-mers |
| Q99630676 | Evaluation of computational methods for human microbiome analysis using simulated data |
| Q41694505 | Evaluation of ddRADseq for reduced representation metagenome sequencing. |
| Q35832785 | Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. |
| Q33764379 | Evidence of natural Wolbachia infections in field populations of Anopheles gambiae |
| Q36273126 | Evolutionary Patterns and Processes: Lessons from Ancient DNA. |
| Q61811295 | Evolutionary dynamics of bacteria in the gut microbiome within and across hosts |
| Q35668246 | Excretion of Host DNA in Feces Is Associated with Risk of Clostridium difficile Infection |
| Q21128781 | Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis |
| Q38953346 | Experimental metagenomics and ribosomal profiling of the human skin microbiome |
| Q34502386 | Exploration and retrieval of whole-metagenome sequencing samples |
| Q90095571 | Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults |
| Q34072406 | Exploring neighborhoods in the metagenome universe |
| Q35829641 | Extensive Modulation of the Fecal Metagenome in Children With Crohn's Disease During Exclusive Enteral Nutrition |
| Q61810125 | Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle |
| Q64992112 | Extrathymically Generated Regulatory T Cells Establish a Niche for Intestinal Border-Dwelling Bacteria and Affect Physiologic Metabolite Balance. |
| Q30842743 | FASTQSim: platform-independent data characterization and in silico read generation for NGS datasets |
| Q33764799 | FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares |
| Q33982182 | Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification |
| Q47552694 | FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data |
| Q92784770 | Fecal dysbiosis in infants with cystic fibrosis is associated with early linear growth failure |
| Q35085234 | Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn's disease. |
| Q52691475 | Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice. |
| Q31137728 | Filtration and Normalization of Sequencing Read Data in Whole-Metagenome Shotgun Samples |
| Q56890690 | Fine-scale differentiation between and group signatures in metagenome shotgun data |
| Q89452333 | Flavin monooxygenase 3, the host hepatic enzyme in the metaorganismal trimethylamine N-oxide-generating pathway, modulates platelet responsiveness and thrombosis risk |
| Q37445053 | Functional metagenomic profiling of intestinal microbiome in extreme ageing |
| Q37541474 | GABA-producing Bifidobacterium dentium modulates visceral sensitivity in the intestine |
| Q90029276 | GMrepo: a database of curated and consistently annotated human gut metagenomes |
| Q36070871 | GUTSS: An Alignment-Free Sequence Comparison Method for Use in Human Intestinal Microbiome and Fecal Microbiota Transplantation Analysis |
| Q37734902 | Gastrointestinal pathology in juvenile and adult CFTR-knockout ferrets. |
| Q47107402 | Gene-Based Pathogen Detection: Can We Use qPCR to Predict the Outcome of Diagnostic Metagenomics? |
| Q34463958 | Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues |
| Q50315142 | Genome-resolved metagenomics of sugarcane vinasse bacteria |
| Q35764974 | GenomePeek-an online tool for prokaryotic genome and metagenome analysis |
| Q61445485 | Genomic Analyses of Acute Flaccid Myelitis Cases among a Cluster in Arizona Provide Further Evidence of Enterovirus D68 Role |
| Q38833446 | Genomic Analysis of Viral Outbreaks |
| Q37644494 | Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention |
| Q38987535 | Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes |
| Q57213232 | Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia |
| Q64993094 | Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life. |
| Q36295913 | Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics |
| Q60909682 | Global genomic similarity and core genome sequence diversity of the genus as a toolkit to identify closely related bacterial species in complex environments |
| Q33786338 | Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. |
| Q55120679 | Gut Dysbiosis and Muscle Aging: Searching for Novel Targets against Sarcopenia. |
| Q92650360 | Gut Microbiome Biomarkers and Functional Diversity Within an Amazonian Semi-Nomadic Hunter-Gatherer Group |
| Q46565524 | Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism |
| Q90371831 | Gut microbiome structure and metabolic activity in inflammatory bowel disease |
| Q61445387 | Gut microbiota density influences host physiology and is shaped by host and microbial factors |
| Q58798926 | Gut microbiota, short chain fatty acids, and obesity across the epidemiologic transition: the METS-Microbiome study protocol |
| Q30398441 | HIPPI: highly accurate protein family classification with ensembles of HMMs |
| Q49604667 | HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA. |
| Q62486855 | Health Outcomes, Pathogenesis and Epidemiology of Severe Acute Malnutrition (HOPE-SAM): rationale and methods of a longitudinal observational study |
| Q28392058 | High throughput genomic sequencing of bioaerosols in broiler chicken production facilities |
| Q30856812 | High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis. |
| Q35872979 | High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. |
| Q50056664 | High-Throughput DNA sequencing of ancient wood |
| Q84355742 | High-speed microbial community profiling |
| Q46240473 | Higher recall in metagenomic sequence classification exploiting overlapping reads |
| Q89467832 | Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin |
| Q46318762 | Human genetic variation and the gut microbiome in disease |
| Q34980773 | Human gut microbiota changes reveal the progression of glucose intolerance |
| Q34656085 | Human gut microbiota community structures in urban and rural populations in Russia |
| Q42958061 | Human microbiome signatures of differential colorectal cancer drug metabolism |
| Q92767858 | HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples |
| Q36324802 | Identification of Klebsiella capsule synthesis loci from whole genome data |
| Q40158461 | Identification of donor microbe species that colonize and persist long term in the recipient after fecal transplant for recurrent Clostridium difficile. |
| Q35854627 | Identification of low abundance microbiome in clinical samples using whole genome sequencing |
| Q35627668 | Identifying personal microbiomes using metagenomic codes |
| Q37514864 | Identifying species of symbiont bacteria from the human gut that, alone, can induce intestinal Th17 cells in mice |
| Q35031439 | Identifying strains that contribute to complex diseases through the study of microbial inheritance |
| Q96303512 | Impact of DNA Extraction Method on Variation in Human and Built Environment Microbial Community and Functional Profiles Assessed by Shotgun Metagenomics Sequencing |
| Q64911807 | Impact of Host DNA and Sequencing Depth on the Taxonomic Resolution of Whole Metagenome Sequencing for Microbiome Analysis. |
| Q38599048 | Impact of Immunosuppression on the Metagenomic Composition of the Intestinal Microbiome: a Systems Biology Approach to Post-Transplant Diabetes |
| Q64102315 | Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling |
| Q91062698 | Impact of delivery mode-associated gut microbiota dynamics on health in the first year of life |
| Q92049045 | Impact of intestinal parasites on microbiota and cobalamin gene sequences: a pilot study |
| Q99628469 | Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial |
| Q90195017 | Impact of plants on the diversity and activity of methylotrophs in soil |
| Q41351557 | Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease |
| Q58105819 | Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes |
| Q35807983 | Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease |
| Q37658394 | Inhalable microorganisms in Beijing's PM2.5 and PM10 pollutants during a severe smog event |
| Q31162021 | Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis |
| Q50110810 | Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. |
| Q94539772 | Interaction of bacterial communities and indicators of water quality in shoreline sand, sediment, and water of Lake Michigan |
| Q98627341 | Intermittent aeration of landfill simulation bioreactors: Effects on emissions and microbial community |
| Q38616718 | Intestinal Bacterial Communities of Trypanosome-Infected and Uninfected Glossina palpalis palpalis from Three Human African Trypanomiasis Foci in Cameroon |
| Q92071368 | Intestinal Bacteroides sp. Imbalance Associated With the Occurrence of Childhood Undernutrition in China |
| Q35912366 | Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis |
| Q28607510 | Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification |
| Q34663798 | Introducing an environmental assessment and intervention program in inner-city schools |
| Q31151211 | Kingdom-agnostic metagenomics and the importance of complete characterization of enteric microbial communities |
| Q33742022 | Kraken: ultrafast metagenomic sequence classification using exact alignments |
| Q36357968 | LAF: Logic Alignment Free and its application to bacterial genomes classification. |
| Q36102158 | LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes |
| Q57042539 | LVQ-KNN: Composition-based DNA/RNA binning of short nucleotide sequences utilizing a prototype-based k-nearest neighbor approach |
| Q38610350 | Large-scale comparative metagenomics of Blastocystis, a common member of the human gut microbiome |
| Q38368749 | Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing |
| Q34783015 | Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis). |
| Q35770107 | Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota |
| Q36182975 | Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity |
| Q92330377 | Long-term impact of fecal transplantation in healthy volunteers |
| Q91854695 | Long-term impact of oral surgery with or without amoxicillin on the oral microbiome-A prospective cohort study |
| Q35750427 | Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis |
| Q58759873 | Low-dose calcipotriol can elicit wound closure, anti-microbial, and anti-neoplastic effects in epidermolysis bullosa keratinocytes |
| Q42695976 | MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes |
| Q31109557 | MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data |
| Q55297112 | MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. |
| Q42696266 | MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis |
| Q64080144 | MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs |
| Q34508000 | MMseqs software suite for fast and deep clustering and searching of large protein sequence sets |
| Q92857487 | Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks |
| Q36072739 | Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights |
| Q64063238 | Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts |
| Q35646012 | Marked seasonal variation in the wild mouse gut microbiota |
| Q36860756 | Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains |
| Q58700639 | Maternal gut and breast milk microbiota affect infant gut antibiotic resistome and mobile genetic elements |
| Q37693667 | Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery |
| Q92878135 | Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease |
| Q56888712 | Maximal viral information recovery from sequence data using VirMAP |
| Q91933613 | Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue |
| Q92879544 | Meta-transcriptomic identification of hepatitis B virus in cerebrospinal fluid in patients with central nervous system disease |
| Q97542057 | MetaBCC-LR: metagenomics binning by coverage and composition for long reads |
| Q42281181 | MetaGen: reference-free learning with multiple metagenomic samples |
| Q35101532 | MetaID: a novel method for identification and quantification of metagenomic samples |
| Q36139108 | MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples |
| Q57255766 | MetaPhlAn2 for enhanced metagenomic taxonomic profiling |
| Q39429382 | MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures. |
| Q35672275 | MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. |
| Q35033956 | MetaRef: a pan-genomic database for comparative and community microbial genomics |
| Q35233831 | MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning |
| Q47169887 | Metabolic capability and in situ activity of microorganisms in an oil reservoir. |
| Q34822704 | Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules |
| Q31164389 | Metacoder: An R package for visualization and manipulation of community taxonomic diversity data |
| Q97424135 | Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut |
| Q46255672 | Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes. |
| Q56795158 | Metagenomic Analysis of the Saliva Microbiome with Merlin |
| Q64106894 | Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation |
| Q62918832 | Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota |
| Q35964279 | Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants |
| Q41693862 | Metagenomic Shotgun Sequencing and Unbiased Metabolomic Profiling Identify Specific Human Gut Microbiota and Metabolites Associated with Immune Checkpoint Therapy Efficacy in Melanoma Patients |
| Q34700757 | Metagenomic analysis of a tropical composting operation at the são paulo zoo park reveals diversity of biomass degradation functions and organisms |
| Q37545345 | Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum |
| Q28601802 | Metagenomic analysis of microbial consortia enriched from compost: new insights into the role of Actinobacteria in lignocellulose decomposition |
| Q35132034 | Metagenomic analysis of nitrate-reducing bacteria in the oral cavity: implications for nitric oxide homeostasis. |
| Q57059592 | Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages |
| Q90247273 | Metagenomic analysis of relationships between the denitrification process and carbon metabolism in a bioaugmented full-scale tannery wastewater treatment plant |
| Q39560779 | Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community |
| Q57211604 | Metagenomic analysis reveals the prevalence and persistence of antibiotic- and heavy metal-resistance genes in wastewater treatment plant |
| Q36178854 | Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes |
| Q46297436 | Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter |
| Q42362956 | Metagenomic characterization of ambulances across the USA |
| Q100945966 | Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China |
| Q30835908 | Metagenomic data utilization and analysis (MEDUSA) and construction of a global gut microbial gene catalogue |
| Q35945463 | Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis |
| Q40350740 | Metagenomic profiles of antibiotic resistance genes in paddy soils from South China. |
| Q35039243 | Metagenomic profiling of known and unknown microbes with microbeGPS. |
| Q33736416 | Metagenomic search strategies for interactions among plants and multiple microbes |
| Q35021237 | Metagenomic species profiling using universal phylogenetic marker genes |
| Q26799820 | Metagenomic surveys of gut microbiota |
| Q91728214 | Metagenomics analysis reveals features unique to Indian distal gut microbiota |
| Q36068973 | Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. |
| Q89433453 | Metagenomics for Clinical Infectious Disease Diagnostics Steps Closer to Reality |
| Q37593138 | Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods |
| Q33867106 | Metagenomics: The Next Culture-Independent Game Changer. |
| Q30953199 | Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies |
| Q35366212 | Metatranscriptomic evidence for co-occurring top-down and bottom-up controls on toxic cyanobacterial communities |
| Q53079633 | Metaviz: interactive statistical and visual analysis of metagenomic data. |
| Q64263872 | Methanethiol and Dimethylsulfide Cycling in Stiffkey Saltmarsh |
| Q64997999 | MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples. |
| Q59328967 | Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants |
| Q90050523 | Microbial Communities Associated With Passive Acidic Abandoned Coal Mine Remediation |
| Q90114640 | Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome |
| Q34531231 | Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring |
| Q37366382 | Microbial Succession and Flavor Production in the Fermented Dairy Beverage Kefir |
| Q28081332 | Microbial bioinformatics for food safety and production |
| Q89931322 | Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists |
| Q91673905 | Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage |
| Q38255274 | Microbial genome-enabled insights into plant-microorganism interactions |
| Q34137586 | Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer |
| Q89695831 | Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data |
| Q37735523 | Microbial strain-level population structure and genetic diversity from metagenomes |
| Q50801598 | Microbiology: Learning about who we are. |
| Q31152913 | Microbiota present in cystic fibrosis lungs as revealed by whole genome sequencing |
| Q35541605 | Microbiota-mediated inflammation and antimicrobial defense in the intestine |
| Q92217859 | Microfluidics-Based Enrichment and Whole-Genome Amplification Enable Strain-Level Resolution for Airway Metagenomics |
| Q47138783 | MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage |
| Q57518109 | Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women |
| Q62731347 | Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome |
| Q55243928 | Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers. |
| Q47731422 | Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease. |
| Q57285302 | Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches |
| Q110949519 | Multiple comparative metagenomics using multisetk-mer counting |
| Q37275280 | Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability |
| Q36238500 | Noninvasive monitoring of infection and rejection after lung transplantation |
| Q28829468 | Not All Particles Are Equal: The Selective Enrichment of Particle-Associated Bacteria from the Mediterranean Sea |
| Q92188489 | Novel Isoprene-Degrading Proteobacteria From Soil and Leaves Identified by Cultivation and Metagenomics Analysis of Stable Isotope Probing Experiments |
| Q38723919 | Novel Strategies for Applied Metagenomics. |
| Q34284507 | Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis. |
| Q52331906 | Opportunities and obstacles for deep learning in biology and medicine. |
| Q40034894 | Optimization of alignment-based methods for taxonomic binning of metagenomics reads |
| Q35612782 | Optimized DNA extraction and metagenomic sequencing of airborne microbial communities |
| Q91405102 | Oral microbiome diversity in chimpanzees from Gombe National Park |
| Q28657611 | Orione, a web-based framework for NGS analysis in microbiology |
| Q41951395 | Overexpression of antibiotic resistance genes in hospital effluents over time |
| Q30833683 | PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data |
| Q41480121 | Pan-genome analysis of Bacillus for microbiome profiling |
| Q30770115 | Parallel-META 2.0: enhanced metagenomic data analysis with functional annotation, high performance computing and advanced visualization |
| Q31155417 | Parasite infection of public databases: a data mining approach to identify apicomplexan contaminations in animal genome and transcriptome assemblies |
| Q61919651 | Parkinson's disease and bacteriophages as its overlooked contributors |
| Q34182467 | PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples |
| Q34811411 | Pathoscope: species identification and strain attribution with unassembled sequencing data |
| Q57041999 | Patients with Chronic Obstructive Pulmonary Disease harbour a variation of Haemophilus species |
| Q37368628 | Pharmacometabolomics Informs Viromics toward Precision Medicine |
| Q34363801 | PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes |
| Q38342057 | PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes |
| Q41882289 | PhyloSift: phylogenetic analysis of genomes and metagenomes |
| Q97542472 | Phylogenetic double placement of mixed samples |
| Q90135322 | Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method |
| Q34692435 | Phylogenetics and the human microbiome |
| Q35623482 | Population-Sequencing as a Biomarker for Sample Characterization |
| Q36002388 | Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity |
| Q40129363 | Potential for Monitoring Gut Microbiota for Diagnosing Infections and Graft-versus-Host Disease in Cancer and Stem Cell Transplant Patients. |
| Q91968027 | Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences |
| Q28652656 | Prehistoric genomes reveal the genetic foundation and cost of horse domestication |
| Q28534801 | Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans |
| Q38921638 | Probiotics, gut microbiota, and their influence on host health and disease. |
| Q46256606 | Progressive Colonization of Bacteria and Degradation of Rice Straw in the Rumen by Illumina Sequencing |
| Q28647668 | Pros and cons of methylation-based enrichment methods for ancient DNA |
| Q99616793 | Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years |
| Q36761234 | Protein signature-based estimation of metagenomic abundances including all domains of life and viruses |
| Q58569890 | Purification of oocysts obtained from human stool specimens for whole genome sequencing |
| Q35161789 | Purifying the impure: sequencing metagenomes and metatranscriptomes from complex animal-associated samples |
| Q57652324 | Pyrosequencing of rpoB uncovers a significant biogeographical pattern of rhizobial species in soybean rhizosphere |
| Q34532504 | Pyrosequencing reveals the influence of organic and conventional farming systems on bacterial communities |
| Q92538282 | Quantification of Human Oral and Fecal Streptococcus parasanguinis by Use of Quantitative Real-Time PCR Targeting the groEL Gene |
| Q91905094 | Quantifying spatiotemporal variability and noise in absolute microbiota abundances using replicate sampling |
| Q100736953 | Quantitative characterization of Clostridioides difficile population in the gut microbiome of patients with C. difficile infection and their association with clinical factors |
| Q35154395 | RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets |
| Q92382977 | Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy |
| Q27342229 | Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis |
| Q24286921 | Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella |
| Q37049410 | Rapid evolution of the human gut virome |
| Q33751206 | Ray Meta: scalable de novo metagenome assembly and profiling. |
| Q91869091 | Reads Binning Improves Alignment-Free Metagenome Comparison |
| Q35657312 | Reconstructing ancient genomes and epigenomes |
| Q35022283 | Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution |
| Q40065742 | Reconstruction of Bacterial and Viral Genomes from Multiple Metagenomes. |
| Q90615407 | Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients |
| Q33730723 | Relating the metatranscriptome and metagenome of the human gut. |
| Q63647898 | Removing contaminants from databases of draft genomes |
| Q47559233 | ReprDB and panDB: minimalist databases with maximal microbial representation |
| Q64121080 | Resolving Phylogenetic Relationships for Streptococcus mitis and Streptococcus oralis through Core- and Pan-Genome Analyses |
| Q46251995 | Resources and tools for the high-throughput, multi-omic study of intestinal microbiota |
| Q90950487 | Retinal artery occlusion is associated with compositional and functional shifts in the gut microbiome and altered trimethylamine-N-oxide levels |
| Q99570296 | Revealing antimicrobial resistance in stormwater with MinION |
| Q34129372 | Rural and urban microbiota: To be or not to be? |
| Q98243935 | STROBE-metagenomics: a STROBE extension statement to guide the reporting of metagenomics studies |
| Q31004139 | SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data |
| Q55899829 | Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico |
| Q47343176 | Salt-responsive gut commensal modulates TH17 axis and disease |
| Q37662549 | Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research |
| Q34355671 | Scalable metagenomic taxonomy classification using a reference genome database |
| Q90312531 | Scaling read aligners to hundreds of threads on general-purpose processors |
| Q36276433 | Scaling statistical multiple sequence alignment to large datasets |
| Q35924484 | Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River |
| Q57094607 | Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research |
| Q93161105 | Selective colonization ability of human fecal microbes in different mouse gut environments |
| Q89662507 | Separating the signal from the noise in metagenomic cell-free DNA sequencing |
| Q113306949 | Sepia, a taxonomy oriented read classifier in Rust |
| Q35615383 | Sequencing and beyond: integrating molecular 'omics' for microbial community profiling |
| Q39608380 | Severe Gut Microbiota Dysbiosis Is Associated With Poor Growth in Patients With Short Bowel Syndrome |
| Q91722743 | Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades |
| Q47340519 | Shotgun metagenomics and volatilome profile of the microbiota of fermented sausages |
| Q40045674 | Shotgun metagenomics, from sampling to analysis |
| Q35115454 | Shotgun microbial profiling of fossil remains |
| Q28652492 | Sigma: strain-level inference of genomes from metagenomic analysis for biosurveillance |
| Q64075192 | Signal enrichment with strain-level resolution in metagenomes using topological data analysis |
| Q36828490 | Skin Microbiome Surveys Are Strongly Influenced by Experimental Design |
| Q35232637 | Social networks predict gut microbiome composition in wild baboons. |
| Q30573684 | Species-level analysis of DNA sequence data from the NIH Human Microbiome Project |
| Q58064075 | Species-level functional profiling of metagenomes and metatranscriptomes |
| Q34648507 | Stability of gut enterotypes in Korean monozygotic twins and their association with biomarkers and diet |
| Q34792396 | Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model. |
| Q36105723 | Stool microbiome reveals diverse bacterial ureases as confounders of oral urea breath testing for Helicobacter pylori and Mycobacterium tuberculosis in Bamako, Mali |
| Q47256192 | Strain profiling and epidemiology of bacterial species from metagenomic sequencing. |
| Q46088920 | Strain recovery from metagenomes |
| Q62731352 | Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life |
| Q36216248 | Strain-Level Discrimination of Shiga Toxin-Producing Escherichia coli in Spinach Using Metagenomic Sequencing |
| Q91809427 | Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps |
| Q35964692 | Strain-level microbial epidemiology and population genomics from shotgun metagenomics |
| Q37734380 | Strain/species identification in metagenomes using genome-specific markers |
| Q37719248 | Strategies to improve reference databases for soil microbiomes |
| Q37126000 | Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION(TM) sequencing |
| Q101133097 | Strong oral plaque microbiome signatures for dental implant diseases identified by strain-resolution metagenomics |
| Q35657711 | Strong spurious transcription likely contributes to DNA insert bias in typical metagenomic clone libraries |
| Q49562676 | Structural Modulation of Gut Microbiota during Alleviation of Suckling Piglets Diarrhoea with Herbal Formula |
| Q35755078 | Structure and function of the healthy pre-adolescent pediatric gut microbiome |
| Q24626370 | Structure, function and diversity of the healthy human microbiome |
| Q51146477 | Studying microbial functionality within the gut ecosystem by systems biology. |
| Q35925547 | Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes |
| Q64062867 | Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments |
| Q47210600 | Surveillance of Foodborne Pathogens: Towards Diagnostic Metagenomics of Fecal Samples. |
| Q38985658 | Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics |
| Q38767286 | Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome |
| Q35023038 | Systematic identification of gene families for use as "markers" for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups |
| Q38096025 | Systems level immune response analysis and personalized medicine |
| Q34621406 | TIPP: taxonomic identification and phylogenetic profiling |
| Q42379271 | TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms. |
| Q35233987 | Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods. |
| Q47242947 | Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals |
| Q93356450 | Thanatomicrobiome composition profiling as a tool for forensic investigation |
| Q52648684 | The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn's Disease-Like Ileitis. |
| Q26766414 | The Challenge and Potential of Metagenomics in the Clinic |
| Q98164079 | The Challenges of Using Oropharyngeal Samples To Measure Pneumococcal Carriage in Adults |
| Q35652679 | The Complete Mitochondrial Genome of the Foodborne Parasitic Pathogen Cyclospora cayetanensis |
| Q46265536 | The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. |
| Q60958129 | The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics |
| Q34384120 | The Human Microbiome Project: a community resource for the healthy human microbiome |
| Q93270199 | The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities |
| Q35751434 | The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults |
| Q64108290 | The Promises and Pitfalls of Machine Learning for Detecting Viruses in Aquatic Metagenomes |
| Q54967862 | The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data. |
| Q92153641 | The Supragingival Biofilm in Early Childhood Caries: Clinical and Laboratory Protocols and Bioinformatics Pipelines Supporting Metagenomics, Metatranscriptomics, and Metabolomics Studies of the Oral Microbiome |
| Q33574757 | The Use of Next-Generation Sequencing in the Identification of a Fastidious Pathogen: A Lesson From a Clinical Setup |
| Q36286405 | The distinct features of microbial 'dysbiosis' of Crohn's disease do not occur to the same extent in their unaffected, genetically-linked kindred |
| Q35557877 | The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes |
| Q26748672 | The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation |
| Q35987618 | The gut microbiota and metabolic disease: current understanding and future perspectives |
| Q35642328 | The human microbiome in hematopoiesis and hematologic disorders |
| Q34498930 | The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. |
| Q26749040 | The implications of whole-genome sequencing in the control of tuberculosis |
| Q34525463 | The intestinal microbiome of fish under starvation. |
| Q89556854 | The landscape of viral associations in human cancers |
| Q48743597 | The liver-gut microbiota axis modulates hepatotoxicity of tacrine in the rat. |
| Q90589397 | The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography |
| Q35578734 | The perinatal microbiome and pregnancy: moving beyond the vaginal microbiome |
| Q35171983 | The placenta harbors a unique microbiome |
| Q34456447 | The preterm placental microbiome varies in association with excess maternal gestational weight gain |
| Q33610082 | The prevalence of species and strains in the human microbiome: a resource for experimental efforts |
| Q26315521 | The reproductive tracts of two malaria vectors are populated by a core microbiome and by gender- and swarm-enriched microbial biomarkers |
| Q35785593 | The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome |
| Q99400889 | The role of the gut microbiome in graft fibrosis after pediatric liver transplantation |
| Q35884681 | The role of the intestinal microbiota in type 1 diabetes mellitus |
| Q35567838 | The skin microbiome: Associations between altered microbial communities and disease |
| Q36383442 | The transcriptional profile of coronary arteritis in Kawasaki disease |
| Q92382971 | The vaginal microbiome and preterm birth |
| Q50059521 | Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion for efficient hydrogen and methane production from waste activated sludge: Focusing on dynamics of bacterial pathogens as revealed by the combination of metagenomic and qP |
| Q31117238 | Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis |
| Q36080191 | Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma |
| Q62492934 | Tongue coating microbiome as a potential biomarker for gastritis including precancerous cascade |
| Q28076421 | Toward Accurate and Quantitative Comparative Metagenomics |
| Q90571574 | Toward a dynamical understanding of microbial communities |
| Q55245667 | Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. |
| Q37644057 | Transcriptomic responses in the bloom-forming cyanobacterium Microcystis induced during exposure to zooplankton |
| Q57301623 | Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions |
| Q37327689 | Two-stage microbial community experimental design |
| Q91622714 | Type 1 Diabetes: an Association Between Autoimmunity, the Dynamics of Gut Amyloid-producing E. coli and Their Phages |
| Q64079758 | UltraStrain: An NGS-Based Ultra Sensitive Strain Typing Method for |
| Q36051066 | Unbiased probabilistic taxonomic classification for DNA barcoding |
| Q39442695 | Uncovering oral Neisseria tropism and persistence using metagenomic sequencing |
| Q30951410 | Under-detection of endospore-forming Firmicutes in metagenomic data |
| Q59801363 | Understanding the microbial basis of body odor in pre-pubescent children and teenagers |
| Q38843831 | Understanding the role of the microbiome in chronic obstructive pulmonary disease: principles, challenges, and future directions |
| Q33826257 | Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis |
| Q37314891 | Unique Features of Ethnic Mongolian Gut Microbiome revealed by metagenomic analysis |
| Q98158314 | Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach |
| Q93217452 | Updated review of research on the gut microbiota and their relation to depression in animals and human beings |
| Q37349245 | Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment |
| Q47096169 | Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities |
| Q92669580 | Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data |
| Q35618499 | Using populations of human and microbial genomes for organism detection in metagenomes |
| Q35626830 | Using the taxon-specific genes for the taxonomic classification of bacterial genomes |
| Q28391825 | Validation of high throughput sequencing and microbial forensics applications |
| Q36076898 | Vancomycin gene selection in the microbiome of urban Rattus norvegicus from hospital environment |
| Q37222642 | Virtual microfluidics for digital quantification and single-cell sequencing |
| Q36147538 | WEVOTE: Weighted Voting Taxonomic Identification Method of Microbial Sequences |
| Q35120230 | WGSQuikr: fast whole-genome shotgun metagenomic classification |
| Q92118670 | Water and microbial monitoring technologies towards the near future space exploration |
| Q58613618 | What we can see from very small size sample of metagenomic sequences |
| Q55284923 | When old metagenomic data meet newly sequenced genomes, a case study. |
| Q48094534 | Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare |
| Q27324451 | Whole-Metagenome-Sequencing-Based Community Profiles of Vitis vinifera L. cv. Corvina Berries Withered in Two Post-harvest Conditions. |
| Q30300187 | Whole-genome sequencing in outbreak analysis |
| Q91827145 | You are what you eat: diet, health and the gut microbiota |
| Q52677595 | [Gut microbiota, the key for a better diet?] |
| Q47294839 | bioBakery: A meta'omic analysis environment |
| Q58547518 | gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data |
| Q58617812 | imGLAD: accurate detection and quantification of target organisms in metagenomes |
| Q31148641 | k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets |
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