| 1 | Improving microbial phylogeny with citizen science within a mass-market video game | 25.8 | 7 | Citations (PDF) |
| 2 | Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases | 2.7 | 17 | Citations (PDF) |
| 3 | Global branches and local states of the human gut microbiome define associations with environmental and intrinsic factors | 14.2 | 32 | Citations (PDF) |
| 4 | Testing GitHub projects on custom resources using unprivileged Kubernetes runners 2023, , 332-335 | | 1 | Citations (PDF) |
| 5 | Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection | 1.4 | 12 | Citations (PDF) |
| 6 | A posteriori dietary patterns better explain variations of the gut microbiome than individual markers in the American Gut Project | 5.4 | 65 | Citations (PDF) |
| 7 | Applications and Comparison of Dimensionality Reduction Methods for Microbiome Data | 3.8 | 49 | Citations (PDF) |
| 8 | Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases | 4.6 | 19 | Citations (PDF) |
| 9 | Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy | 4.6 | 98 | Citations (PDF) |
| 10 | Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype | 4.6 | 20 | Citations (PDF) |
| 11 | Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase | 4.6 | 9 | Citations (PDF) |
| 12 | Enhancing untargeted metabolomics using metadata-based source annotation | 25.8 | 64 | Citations (PDF) |
| 13 | Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission | 34.3 | 443 | Citations (PDF) |
| 14 | Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species | 14.2 | 71 | Citations (PDF) |
| 15 | Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity | 16.5 | 148 | Citations (PDF) |
| 16 | Fecal Microbiota Transplantation Is Highly Effective in Real-World Practice: Initial Results From the FMT National Registry | 1.0 | 180 | Citations (PDF) |
| 17 | High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing | 24.0 | 357 | Citations (PDF) |
| 18 | Reply to: Examining microbe–metabolite correlations by linear methods | 24.0 | 9 | Citations (PDF) |
| 19 | Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment | 11.4 | 21 | Citations (PDF) |
| 20 | Evaluation of the Effect of Storage Methods on Fecal, Saliva, and Skin Microbiome Composition | 4.6 | 61 | Citations (PDF) |
| 21 | Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection | 11.4 | 67 | Citations (PDF) |
| 22 | EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets | 4.6 | 51 | Citations (PDF) |
| 23 | SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment | 11.4 | 54 | Citations (PDF) |
| 24 | Accelerating Key Bioinformatics Tasks 100-fold by Improving Memory Access 2021, 33, 1-5 | | 0 | Citations (PDF) |
| 25 | Nutritional Interventions and the Gut Microbiome in Children | 11.4 | 29 | Citations (PDF) |
| 26 | Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus | 4.6 | 131 | Citations (PDF) |
| 27 | Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding | 5.3 | 73 | Citations (PDF) |
| 28 | Efficient computation of Faith's phylogenetic diversity with applications in characterizing microbiomes | 4.7 | 38 | Citations (PDF) |
| 29 | The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder | 4.6 | 11 | Citations (PDF) |
| 30 | Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity | 8.1 | 43 | Citations (PDF) |
| 31 | Effects of the microalgae Chlamydomonas on gastrointestinal health | 3.6 | 92 | Citations (PDF) |
| 32 | Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India | 3.1 | 27 | Citations (PDF) |
| 33 | Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome | 4.6 | 14 | Citations (PDF) |
| 34 | Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV | 4.6 | 2 | Citations (PDF) |
| 35 | Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome | 4.6 | 137 | Citations (PDF) |
| 36 | Multiple-Disease Detection and Classification across Cohorts via Microbiome Search | 4.6 | 20 | Citations (PDF) |
| 37 | Chemically informed analyses of metabolomics mass spectrometry data with Qemistree | 12.5 | 100 | Citations (PDF) |
| 38 | Context-aware dimensionality reduction deconvolutes gut microbial community dynamics | 25.8 | 88 | Citations (PDF) |
| 39 | Reply to Sun et al., “Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy” | 4.5 | 0 | Citations (PDF) |
| 40 | Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 | 25.8 | 18,874 | Citations (PDF) |
| 41 | Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny | 8.1 | 70 | Citations (PDF) |
| 42 | Species abundance information improves sequence taxonomy classification accuracy | 14.2 | 173 | Citations (PDF) |
| 43 | Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity | 8.1 | 133 | Citations (PDF) |
| 44 | redbiom: a Rapid Sample Discovery and Feature Characterization System | 4.6 | 46 | Citations (PDF) |
| 45 | The impact of skin care products on skin chemistry and microbiome dynamics | 4.0 | 154 | Citations (PDF) |
| 46 | Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults | 4.6 | 318 | Citations (PDF) |
| 47 | Calour: an Interactive, Microbe-Centric Analysis Tool | 4.6 | 33 | Citations (PDF) |
| 48 | Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces | 11.4 | 209 | Citations (PDF) |
| 49 | Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea | 14.2 | 316 | Citations (PDF) |
| 50 | Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians | 6.1 | 266 | Citations (PDF) |
| 51 | Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects | 2.4 | 227 | Citations (PDF) |
| 52 | The emergence of microbiome centres | 16.5 | 19 | Citations (PDF) |
| 53 | Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information | 4.6 | 483 | Citations (PDF) |
| 54 | Identifying and Predicting Novelty in Microbiome Studies | 4.5 | 34 | Citations (PDF) |
| 55 | Qiita: rapid, web-enabled microbiome meta-analysis | 24.0 | 596 | Citations (PDF) |
| 56 | Striped UniFrac: enabling microbiome analysis at unprecedented scale | 24.0 | 87 | Citations (PDF) |
| 57 | American Gut: an Open Platform for Citizen Science Microbiome Research | 4.6 | 780 | Citations (PDF) |
| 58 | Best practices for analysing microbiomes | 64.7 | 1,528 | Citations (PDF) |
| 59 | Methods for phylogenetic analysis of microbiome data | 16.5 | 89 | Citations (PDF) |
| 60 | Are microbiome studies ready for hypothesis-driven research? | 7.7 | 30 | Citations (PDF) |
| 61 | Regional variation limits applications of healthy gut microbiome reference ranges and disease models | 36.5 | 797 | Citations (PDF) |
| 62 | Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome | 4.6 | 122 | Citations (PDF) |
| 63 | GABA-modulating bacteria of the human gut microbiota | 16.5 | 939 | Citations (PDF) |
| 64 | Balance Trees Reveal Microbial Niche Differentiation | 4.6 | 308 | Citations (PDF) |
| 65 | Bringing the Dynamic Microbiome to Life with Animations | 10.6 | 117 | Citations (PDF) |
| 66 | Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns | 4.6 | 1,727 | Citations (PDF) |
| 67 | Dynamics of the human gut microbiome in inflammatory bowel disease | 16.5 | 1,055 | Citations (PDF) |
| 68 | The Microbiome and Human Biology | 7.5 | 309 | Citations (PDF) |
| 69 | A communal catalogue reveals Earth’s multiscale microbial diversity | 34.3 | 2,538 | Citations (PDF) |
| 70 | Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping | 4.6 | 131 | Citations (PDF) |
| 71 | Strains, functions and dynamics in the expanded Human Microbiome Project | 34.3 | 1,179 | Citations (PDF) |
| 72 | Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project | 1.9 | 44 | Citations (PDF) |
| 73 | Extreme Dysbiosis of the Microbiome in Critical Illness | 3.1 | 358 | Citations (PDF) |
| 74 | The Treatment-Naive Microbiome in New-Onset Crohn’s Disease | 10.6 | 3,062 | Citations (PDF) |
| 75 | Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences | 25.8 | 9,195 | Citations (PDF) |
| 76 | The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome | 3.4 | 746 | Citations (PDF) |
| 77 | An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea | 9.2 | 5,046 | Citations (PDF) |
| 78 | QIIME allows analysis of high-throughput community sequencing data | 24.0 | 35,018 | Citations (PDF) |
