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| 37310549 | Gut Microbiome Composition in Lynch Syndrome With and Without History of Colorectal Neoplasia and Non-Lynch Controls. | J Gastrointest Cancer | 2024 |
| 38054712 | Waste not, want not: revisiting the analysis that called into question the practice of rarefaction. | mSphere | 2024 |
| 36651754 | The Riffomonas YouTube Channel: An Educational Resource To Foster Reproducible Research Practices. | Microbiol Resour Announc | 2023 |
| 37909768 | More evidence of Impact Factor Mania. | Microbiol Spectr | 2023 |
| 37615431 | Machine learning classification by fitting amplicon sequences to existing OTUs. | mSphere | 2023 |
| 34689185 | Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways. | ISME J | 2022 |
| 35856563 | The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity. | mBio | 2022 |
| 35900107 | Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides difficile Colonization in a Mouse Model of Colitis. | mBio | 2022 |
| 35913161 | Diluted Fecal Community Transplant Restores Clostridioides difficile Colonization Resistance to Antibiotic-Perturbed Murine Communities. | mBio | 2022 |
| 35224460 | Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research. | J Open Source Educ | 2022 |
| 35012354 | A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer. | mBio | 2022 |
| 35107341 | OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs. | mSphere | 2022 |
| 33144320 | The Decision To Publish Gutierrez-Alvarez et al., "Middle East Respiratory Syndrome Coronavirus Gene 5 Modulates Pathogenesis in Mice". | J Virol | 2021 |
| 33785619 | Protection from Lethal Clostridioides difficile Infection via Intraspecies Competition for Cogerminant. | mBio | 2021 |
| 33758094 | Erratum for Hagan et al., "Women Are Underrepresented and Receive Differential Outcomes at ASM Journals: a Six-Year Retrospective Analysis". | mBio | 2021 |
| 34789871 | Reporting guidelines for human microbiome research: the STORMS checklist. | Nat Med | 2021 |
| 34585964 | An Osmotic Laxative Renders Mice Susceptible to Prolonged Clostridioides difficile Colonization and Hinders Clearance. | mSphere | 2021 |
| 34414351 | mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines. | J Open Source Softw | 2021 |
| 34287003 | Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters. | mSphere | 2021 |
| 33952668 | Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes. | mSphere | 2021 |
| 32193230 | Coding-Complete RNA Virus Genomes Assembled from Murine Cecal Metatranscriptomes. | Microbiol Resour Announc | 2020 |
| 31704678 | Reintroducing mothur: 10 Years Later. | Appl Environ Microbiol | 2020 |
| 33087520 | The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice. | mSphere | 2020 |
| 33262256 | Women Are Underrepresented and Receive Differential Outcomes at ASM Journals: a Six-Year Retrospective Analysis. | mBio | 2020 |
| 32737035 | The ASM Journals Committee Values the Contributions of Black Microbiologists. | Clin Microbiol Rev | 2020 |
| 32853198 | Ten simple rules to increase computational skills among biologists with Code Clubs. | PLoS Comput Biol | 2020 |
| 32788948 | The ASM Journals Committee Values the Contributions of Black Microbiologists. | J Microbiol Biol Educ | 2020 |
| 32518182 | A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems. | mBio | 2020 |
| 32268087 | Gut Microbiota Modulate CD8Â T Cell Responses to Influence Colitis-Associated Tumorigenesis. | Cell Rep | 2020 |
| 30622186 | Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate <i>Clostridium difficile</i> Colitis while Dysregulating the Inflammatory Response. | mBio | 2019 |
| 31748246 | The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model. | mSphere | 2019 |
| 31530677 | Explaining Order among Those Who Share Positions in the Author Byline. | mBio | 2019 |
| 31266879 | Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure. | mBio | 2019 |
| 31118305 | Erratum for Baxter et al., "The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome". | mSphere | 2019 |
| 31118299 | The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data. | mSphere | 2019 |
| 30728281 | The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome. | mSphere | 2019 |
| 30679363 | Toward unrestricted use of public genomic data. | Science | 2019 |
| 29535202 | Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn's Disease Patients. | mBio | 2018 |
| 34386723 | The Riffomonas Reproducible Research Tutorial Series. | J Open Source Educ | 2018 |
| 29871916 | Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors. | mBio | 2018 |
| 29871915 | Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research. | mBio | 2018 |
| 29950381 | <i>Clostridium difficile</i> Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization. | mSphere | 2018 |
| 30459201 | Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome. | mBio | 2018 |
| 30327440 | Erratum for Sze and Schloss, "Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors". | mBio | 2018 |
| 29636352 | Spatial Variation of the Native Colon Microbiota in Healthy Adults. | Cancer Prev Res (Phila) | 2018 |
| 29668682 | Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome. | PLoS Comput Biol | 2018 |
| 29720529 | In Defense of an Academic Career in Microbiology. | mSphere | 2018 |
| 28761936 | <i>Clostridium difficile</i> Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes. | mSystems | 2017 |
| 28445725 | NLRP6 Protects Il10<sup>-/-</sup> Mice from Colitis by Limiting Colonization of Akkermansia muciniphila. | Cell Rep | 2017 |
| 28289728 | OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units. | mSphere | 2017 |