P. Schloss

发表

A framework for human microbiome research

Katherine H. Huang, Daniel D. Sommer, Zhengyuan O. Wang, 2012, Nature.

Toward unrestricted use of public genomic data

Rick L. Stevens, G. Weinstock, P. Bork, 2019, Science.

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

Sarah L. Westcott, P. Schloss, S. Highlander, 2013, Applied and Environmental Microbiology.

In Defense of an Academic Career in Microbiology

P. Schloss, 2018, mSphere.

Structure, Function and Diversity of the Healthy Human Microbiome

Katherine H. Huang, Daniel D. Sommer, Zhengyuan O. Wang, 2012, Nature.

Stabilization of the murine gut microbiome following weaning

J. Petrosino, P. Schloss, Alyxandria M. Schubert, 2012, Gut microbes.

The Human Gut Microbiome as a Screening Tool for Colorectal Cancer

P. Schloss, M. Rogers, M. Ruffin, 2014, Cancer Prevention Research.

Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

P. Schloss, M. Rogers, M. Ruffin, 2016, Genome Medicine.

Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters

P. Schloss, 2021, bioRxiv.

Amplicon Sequence Variants Artificially Split Bacterial Genomes into Separate Clusters

P. Schloss, 2021, mSphere.

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

Sarah L. Westcott, P. Schloss, S. Westcott, 2015, PeerJ.

Removal of rare amplicon sequence variants from 16S rRNA gene sequence surveys biases the interpretation of community structure data

P. Schloss, 2020, bioRxiv.

The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data

P. Schloss, Marc A Sze, 2019, bioRxiv.

The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on 16S rRNA Gene Sequence Data

P. Schloss, Marc A Sze, Marc A. Sze, 2019, mSphere.

Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Emily S. Charlson, Chris I. Hunter, B. Birren, 2011, Nature Biotechnology.

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

Lynn K. Carmichael, N. Lennon, B. Haas, 2012, PloS one.

Dynamics and associations of microbial community types across the human body

P. Schloss, Tao Ding, 2014, Nature.

Metagenomics: genomic analysis of microbial communities.

J. Handelsman, P. Schloss, C. S. Riesenfeld, 2004, Annual review of genetics.

Gut Microbiota of an Invasive Subcortical Beetle, Agrilus planipennis Fairmaire, Across Various Life Stages

J. Handelsman, P. Schloss, K. Raffa, 2008, Environmental entomology.

What is the extent of prokaryotic diversity?

W. Sloan, P. Schloss, I. Head, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

Status of the Microbial Census

J. Handelsman, P. Schloss, 2004, Microbiology and Molecular Biology Reviews.

Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial Community Memberships and Structures

J. Handelsman, P. Schloss, 2006, Applied and Environmental Microbiology.

Introducing TreeClimber, a Test To Compare Microbial Community Structures

J. Handelsman, P. Schloss, 2006, Applied and Environmental Microbiology.

A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

P. Schloss, 2009, PloS one.

Secondary structure improves OTU assignments of 16S rRNA gene sequences

P. Schloss, 2012, The ISME Journal.

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

Ryan A. Lesniewski, Karthik Anantharaman, P. Schloss, 2012, The ISME Journal.

Introducing DOTUR, a Computer Program for Defining Operational Taxonomic Units and Estimating Species Richness

J. Handelsman, P. Schloss, 2005, Applied and Environmental Microbiology.

Preprinting Microbiology

P. Schloss, 2017, mBio.

Intracellular Screen To Identify Metagenomic Clones That Induce or Inhibit a Quorum-Sensing Biosensor

Heather K. Allen, J. Handelsman, P. Schloss, 2005, Applied and Environmental Microbiology.

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

Patrick D. Schloss, Matthew L. Jenior, Sarah L. Westcott, 2016, PeerJ.

Biotechnological prospects from metagenomics.

Jo Handelsman, Patrick D Schloss, J. Handelsman, 2003, Current opinion in biotechnology.

Metabolomics and the Microbiome: Characterizing Molecular Diversity in Complex Microbial Communities

Sara P. Puckett, Marcy J. Balunas, P. Schloss, 2020 .

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

Patrick D. Schloss, Sarah L. Westcott, P. Schloss, 2011, Applied and Environmental Microbiology.

Microbiome Data Distinguish Patients with Clostridium difficile Infection and Non-C. difficile-Associated Diarrhea from Healthy Controls

Patrick D. Schloss, Vincent B. Young, D. Aronoff, 2014, mBio.

Status of the Archaeal and Bacterial Census: an Update

Patrick D. Schloss, J. C. Thrash, P. Schloss, 2016, mBio.

Gut bacteria of bark and wood boring beetles

J. Handelsman, P. Schloss, K. Raffa, 2007 .

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

Patrick D. Schloss, Dirk Gevers, Sarah L. Westcott, 2011, PloS one.

The Diagnostic Potential & Interactive Dynamics of the Colorectal Cancer Virome

Geoffrey D. Hannigan, P. Schloss, M. Ruffin, 2017, bioRxiv.

Quantifying bacterial population dynamics in compost using 16S rRNA gene probes

J. Gossett, P. Schloss, L. Walker, 2004, Applied Microbiology and Biotechnology.

Tracking temporal changes of bacterial community fingerprints during the initial stages of composting.

P. Schloss, L. Walker, D. Wilson, 2003, FEMS microbiology ecology.

Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract

Casey M. Theriot, Patrick D. Schloss, Vincent B. Young, 2014, Infection and Immunity.

Clostridium difficile alters the structure and metabolism of distinct cecal microbiomes during initial infection to promote sustained colonization

P. Schloss, V. Young, M. Jenior, 2018 .

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut microbiomes

P. Schloss, V. Young, M. Jenior, 2017, bioRxiv.

Clostridium difficile differentially alters the structure and metabolism of distinct cecal microbiomes to promote persistent colonization during infection

Matthew L. Jenior, P. Schloss, V. Young, 2017, bioRxiv.

Microbial Characterization of Qatari Barchan Sand Dunes

M. Louge, P. Schloss, A. Sultan, 2016, PloS one.

Structures Community Memberships and Comparisons of Microbial Operational Taxonomic Unit-Based Introducing SONS , a Tool for

J. Handelsman, P. Schloss, 2006 .

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model

P. Schloss, M. Rogers, M. Ruffin, 2016, Microbiome.

DNA from fecal immunochemical test can replace stool for microbiota-based colorectal cancer screening

P. Schloss, M. Rogers, M. Ruffin, 2016, bioRxiv.

The last word: books as a statistical metaphor for microbial communities.

J. Handelsman, P. Schloss, 2007, Annual review of microbiology.

Spatial Variation of the Native Colon Microbiota in Healthy Adults

Kaitlin J. Flynn, P. Schloss, M. Ruffin, 2017, Cancer Prevention Research.

Association of bacterial community types, functional microbial processes and lung disease in cystic fibrosis airways

P. Schloss, S. Widder, J. Lipuma, 2021, The ISME Journal.

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

P. Schloss, Alyxandria M. Schubert, H. Sinani, 2015, mBio.

The dynamics of a family’s gut microbiota reveal variations on a theme

J. Petrosino, P. Schloss, Kathryn Iverson, 2014, Microbiome.

Species Richness Taxonomic Units and Estimating Program for Defining Operational Introducing DOTUR , a Computer

J. Handelsman, P. Schloss, 2005 .

Microbial community function and biomarker discovery in the human microbiome

C. Huttenhower, N. Segata, L. Waldron, 2011, Genome Biology.

Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes

Nicholas A. Lesniak, P. Schloss, Alyxandria M. Schubert, 2020, bioRxiv.

Metagenomics for studying unculturable microorganisms: cutting the Gordian knot

Jo Handelsman, Patrick D Schloss, J. Handelsman, 2005, Genome Biology.

Women Are Underrepresented and Receive Differential Outcomes at ASM Journals: a Six-Year Retrospective Analysis

P. Schloss, H. Barton, B. D. Topçuoglu, 2020, mBio.

Diluted Fecal Community Transplant Restores Clostridioides difficile Colonization Resistance to Antibiotic-Perturbed Murine Communities

Nicholas A. Lesniak, P. Schloss, Lucas Bishop, 2022, bioRxiv.

The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model

Nicholas A. Lesniak, P. Schloss, Lucas Bishop, 2019, mSphere.

The Proton Pump Inhibitor Omeprazole Does Not Promote Clostridioides difficile Colonization in a Murine Model

Nicholas A. Lesniak, P. Schloss, Lucas Bishop, 2019, mSphere.

The initial gut microbiota and response to antibiotic perturbation influence Clostridioides difficile colonization in mice

P. Schloss, Lucas Bishop, Sarah Tomkovich, 2020, bioRxiv.

Impact of Enhanced Staphylococcus DNA Extraction on Microbial Community Measures in Cystic Fibrosis Sputum

J. Petrosino, P. Schloss, V. Young, 2012, PloS one.

MOLECULAR ASSESSMENT OF INOCULUM EFFICACY AND PROCESS REPRODUCIBILITY IN COMPOSTING USING ARISA

P. Schloss, L. Walker, David B. Wilson, 2003 .

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Martin Hartmann, Patrick D Schloss, Sarah L Westcott, 2009, Applied and Environmental Microbiology.

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research

Patrick D Schloss, P. Schloss, 2018, mBio.

Application of database-independent approach to assess the quality of OTU picking methods

P. Schloss, 2016, bioRxiv.

The Riffomonas Reproducible Research Tutorial Series

Patrick D Schloss, P. Schloss, 2018, The Journal of open source education.

Microbial community function and biomarker discovery in the human microbiome

C. Huttenhower, N. Segata, L. Waldron, 2011, Genome Biology.

Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome

Patrick D. Schloss, P. Schloss, Marc A. Sze, 2016, mBio.

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome

Nicholas A. Lesniak, P. Schloss, Nielson T. Baxter, 2019, mSphere.

Intra- and Interindividual Variations Mask Interspecies Variation in the Microbiota of Sympatric Peromyscus Populations

Matthew L. Jenior, P. Schloss, Alyxandria M. Schubert, 2014, Applied and Environmental Microbiology.

Decade-long bacterial community dynamics in cystic fibrosis airways

Susan Murray, Patrick D. Schloss, Jun Z. Li, 2012, Proceedings of the National Academy of Sciences.

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Bernard Henrissat, Brandi L. Cantarel, Curtis Huttenhower, 2012, PLoS Comput. Biol..

Structure of the gut microbiome following colonization with human feces determines colonic tumor burden

Patrick D Schloss, Joseph P Zackular, P. Schloss, 2014, Microbiome.

NLRP6 Protects Il10-/- Mice from Colitis by Limiting Colonization of Akkermansia muciniphila.

P. Schloss, Nielson T. Baxter, E. Martens, 2017, Cell reports.

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

Mack T. Ruffin, Patrick D. Schloss, Geoffrey D. Hannigan, 2018, mBio.

Viral and Bacterial Communities of Colorectal Cancer

Geoffrey D. Hannigan, P. Schloss, M. Ruffin, 2017 .

Fecal Microbiota Signatures Are Associated with Response to Ustekinumab Therapy among Crohn’s Disease Patients

P. Schloss, S. Telesco, Tao Ding, 2018, mBio.

Integration of Microbial Ecology and Statistics: a Test To Compare Gene Libraries

Jo Handelsman, Patrick D. Schloss, J. Handelsman, 2004, Applied and Environmental Microbiology.

Fecal Short-Chain Fatty Acids Are Not Predictive of Colonic Tumor Status and Cannot Be Predicted Based on Bacterial Community Structure

Nicholas A. Lesniak, P. Schloss, M. Ruffin, 2019, mBio.

Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes

Patrick D. Schloss, Matthew L. Jenior, Vincent B. Young, 2017, mSystems.

EPIGENETIC REGULATION OF CELLULAR MEMORY BY THE POLYCOMB AND TRITHORAX GROUP PROTEINS

Jo Handelsman, Julian Parkhill, David Haig, 2008 .

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

Jo Handelsman, Patrick D. Schloss, J. Handelsman, 2008, BMC Bioinformatics.

Intra-and inter-individual variation masks inter-species variation 1 in the microbiota of sympatric Peromyscus populations 2 3 Running title : Variation in the Peromyscus microbiota 4 5

Matthew L. Jenior, P. Schloss, Alyxandria M. Schubert, 2014 .

Gut Microbiota Modulate CD8 T Cell Responses to Influence Colitis-Associated Tumorigenesis.

P. Schloss, E. Martens, J. Whitfield, 2020, Cell reports.

Reporting guidelines for human microbiome research: the STORMS checklist

Chris I. Hunter, Jennifer M. Fettweis, F. Bushman, 2021, Nature Medicine.

The dynamics of a family’s gut microbiota reveal variations on a theme

J. Petrosino, P. Schloss, Kathryn Iverson, 2014, Microbiome.

Bioinformatics for the Human Microbiome Project

Mihai Pop, Curtis Huttenhower, Patrick D. Schloss, 2012, PLoS Comput. Biol..

The Initial Gut Microbiota and Response to Antibiotic Perturbation Influence Clostridioides difficile Clearance in Mice

P. Schloss, Lucas Bishop, Sarah Tomkovich, 2020, mSphere.

The interplay between microbiome dynamics and pathogen dynamics in a murine model of Clostridium difficile Infection

Patrick D Schloss, P. Schloss, I. Bergin, 2011, Gut microbes.

Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

Patrick D Schloss, Kristina Crothers, Elodie Ghedin, 2013, American journal of respiratory and critical care medicine.

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Emily S. Charlson, F. Bushman, G. Weinstock, 2015, American journal of respiratory and critical care medicine.

Mathematical modeling of primary succession of murine intestinal microbiota

Simeone Marino, Patrick D. Schloss, J. Petrosino, 2013, Proceedings of the National Academy of Sciences.

Multiphasic analysis of the temporal development of the distal gut microbiota in patients following ileal pouch anal anastomosis

Folker Meyer, Patrick D Schloss, Dongjuan Dai, 2013, Microbiome.

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

Patrick D Schloss, Jenna Wiens, Mack T Ruffin, 2020, mBio.

1 A framework for effective application of machine learning to microbiome-1 based classification problems 2 3 4 5 6 Running title : Machine learning framework to model microbiome data 7 8 9 10 11

Nicholas A. Lesniak, J. Wiens, P. Schloss, 2020 .

A Framework for Effective Application of Machine Learning to Microbiome-Based Classification Problems

Jenna Wiens, Mack T. Ruffin, Begüm D. Topçuoğlu, 2019, mBio.

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Danai Koutra, Melissa Beth Duhaime, Patrick D. Schloss, 2017, bioRxiv.

Biogeography & environmental conditions shape bacteriophage-bacteria networks across the human microbiome

Geoffrey D. Hannigan, Danai Koutra, P. Schloss, 2017, bioRxiv.

Novelty and Uniqueness Patterns of Rare Members of the Soil Biosphere

Noha H. Youssef, Vanessa L. Bailey, Mostafa S. Elshahed, 2008, Applied and Environmental Microbiology.

Toward a Census of Bacteria in Soil

Jo Handelsman, Patrick D. Schloss, J. Handelsman, 2006, PLoS Comput. Biol..

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

Patrick D Schloss, Sarah L Westcott, Sarah L. Westcott, 2017, mSphere.

Evaluating different approaches that test whether microbial communities have the same structure

Patrick D Schloss, P. Schloss, 2008, The ISME Journal.

Psychrotrophic strain of Janthinobacterium lividum from a cold Alaskan soil produces prodigiosin.

Heather K. Allen, J. Handelsman, J. Clardy, 2010, DNA and cell biology.

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

Patrick D. Schloss, P. Schloss, 2010, PLoS Comput. Biol..

NLRP6 Protects Il10-/- Mice from Colitis by Limiting Colonization of Akkermansia muciniphila.

P. Schloss, Nielson T. Baxter, E. Martens, 2017, Cell reports.

Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions

P. Schloss, M. Rogers, M. Ruffin, 2016, Genome Medicine.

The Gut Microbiome Modulates Colon Tumorigenesis

J. Petrosino, P. Schloss, Nielson T. Baxter, 2013, mBio.

Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis

Patrick D. Schloss, Joseph P. Zackular, P. Schloss, 2015, mSphere.

Nonsteroidal Anti-inflammatory Drugs Alter the Microbiota and Exacerbate Clostridium difficile Colitis while Dysregulating the Inflammatory Response

Eric P. Skaar, M. Washington, D. Aronoff, 2018, mBio.

Low prevalence of Clostridium septicum fecal carriage in an adult population.

D. Aronoff, P. Schloss, Alyxandria M. Schubert, 2015, Anaerobe.

The status of the microbial census: an update

J. C. Thrash, P. Schloss, Rene A. Girard, 2016, bioRxiv.

Robustness of the Bacterial Community in the Cabbage White Butterfly Larval Midgut

Courtney J. Robinson, J. Handelsman, P. Schloss, 2009, Microbial Ecology.

mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines

Jenna Wiens, Zena Lapp, Kelly L. Sovacool, 2021, J. Open Source Softw..

An Osmotic Laxative Renders Mice Susceptible to Prolonged Clostridioides difficile Colonization and Hinders Clearance

Nicholas A. Lesniak, P. Schloss, I. Bergin, 2021, bioRxiv.

The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity

Nicholas A. Lesniak, Kaitlin J. Flynn, P. Schloss, 2022, bioRxiv.

Composition of the bacterial community in the gut of the pine engraver, Ips pini (Say) (Coloptera) colonizing red pine

J. Handelsman, P. Schloss, K. Raffa, 2007 .

Characterization of Gut-Associated Bacteria in Larvae and Adults of the Southern Pine Beetle, Dendroctonus frontalis Zimmermann

J. Handelsman, P. Schloss, K. Raffa, 2006 .

Intestinal Inflammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides difficile Colonization in a Mouse Model of Colitis

Kelly L. Sovacool, P. Schloss, I. Bergin, 2022, bioRxiv.

Changes in cystic fibrosis airway microbiota at pulmonary exacerbation.

J. Petrosino, P. Schloss, V. Young, 2013, Annals of the American Thoracic Society.

Microbiology: An integrated view of the skin microbiome

P. Schloss, 2014, Nature.

StructuresMemberships and Comparisons of Microbial Operational Taxonomic Unit-Based Introducing SONS, a Tool for

Jo Handelsman, Patrick D. Schloss, J. Handelsman, 2010 .

Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors

P. Schloss, Marc A. Sze, M. Sze, 2018, mBio.

Normalization of the microbiota in patients after treatment for colonic lesions

P. Schloss, M. Rogers, M. Ruffin, 2017, Microbiome.

The effect of treatment on the microbiota of patients diagnosed with colonic lesions

P. Schloss, M. Rogers, M. Ruffin, 2017 .

and Estimating Species Richness for Defining Operational Taxonomic Units Introducing DOTUR , a Computer Program

J. Handelsman, P. Schloss, 2005 .

Libraries Statistics : a Test To Compare Gene Integration of Microbial Ecology and

J. Handelsman, B. Larget, P. Schloss, 2004 .

Reintroducing mothur: 10 Years Later

Patrick D Schloss, P. Schloss, 2019, Applied and Environmental Microbiology.

OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs

Kelly L. Sovacool, Sarah L. Westcott, P. Schloss, 2021, bioRxiv.

Bacteria Associated with the Guts of Two Wood-Boring Beetles: Anoplophora glabripennis and Saperda vestita (Cerambycidae)

J. Handelsman, P. Schloss, K. Raffa, 2006 .

Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization

Patrick D. Schloss, Matthew L. Jenior, Vincent B. Young, 2018, mSphere.

Effect of Sample Storage Conditions on Culture-Independent Bacterial Community Measures in Cystic Fibrosis Sputum Specimens

J. Petrosino, P. Schloss, V. Young, 2011, Journal of Clinical Microbiology.

The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation

Z. Abdo, P. Schloss, T. Schmidt, 2015, Microbiome.

Jo Handelsman: Adviser, Teacher, Role Model, Friend

P. Schloss, 2018 .

Molecular characterization of fungal community dynamics in the initial stages of composting.

P. Schloss, L. Walker, A. Hay, 2005, FEMS microbiology ecology.

Running title : Introducing mothur Appropriate Section : Methods

Donovan H. Parks, Ryan A. Lesniewski, Courtney J. Robinson, 2009 .

A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer

Courtney R. Armour, P. Schloss, B. D. Topçuoglu, 2021, bioRxiv.

Clones That Induce or Inhibit a Quorum-Sensing 2005 . Intracellular Screen To Identify Metagenomic

Heather K. Allen, J. Handelsman, P. Schloss, 2005 .

Top 10 research priorities in colorectal cancer: results from the Colorectal Cancer Priority-Setting Partnership

P. Schloss, T. Gronlund, M. Wensing, 2022, Journal of Cancer Research and Clinical Oncology.

OptiClust: Improved method for assigning amplicon-based sequence data to operational taxonomic units

Patrick D. Schloss, Sarah L. Westcott, P. Schloss, 2016, bioRxiv.

Erratum: NLRP6 Protects Il10−/− Mice from Colitis by Limiting Colonization of Akkermansia muciniphila (Cell Reports (2017) 19(4) (733–745) (S2211124717304576) (10.1016/j.celrep.2017.03.080))

P. Schloss, Nielson T. Baxter, E. Martens, 2017 .

Sociality does not predict oral microbiome composition or diversity in free-living prairie voles

P. Schloss, Connor T. Lambert, Lauren Petrullo, 2023, Animal Behaviour.

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer

Kaitlin J. Flynn, P. Schloss, Nielson T. Baxter, 2016, mSphere.

DNA from fecal immunochemical test can replace stool for detection of colonic lesions using a microbiota-based model

P. Schloss, M. Rogers, M. Ruffin, 2016, Microbiome.

Mo1796 The Gut Microbiome Differentiates Clinical Phenotypes in Moderate to Severe Crohn's Disease: Results From the CERTIFI Study

Tanya Yatsunenko, P. Schloss, S. Telesco, 2015 .

Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods

Patrick D Schloss, P. Schloss, 2016, mSystems.

Waste not, want not: Revisiting the analysis that called into question the practice of rarefaction

P. Schloss, 2023, bioRxiv.

Protection from Lethal Clostridioides difficile Infection via Intraspecies Competition for Cogerminant

Matthew L. Jenior, P. Schloss, I. Bergin, 2021, mBio.

Normalization of the microbiota in patients after treatment for colonic lesions

P. Schloss, M. Rogers, M. Ruffin, 2017, bioRxiv.

Intestinal In ﬂ ammation Reversibly Alters the Microbiota to Drive Susceptibility to Clostridioides dif ﬁ cile Colonization in a Mouse Model of Colitis

Kelly L. Sovacool, P. Schloss, I. Bergin, 2022 .

Application of database-independent approach to assess the quality of OTU picking methods

Patrick D. Schloss, P. Schloss, 2016, bioRxiv.

Support Science by Publishing in Scientific Society Journals

A. Casadevall, P. Schloss, Mark Johnston, 2017, mBio.

Coding-Complete RNA Virus Genomes Assembled from Murine Cecal Metatranscriptomes

P. Schloss, Andrew J. Beaudoin, Joshua M A Stough, 2020, Microbiology Resource Announcements.

Evaluation of software impact designed for biomedical research: Are we measuring what’s meaningful?

Cambridge, Northern Arizona University, Seattle, 2023, ArXiv.

Gut Microbiome Composition in Lynch Syndrome With and Without History of Colorectal Neoplasia and Non-Lynch Controls.

P. Schloss, E. Stoffel, S. Rifkin, 2023, Journal of gastrointestinal cancer.

Clostridium difficile colonizes alternative nutrient niches during infection across distinct murine gut environments

Matthew L. Jenior, P. Schloss, V. Young, 2016 .

Machine learning classification by fitting amplicon sequences to existing OTUs

Kelly L. Sovacool, J. Wiens, P. Schloss, 2023, bioRxiv.

Analysis of 2,440 human exomes highlights the evolution and functional impact of rare coding variation

C. Huttenhower, N. Segata, L. Waldron, 2011, Genome Biology.

Status of the Archaeal and Bacterial Census: an Update

J. C. Thrash, P. Schloss, Thomas M. Martin, 2016, mBio.

Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses

P. Schloss, 2023, bioRxiv.

Microbial community function and biomarker discovery in the human microbiome

C. Huttenhower, N. Segata, L. Waldron, 2011, Genome Biology.

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Donovan H. Parks, Ryan A. Lesniewski, Courtney J. Robinson, 2009, Applied and Environmental Microbiology.

Multicenter Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals.

Emily S. Charlson, F. Bushman, G. Weinstock, 2015, American journal of respiratory and critical care medicine.

Comparison of the respiratory microbiome in healthy nonsmokers and smokers.

G. Weinstock, J. Curtis, E. Sodergren, 2013, American journal of respiratory and critical care medicine.

The Diagnostic Potential & Interactive Dynamics of the Colorectal Cancer Virome

Geoffrey D. Hannigan, P. Schloss, M. Ruffin, 2017, bioRxiv.

DNA from fecal immunochemical test can replace stool for microbiota-based colorectal cancer screening

P. Schloss, M. Rogers, M. Ruffin, 2016, bioRxiv.

The Diagnostic Potential & Interactive Dynamics of the 1 Colorectal Cancer Virome

Geoffrey D. Hannigan, P. Schloss, M. Ruffin, 2018 .

Sequencing 16 S rRNA gene fragments using the PacBio SMRT DNA sequencing system

Matthew L. Jenior, Sarah L. Westcott, P. Schloss, 2017 .

Diagnostic Potential & the Interactive Dynamics of the Colorectal Cancer Virome

Geoffrey D. Hannigan, P. Schloss, M. Ruffin, 2017 .

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

J. Handelsman, P. Schloss, 2008, BMC Bioinformatics.

Assigning 16 S rRNA gene sequences to operational taxonomic units ( OTUs ) allows microbial

P. Schloss, 2016 .