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List of works by Patrick D. Schloss

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

scientific article published on 09 June 2020

A framework for human microbiome research

scientific article

A high-throughput DNA sequence aligner for microbial ecology studies

scientific article

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

scientific article

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

scientific article published on 14 July 2015

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

scientific article published on March 2016

Assessing and improving methods used in operational taxonomic unit-based approaches for 16S rRNA gene sequence analysis

scientific article

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

scientific article

Bioinformatics for the Human Microbiome Project

scientific article

Biotechnological prospects from metagenomics

scientific article

Changes in cystic fibrosis airway microbiota at pulmonary exacerbation

scientific article

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

scientific article

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

scientific article

Coding-Complete RNA Virus Genomes Assembled from Murine Cecal Metatranscriptomes

scientific article published on 19 March 2020

Comparison of the respiratory microbiome in healthy nonsmokers and smokers

scientific article published on May 2013

Consent insufficient for data release-Response

scientific article published on 01 May 2019

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

scientific article

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

scientific article published on 8 December 2015

Decade-long bacterial community dynamics in cystic fibrosis airways

scientific article

Developing and deploying an integrated workshop curriculum teaching computational skills for reproducible research

scientific article published in 2022

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

scientific article

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

scientific article published on 20 November 2018

Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract

scientific article

Effect of sample storage conditions on culture-independent bacterial community measures in cystic fibrosis sputum specimens

scientific article published on 24 August 2011

Erratum for Schloss et al., "Support Science by Publishing in Scientific Society Journals".

scientific article

Erratum for Sze and Schloss, "Leveraging Existing 16S rRNA Gene Surveys To Identify Reproducible Biomarkers in Individuals with Colorectal Tumors"

article

Erratum for Sze and Schloss, "Looking for a Signal in the Noise: Revisiting Obesity and the Microbiome".

scientific article published on 5 December 2017

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

scientific article published on 31 January 2008

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

scientific article

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

scientific article published on 02 July 2019

Gut microbiota of an invasive subcortical beetle, Agrilus planipennis Fairmaire, across various life stages

scientific article published on October 2008

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

scientific article published on 5 June 2018

Impact of enhanced Staphylococcus DNA extraction on microbial community measures in cystic fibrosis sputum

scientific article

In Defense of an Academic Career in Microbiology.

scientific article

Integration of microbial ecology and statistics: a test to compare gene libraries

scientific article

Intra- and interindividual variations mask interspecies variation in the microbiota of sympatric peromyscus populations.

scientific article

Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor

scientific article published in October 2005

Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness

scientific article

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures

scientific article

Introducing TreeClimber, a test to compare microbial community structures

scientific article published in April 2006

Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities

scientific article

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

scientific article published on 5 June 2018

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

scientific article

Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis

scientific article published on 4 November 2015

Mathematical modeling of primary succession of murine intestinal microbiota.

scientific article

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer

scientific article

Metabolic reconstruction for metagenomic data and its application to the human microbiome

scientific article published in 2012

Metagenomics for studying unculturable microorganisms: cutting the Gordian knot

scientific article

Metagenomics: genomic analysis of microbial communities

scientific article

Microbial Characterization of Qatari Barchan Sand Dunes

scientific article

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

scientific article

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

scientific article

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

scientific article published in January 2005

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

scientific article published on 6 August 2015

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

scientific article published on 04 March 2013

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

scientific article published on 08 January 2019

Normalization of the microbiota in patients after treatment for colonic lesions.

scientific article published on 16 November 2017

Novelty and uniqueness patterns of rare members of the soil biosphere

scientific article

Nurturing the microbiome field

scientific article published in November 2015

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

scientific article

Preprinting Microbiology

scientific article (publication date: 23 May 2017)

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

scientific article

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

scientific article published on 11 September 2004

Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies

scientific article

Reintroducing mothur: 10 Years Later

scientific article published on 07 January 2020

Robustness of the bacterial community in the cabbage white butterfly larval midgut

scientific article

Secondary structure improves OTU assignments of 16S rRNA gene sequences ⬇️

scientific article published on September 27, 2012

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

scientific article

Spatial Variation of the Native Colon Microbiota in Healthy Adults

scientific article published on 10 April 2018

Stabilization of the murine gut microbiome following weaning

scientific article

Status of the Archaeal and Bacterial Census: an Update

scientific article

Status of the Microbial Census

scientific article

Structure, function and diversity of the healthy human microbiome

scientific article

Support Science by Publishing in Scientific Society Journals

scientific article published on 26 September 2017

Ten simple rules to increase computational skills among biologists with Code Clubs

scientific article published on 27 August 2020

The ASM Journals Committee Values the Contributions of Black Microbiologists

scientific article published on 31 July 2020

The ASM Journals Committee Values the Contributions of Black Microbiologists

scholarly article published in 2020

The Decision to Publish Gutierrez-Alvarez et al., "Middle East Respiratory Syndrome Coronavirus Gene 5 Modulates Pathogenesis in Mice"

scientific article published on 03 November 2020

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

scientific article published on 06 February 2019

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

article

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

scientific article published on 20 November 2019

The Riffomonas Reproducible Research Tutorial Series

scientific article published in 2018

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

scientific article

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies

scientific article

The gut microbiome modulates colon tumorigenesis

scientific article

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

scientific article published on May 1, 2011

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

scientific article published on January 2007

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

scientific article

Toward a census of bacteria in soil

scientific article

Toward unrestricted use of public genomic data:

scientific article

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

scientific article

What is the extent of prokaryotic diversity?

scientific article

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

scientific article published on 14 May 2021

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