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List of works by Daniel McDonald

A communal catalogue reveals Earth's multiscale microbial diversity

scientific article published in November 2017

Activating and inhibiting connections in biological network dynamics

scientific article

Age- and Sex-Dependent Patterns of Gut Microbial Diversity in Human Adults

scientific article published on 14 May 2019

American Gut: an Open Platform for Citizen Science Microbiome Research

article

Are microbiome studies ready for hypothesis-driven research?

scientific article published on 27 July 2018

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection

scientific article published in 2021

Author Correction: Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

scientific article published on 25 February 2020

Author Correction: Regional variation limits applications of healthy gut microbiome reference ranges and disease models

scientific article published on 01 December 2018

Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 September 2019

Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity

scientific article published on 18 August 2020

Balance Trees Reveal Microbial Niche Differentiation.

scientific article published on 17 January 2017

Best practices for analysing microbiomes

scientific article published on 01 July 2018

Boulder ALignment Editor (ALE): a web-based RNA alignment tool

scientific article

Bringing the Dynamic Microbiome to Life with Animations

scientific article published in January 2017

Calour: an Interactive, Microbe-Centric Analysis Tool

Characterization of the total and viable bacterial and fungal communities associated with the International Space Station surfaces

scientific article published on 08 April 2019

Chemically informed analyses of metabolomics mass spectrometry data with Qemistree

scientific article published on 16 November 2020

Collaborative cloud-enabled tools allow rapid, reproducible biological insights ⬇️

scientific article published on October 25, 2012

Comparison of methods for estimating the nucleotide substitution matrix

scientific article

Comparison of the vaginal microbial communities in women with recurrent genital HSV receiving acyclovir intravaginal rings

scientific article

Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype

scientific article published in 2022

Consumption of Fermented Foods Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

scientific article published on 17 March 2020

Context and the human microbiome

scientific article

Context-aware dimensionality reduction deconvolutes gut microbial community dynamics

scientific article published on 31 August 2020

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

scientific article published on 08 October 2019

Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

scientific article published on 07 March 2017

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

scientific article published on 07 March 2017

Depression in Individuals Coinfected with HIV and HCV Is Associated with Systematic Differences in the Gut Microbiome and Metabolome

scientific article published on 29 September 2020

Differences in gut microbiome composition between persons with chronic schizophrenia and healthy comparison subjects

scientific article published on 26 September 2018

Dynamics of the human gut microbiome in inflammatory bowel disease.

scientific article published on 13 February 2017

EMPress Enables Tree-Guided, Interactive, and Exploratory Analyses of Multi-omic Data Sets

scientific article published on 15 March 2021

Enhancing untargeted metabolomics using metadata-based source annotation

scientific article published in 2022

Ensemble dispatching on an IBM Blue Gene/L for a bioinformatics knowledge environment

article

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project

scientific article published on 12 October 2017

Extreme Dysbiosis of the Microbiome in Critical Illness

scientific article published on July 2016

Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake

scientific article published on 19 October 2016

Feasibility of SARS-CoV-2 virus detection from consumer-grade cotton swabs

scientific article published on 18 May 2020

Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment

scientific article published on 18 August 2020

Fecal Microbiota Transplant is Highly Effective in Real-World Practice: Initial Results from the FMT National Registry

scientific article published on 30 September 2020

Forensic identification using skin bacterial communities

scientific article published on 15 March 2010

From Animalcules to an Ecosystem: Application of Ecological Concepts to the Human Microbiome

article

From molecules to dynamic biological communities

scientific article

GABA-modulating bacteria of the human gut microbiota

scientific article published on 10 December 2018

Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

scientific article

Gut microbiome composition in the Hispanic Community Health Study/Study of Latinos is shaped by geographic relocation, environmental factors, and obesity

scientific article published on 01 November 2019

Human Immunodeficiency Virus nef signature sequences are associated with pulmonary hypertension

scientific article

Identifying and Predicting Novelty in Microbiome Studies

scientific article published in 2018

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome.

scientific article published in May 2018

Meeting report: fungal its workshop (october 2012).

scientific article published on 15 April 2013

Methods for phylogenetic analysis of microbiome data

scientific article published on 24 May 2018

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity

scientific article published on 10 December 2021

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

scientific article published on 5 September 2010

Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment

scientific article published on 22 November 2020

Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians

scientific article published on 18 September 2018

Multi-omics profiling of Earth’s biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

scientific article published on 6 June 2021

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search

scientific article published on 17 March 2020

Nucleotides that are essential but not conserved; a sufficient L-tryptophan site in RNA.

scientific article

Nutrition and the Gut Microbiota in 10- to 18-Month-Old Children Living in Urban Slums of Mumbai, India

scientific article published on 23 September 2020

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information.

scientific article published on 17 April 2018

Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat.

scientific article

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

scientific article published on 02 December 2019

Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy

scientific article published on 04 April 2022

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

scientific article (publication date: September 2013)

PyCogent: a toolkit for making sense from sequence

scientific article published in January 2007

QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

scientific article published on 01 June 2020

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

QIIME allows analysis of high-throughput community sequencing data

scientific article

Qiita: rapid, web-enabled microbiome meta-analysis

scientific article published on 01 October 2018

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

scientific article

Rapid, Large-Scale Wastewater Surveillance and Automated Reporting System Enable Early Detection of Nearly 85% of COVID-19 Cases on a University Campus

scientific article published on 10 August 2021

Rapid, large-scale wastewater surveillance and automated reporting system enabled early detection of nearly 85% of COVID-19 cases on a University campus

preprint

Reduced Independence in Daily Living Is Associated with the Gut Microbiome in People with HIV and HCV

scientific article published in 2020

Regional variation limits applications of healthy gut microbiome reference ranges and disease models

scientific article published on 27 August 2018

Reply to Sun et al., "Identifying Composition Novelty in Microbiome Studies: Improvement of Prediction Accuracy"

scientific article published on 06 August 2019

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

scientific article published on 01 August 2019

Rethinking "enterotypes".

scientific article

Ribosomal RNA, the lens into life

scientific article published in April 2015

Role of the microbiome, probiotics, and 'dysbiosis therapy' in critical illness

scientific article published on 18 June 2016

SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital environment

scientific article published on 08 June 2021

Species abundance information improves sequence taxonomy classification accuracy

scientific article published on 11 October 2019

Strains, functions and dynamics in the expanded Human Microbiome Project

scientific article

Striped UniFrac: enabling microbiome analysis at unprecedented scale

scientific article published on 01 November 2018

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

scientific article

Testing GitHub projects on custom resources using unprivileged Kubernetes runners

scientific article published on 10 September 2023

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

2012 scientific article

The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder

scientific article published in 2021

The Microbiome and Human Biology.

scientific article published on 20 March 2017

The emergence of microbiome centres

scientific article published on 01 January 2020

The impact of skin care products on skin chemistry and microbiome dynamics

scientific article published on 12 June 2019

The treatment-naive microbiome in new-onset Crohn's disease

scientific article

Towards large-cohort comparative studies to define the factors influencing the gut microbial community structure of ASD patients

scientific article

Tracking Human Gut Microbiome Changes Resulting from a Colonoscopy

scientific article published on 01 January 2017

Turning Participatory Microbiome Research into Usable Data: Lessons from the American Gut Project

scientific article

Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

scientific article published in September 2022

Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission

preprint

microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data ⬇️

scientific article published in 2024

redbiom: a Rapid Sample Discovery and Feature Characterization System

scientific article published on 25 June 2019

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