List of works - Todd Z. DeSantis

A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data

scientific article published on 04 December 2020

A data analysis and coordination center for the human microbiome project.

scientific article

A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis

scientific article

A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

scientific article

Abstract 1490: Novel microbiome-derived peptides activate the host innate immune system by regulation of TLR signaling

scholarly article

Abstract 4963: A novel intestinal microbiome-derived peptide modulates immune cell activity and the tumor microenvironment

scholarly article

Abstract 576: A novel intestinal microbiome-derived peptide modulates host T cell activation

scholarly article

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

scientific article published on 22 August 2008

Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma

scientific article

An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile

scientific article

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn's Disease.

scientific article published on 27 June 2014

Animal-to-animal variation in fecal microbial diversity among beef cattle

scientific article

Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation

scientific article

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool

scientific article

Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia

article

Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces

scientific article published on 9 January 2011

Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata

scientific article

Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland

scientific article

Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil

scientific article

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

scientific article

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

scientific article (publication date: March 2011)

Chronic kidney disease alters intestinal microbial flora

scientific article published on 19 September 2012

Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains

scientific article published on 21 March 2008

Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays.

scientific article

Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

scientific article

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.

scientific article

Correction to: Piphillin predicts metagenomic composition and dynamics from DADA2- corrected 16S rDNA sequences

scientific article published on 31 January 2020

Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species

scientific article (publication date: 2014)

Deciphering the rhizosphere microbiome for disease-suppressive bacteria

scientific article

Deep-sea oil plume enriches indigenous oil-degrading bacteria

scientific article

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

scientific article

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes.

scientific article

Diversity of 16S rRNA genes within individual prokaryotic genomes.

scientific article

Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis

scientific article

Environmental genomics reveals a single-species ecosystem deep within Earth

scientific article

Environmental microarray analyses of Antarctic soil microbial communities

scientific article

Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD.

scientific article

Foregut microbiome in development of esophageal adenocarcinoma

Gut microbiota in multiple sclerosis: possible influence of immunomodulators

scientific article published on June 2015

High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

scientific article

High-density microarray of small-subunit ribosomal DNA probes

scientific article

High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment

scientific article

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

scientific article

Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers

scientific article published on 19 October 2021

Influence of geogenic factors on microbial communities in metallogenic Australian soils.

scientific article

Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray

scientific article

Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer

scientific article

Long-term sustainability of a high-energy, low-diversity crustal biome

scientific article

Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice

scientific article published on 9 January 2018

Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes

scientific article

Microbial markers in the diagnosis of colorectal cancer: the promise, reality and challenge

scientific article

Microbial secondary succession in a chronosequence of chalk grasslands

scientific article

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

scientific article

Molecular bacterial community analysis of clean rooms where spacecraft are assembled

scientific article

New perspectives on microbial community distortion after whole-genome amplification

scientific article published on 26 May 2015

PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip

scientific article

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

scientific article

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

scientific article published on 17 January 2020

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

scientific article

PyNAST: a flexible tool for aligning sequences to a template alignment

scientific article (publication date: 15 January 2010)

Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray

scientific article

Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer

scientific article published in PLoS ONE

Section 3 Update - High density DNA microarray analysis for monitoring microbial community composition and dynamics

article

Selective progressive response of soil microbial community to wild oat roots

scientific article

Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems

scholarly article by Steven A. Wakelin et al published February 2013 in Soil Biology and Biochemistry

Simrank: Rapid and sensitive general-purpose k-mer search tool

scientific article

Supervised classification of microbiota mitigates mislabeling errors

scientific article

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

scientific article

The "most wanted" taxa from the human microbiome for whole genome sequencing

scientific article

The microbial community of the cystic fibrosis airway is disrupted in early life

scientific article

The response of marine picoplankton to ocean acidification

scientific article

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Truffle brûlés have an impact on the diversity of soil bacterial communities

scientific article

Urban aerosols harbor diverse and dynamic bacterial populations

scholarly article

List of works by Todd Z. DeSantis

A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data

A data analysis and coordination center for the human microbiome project.

A microbiota signature associated with experimental food allergy promotes allergic sensitization and anaphylaxis

A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells

Abstract 1490: Novel microbiome-derived peptides activate the host innate immune system by regulation of TLR signaling

Abstract 4963: A novel intestinal microbiome-derived peptide modulates immune cell activity and the tumor microenvironment

Abstract 576: A novel intestinal microbiome-derived peptide modulates host T cell activation

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

Airway microbiota and bronchial hyperresponsiveness in patients with suboptimally controlled asthma

An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn's Disease.

Animal-to-animal variation in fecal microbial diversity among beef cattle

Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool

Bacterial communities associated with a mineral weathering profile at a sulphidic mine tailings dump in arid Western Australia

Bacterial community analysis of beef cattle feedlots reveals that pen surface is distinct from feces

Bacterial diversity and White Plague Disease-associated community changes in the Caribbean coral Montastraea faveolata

Bacterial diversity of terrestrial crystalline volcanic rocks, Iceland

Changes in the microbial community structure of bacteria, archaea and fungi in response to elevated CO(2) and warming in an Australian native grassland soil

Characterization of coastal urban watershed bacterial communities leads to alternative community-based indicators

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

Chronic kidney disease alters intestinal microbial flora

Comparative genomics of "Dehalococcoides ethenogenes" 195 and an enrichment culture containing unsequenced "Dehalococcoides" strains

Comparing bacterial community composition between healthy and white plague-like disease states in Orbicella annularis using PhyloChip™ G3 microarrays.

Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean

Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.

Correction to: Piphillin predicts metagenomic composition and dynamics from DADA2- corrected 16S rDNA sequences

Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species

Deciphering the rhizosphere microbiome for disease-suppressive bacteria

Deep-sea oil plume enriches indigenous oil-degrading bacteria

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes.

Diversity of 16S rRNA genes within individual prokaryotic genomes.

Diversity of bacterioplankton in contrasting Tibetan lakes revealed by high-density microarray and clone library analysis

Environmental genomics reveals a single-species ecosystem deep within Earth

Environmental microarray analyses of Antarctic soil microbial communities

Expansion of urease- and uricase-containing, indole- and p-cresol-forming and contraction of short-chain fatty acid-producing intestinal microbiota in ESRD.

Foregut microbiome in development of esophageal adenocarcinoma

Gut microbiota in multiple sclerosis: possible influence of immunomodulators

High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

High-density microarray of small-subunit ribosomal DNA probes

High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers

Influence of geogenic factors on microbial communities in metallogenic Australian soils.

Integrated microbial survey analysis of prokaryotic communities for the PhyloChip microarray

Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer

Long-term sustainability of a high-energy, low-diversity crustal biome

Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice

Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes

Microbial markers in the diagnosis of colorectal cancer: the promise, reality and challenge

Microbial secondary succession in a chronosequence of chalk grasslands

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

Molecular bacterial community analysis of clean rooms where spacecraft are assembled

New perspectives on microbial community distortion after whole-genome amplification

PCR amplification-independent methods for detection of microbial communities by the high-density microarray PhyloChip

PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

PyNAST: a flexible tool for aligning sequences to a template alignment

Rapid quantification and taxonomic classification of environmental DNA from both prokaryotic and eukaryotic origins using a microarray

Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer

Section 3 Update - High density DNA microarray analysis for monitoring microbial community composition and dynamics

Selective progressive response of soil microbial community to wild oat roots

Shifts in the phylogenetic structure and functional capacity of soil microbial communities follow alteration of native tussock grassland ecosystems

Simrank: Rapid and sensitive general-purpose k-mer search tool

Supervised classification of microbiota mitigates mislabeling errors

Tackling the minority: sulfate-reducing bacteria in an archaea-dominated subsurface biofilm

The "most wanted" taxa from the human microbiome for whole genome sequencing

The microbial community of the cystic fibrosis airway is disrupted in early life

The response of marine picoplankton to ocean acidification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

The “Minimum Information about an ENvironmental Sequence” (MIENS) specification

Truffle brûlés have an impact on the diversity of soil bacterial communities

Urban aerosols harbor diverse and dynamic bacterial populations