Publications by authors named "Todd DeSantis"

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Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease.
Jill O'Sullivan, Shriram Patel, Gabriel E Leventhal, Rachel S Fitzgerald, Emilio J Laserna-Mendieta, Todd Z DeSantis

Gut Microbes· December 2025

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Greengenes2 unifies microbial data in a single reference tree.
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Todd DeSantis

Nat Biotechnol· May 2024

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Author Correction: Greengenes2 unifies microbial data in a single reference tree.
Daniel McDonald, Yueyu Jiang, Metin Balaban, Kalen Cantrell, Qiyun Zhu, Todd DeSantis

Nat Biotechnol· May 2024

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Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism.
Christine Tataru, Marie Peras, Erica Rutherford, Kaiti Dunlap, Xiaochen Yin, Todd Z DeSantis

Sci Rep· July 2023

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StrainSelect: A novel microbiome reference database that disambiguates all bacterial strains, genome assemblies and extant cultures worldwide.
Todd Z DeSantis, Cesar Cardona, Nicole R Narayan, Satish Viswanatham, Divya Ravichandar

Heliyon· February 2023

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Adaptation of the gut holobiont to malnutrition during mouse pregnancy depends on the type of nutritional adversity.
Kristin L Connor, Enrrico Bloise, Todd Z DeSantis, Stephen J Lye

J Nutr Biochem· January 2023

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Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups.
Kiana A West, Xiaochen Yin, Erica M Rutherford, Brendan Wee, Jinlyung Choi, Todd Z DeSantis

Sci Rep· October 2022

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Strain level and comprehensive microbiome analysis in inflammatory bowel disease multi-technology meta-analysis identifies key bacterial influencers of disease.
Jayamary Divya Ravichandar, Erica Rutherford, Cheryl-Emiliane T Chow, Andrew Han, Mitsuko Lynn Yamamoto, Todd Z DeSantis

Front Microbiol· October 2022

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Longitudinal study of stool-associated microbial taxa in sibling pairs with and without autism spectrum disorder.
Christine Tataru, Austin Martin, Kaitlyn Dunlap, Marie Peras, Brianna S Chrisman, Todd Z DeSantis

ISME Commun· December 2021

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Improved detection of disease-associated gut microbes using 16S sequence-based biomarkers.
Brianna S Chrisman, Kelley M Paskov, Nate Stockham, Jae-Yoon Jung, Maya Varma, Todd Z DeSantis

BMC Bioinformatics· October 2021

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A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data.
Xiaochen Yin, Tomer Altman, Erica Rutherford, Kiana A West, Yonggan Wu, Todd Z DeSantis

Front Microbiol· December 2020

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Piphillin predicts metagenomic composition and dynamics from DADA2-corrected 16S rDNA sequences.
Nicole R Narayan, Thomas Weinmaier, Emilio J Laserna-Mendieta, Marcus J Claesson, Fergus Shanahan, Todd Z DeSantis

BMC Genomics· January 2020

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Correction to: Piphillin predicts metagenomic composition and dynamics from DADA2- corrected 16S rDNA sequences.
Nicole R Narayan, Thomas Weinmaier, Emilio J Laserna-Mendieta, Marcus J Claesson, Fergus Shanahan, Todd Z DeSantis

BMC Genomics· January 2020

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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.
Manasi S Shah, Todd DeSantis, Jose-Miguel Yamal, Tiffany Weir, Elizabeth P Ryan

PLoS One· April 2019

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Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer.
Manasi S Shah, Todd Z DeSantis, Thomas Weinmaier, Paul J McMurdie, Julia L Cope

Gut· May 2018

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Maternal metabolic, immune, and microbial systems in late pregnancy vary with malnutrition in mice.
Kristin L Connor, Christel Chehoud, Adam Altrichter, Luisa Chan, Todd Z DeSantis

Biol Reprod· April 2018

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Microbial markers in the diagnosis of colorectal cancer: the promise, reality and challenge.
Todd Z DeSantis, Manasi S Shah, Julia L Cope, Emily B Hollister

Future Microbiol· November 2017

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Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes.
Shoko Iwai, Thomas Weinmaier, Brian L Schmidt, Donna G Albertson, Neil J Poloso, Todd Z DeSantis

PLoS One· June 2017

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New perspectives on microbial community distortion after whole-genome amplification.
Alexander J Probst, Thomas Weinmaier, Todd Z DeSantis, Jorge W Santo Domingo, Nicholas Ashbolt

PLoS One· February 2016

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The microbial community of the cystic fibrosis airway is disrupted in early life.
Julie Renwick, Paul McNally, Bettina John, Todd DeSantis, Barry Linnane

PLoS One· December 2015

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Coupling genetic and chemical microbiome profiling reveals heterogeneity of archaeome and bacteriome in subsurface biofilms that are dominated by the same archaeal species.
Alexander J Probst, Giovanni Birarda, Hoi-Ying N Holman, Todd Z DeSantis, Gerhard Wanner

PLoS One· October 2015

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Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean.
Christina A Kellogg, Yvette M Piceno, Lauren M Tom, Todd Z DeSantis, Michael A Gray

PLoS One· June 2015

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Gut microbiota in multiple sclerosis: possible influence of immunomodulators.
Brandi L Cantarel, Emmanuelle Waubant, Christel Chehoud, Justin Kuczynski, Todd Z DeSantis

J Investig Med· June 2015

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An in vitro culture model to study the dynamics of colonic microbiota in Syrian golden hamsters and their susceptibility to infection with Clostridium difficile.
Matthew Miezeiewski, Todd Schnaufer, Michele Muravsky, Su Wang, Ivette Caro-Aguilar, Todd DeSantis

ISME J· February 2015

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Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata.
Collin J Closek, Shinichi Sunagawa, Michael K DeSalvo, Yvette M Piceno, Todd Z DeSantis

ISME J· December 2014

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