Publications by authors named "Emily Fogarty"

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Defining the Pangenome and Suggestions for a New Composite Reference Sequence.
Poonam Chitale, Elissa Ocke, Aubrey R Odom, Howard Fan, Alexander Henoch, Emily C Fogarty

bioRxiv· November 2025

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Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.
Iva Veseli, Yiqun T Chen, Matthew S Schechter, Chiara Vanni, Emily C Fogarty

Elife· May 2025

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CGE25-106: MHC II More Effectively Predicts Response to Pembrolizumab Than PD-L1 in HER2 Negative Patients.
Emily Fogarty, Brian Corgiat, Kayla Sparks, Chris Arnell, Emanuel Petricoin

J Natl Compr Canc Netw· March 2025

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Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.
Iva Veseli, Yiqun T Chen, Matthew S Schechter, Chiara Vanni, Emily C Fogarty

bioRxiv· July 2024

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Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess.
Michael K Yu, Emily C Fogarty, A Murat Eren

Nat Microbiol· March 2024

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A cryptic plasmid is among the most numerous genetic elements in the human gut.
Emily C Fogarty, Matthew S Schechter, Karen Lolans, Madeline L Sheahan, Iva Veseli

Cell· February 2024

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Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.
Joseph Runde, Iva Veseli, Emily C Fogarty, Andrea R Watson, Quentin Clayssen

J Crohns Colitis· July 2023

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Metabolic independence drives gut microbial colonization and resilience in health and disease.
Andrea R Watson, Jessika Füssel, Iva Veseli, Johanna Zaal DeLongchamp, Marisela Silva, Emily Fogarty

Genome Biol· April 2023

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A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut.
Emily C Fogarty, Matthew S Schechter, Karen Lolans, Madeline L Sheahan, Iva Veseli

bioRxiv· March 2023

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Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster.
Irmarie Cotto, Katherine J Vilardi, Linxuan Huo, Emily C Fogarty, Wendell Khunjar

Water Res· February 2023

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Author Correction: A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome.
Poonam Chitale, Alexander D Lemenze, Emily C Fogarty, Avi Shah, Courtney Grady

Nat Commun· December 2022

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A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome.
Poonam Chitale, Alexander D Lemenze, Emily C Fogarty, Avi Shah, Courtney Grady

Nat Commun· November 2022

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The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes.
Khashiff Miranda, Brooke L Weigel, Emily C Fogarty, Iva A Veseli, Anne E Giblin

mSystems· October 2022

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High molecular weight DNA extraction strategies for long-read sequencing of complex metagenomes.
Florian Trigodet, Karen Lolans, Emily Fogarty, Alon Shaiber, Hilary G Morrison

Mol Ecol Resour· July 2022

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Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes.
Brooke L Weigel, Khashiff K Miranda, Emily C Fogarty, Andrea R Watson, Catherine A Pfister

mSystems· June 2022

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Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations.
Elizabeth A Landis, Emily Fogarty, John C Edwards, Otilia Popa, A Murat Eren

mSystems· June 2022

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Community-led, integrated, reproducible multi-omics with anvi'o.
A Murat Eren, Evan Kiefl, Alon Shaiber, Iva Veseli, Samuel E Miller, Emily C Fogarty

Nat Microbiol· January 2021

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Credit where credit is due.
Emily Fogarty

Science· November 2020

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