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Emily C Fogarty
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Community-led, integrated, reproducible multi-omics with anvi’o
AM Eren, E Kiefl, A Shaiber, I Veseli, SE Miller, MS Schechter, I Fink, ...
Nature microbiology 6 (1), 3-6, 2021
624*2021
Microbial diversity and interaction specificity in kombucha tea fermentations
EA Landis, E Fogarty, JC Edwards, O Popa, AM Eren, BE Wolfe
Msystems 7 (3), e00157-22, 2022
552022
Metabolic independence drives gut microbial colonization and resilience in health and disease
AR Watson, J Füssel, I Veseli, JZ DeLongchamp, M Silva, F Trigodet, ...
Genome Biology 24 (1), 78, 2023
472023
High molecular weight DNA extraction strategies for long‐read sequencing of complex metagenomes
F Trigodet, K Lolans, E Fogarty, A Shaiber, HG Morrison, L Barreiro, ...
Molecular ecology resources 22 (5), 1786-1802, 2022
402022
Functional insights into the kelp microbiome from metagenome-assembled genomes
BL Weigel, KK Miranda, EC Fogarty, AR Watson, CA Pfister
Msystems 7 (3), e01422-21, 2022
392022
A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
P Chitale, AD Lemenze, EC Fogarty, A Shah, C Grady, AR Odom-Mabey, ...
Nature communications 13 (1), 7068, 2022
302022
Microbes with higher metabolic independence are enriched in human gut microbiomes under stress
I Veseli, YT Chen, MS Schechter, C Vanni, EC Fogarty, AR Watson, ...
bioRxiv, 2023.05. 10.540289, 2024
232024
A cryptic plasmid is among the most numerous genetic elements in the human gut
EC Fogarty, MS Schechter, K Lolans, ML Sheahan, I Veseli, RM Moore, ...
Cell 187 (5), 1206-1222. e16, 2024
222024
Adaptive ecological processes and metabolic independence drive microbial colonization and resilience in the human gut
AR Watson, J Füssel, I Veseli, JZ DeLongchamp, M Silva, F Trigodet, ...
bioRxiv, 2021.03. 02.433653, 2021
182021
The genetic and ecological landscape of plasmids in the human gut
MK Yu, EC Fogarty, AM Eren
biorxiv, 2020.11. 01.361691, 2020
162020
Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster
I Cotto, KJ Vilardi, L Huo, EC Fogarty, W Khunjar, C Wilson, ...
Water Research 229, 119497, 2023
152023
The diversity and functional capacity of microbes associated with coastal macrophytes
K Miranda, BL Weigel, EC Fogarty, IA Veseli, AE Giblin, AM Eren, ...
Msystems 7 (5), e00592-22, 2022
142022
Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess
MK Yu, EC Fogarty, AM Eren
Nature Microbiology 9 (3), 830-847, 2024
132024
Functional insights into the kelp microbiome from metagenome-assembled genomes. mSystems 7, e01422-21
BL Weigel, KK Miranda, EC Fogarty, AR Watson, CA Pfister
122022
Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol. 2021; 6: 3–6
AM Eren, E Kiefl, A Shaiber, I Veseli, SE Miller, MS Schechter, I Fink, ...
12
Transient suppression of bacterial populations associated with gut health is critical in success of exclusive enteral nutrition for children with Crohn’s disease
J Runde, I Veseli, EC Fogarty, AR Watson, Q Clayssen, M Yosef, ...
Journal of Crohn's and Colitis 17 (7), 1103-1113, 2023
62023
A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut
EC Fogarty, MS Schechter, K Lolans, ML Sheahan, I Veseli, R Moore, ...
bioRxiv, 2023
42023
Credit where credit is due
E Fogarty
Science 370 (6520), 1130-1130, 2020
32020
Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster
I Cotto, KJ Vilardi, L Huo, EC Fogarty, W Khunjar, C Wilson, ...
bioRxiv, 2022.06. 11.495745, 2022
12022
Revealing the Ecological Interactions, Evolutionary Histories and Niche Boundaries of Prevalent Human Gut Plasmids
EC Fogarty
The University of Chicago, 2023
2023
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Articles 1–20