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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
440*2021
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
342022
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
342022
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
292022
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
262023
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
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
112022
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
102023
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
102022
The genetic and ecological landscape of plasmids in the human gut
MK Yu, EC Fogarty, AM Eren
biorxiv, 2020.11. 01.361691, 2020
102020
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, ...
10
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
82023
Functional insights into the kelp microbiome from metagenome-assembled genomes. mSystems 7: e0142221
BL Weigel, KK Miranda, EC Fogarty, AR Watson, CA Pfister
62022
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
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
32024
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
32023
Credit where credit is due
E Fogarty
Science 370 (6520), 1130-1130, 2020
22020
Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess
MK Yu, EC Fogarty, AM Eren
Nature Microbiology, 1-18, 2024
12024
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