| 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 | 513* | 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 | 44 | 2022 |
| 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 | 35 | 2022 |
| 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 | 33 | 2023 |
| 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 | 33 | 2022 |
| 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 | 20 | 2022 |
| 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 | 18 | 2021 |
| 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 | 14 | 2023 |
| 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 | 13 | 2022 |
| The genetic and ecological landscape of plasmids in the human gut MK Yu, EC Fogarty, AM Eren biorxiv, 2020.11. 01.361691, 2020 | 13 | 2020 |
| 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 | 11 | 2024 |
| 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 | 11 | 2023 |
| 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, ... | 11 | |
| Functional insights into the kelp microbiome from metagenome-assembled genomes. mSystems 7, e01422-21 BL Weigel, KK Miranda, EC Fogarty, AR Watson, CA Pfister | 8 | 2022 |
| 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 | 5 | 2024 |
| 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 | 4 | 2023 |
| 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 | 4 | 2023 |
| Credit where credit is due E Fogarty Science 370 (6520), 1130-1130, 2020 | 3 | 2020 |
| 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 | 1 | 2022 |
| Revealing the Ecological Interactions, Evolutionary Histories and Niche Boundaries of Prevalent Human Gut Plasmids EC Fogarty The University of Chicago, 2023 | | 2023 |
