| Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes TO Delmont, C Quince, A Shaiber, ÖC Esen, STM Lee, MS Rappé, ... Nature microbiology 3 (7), 804-813, 2018 | 490 | 2018 |
| 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 | 477 | 2021 |
| Accurate and complete genomes from metagenomes LX Chen, K Anantharaman, A Shaiber, AM Eren, JF Banfield Genome research 30 (3), 315-333, 2020 | 319 | 2020 |
| Distinct classes of complex structural variation uncovered across thousands of cancer genome graphs K Hadi, X Yao, JM Behr, A Deshpande, C Xanthopoulakis, H Tian, ... Cell 183 (1), 197-210. e32, 2020 | 175 | 2020 |
| Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome A Shaiber, AD Willis, TO Delmont, S Roux, LX Chen, AC Schmid, ... Genome biology 21, 1-35, 2020 | 153 | 2020 |
| Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions D Butler, C Mozsary, C Meydan, J Foox, J Rosiene, A Shaiber, D Danko, ... Nature communications 12 (1), 1660, 2021 | 145 | 2021 |
| Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics STM Lee, SA Kahn, TO Delmont, A Shaiber, ÖC Esen, NA Hubert, ... Microbiome 5, 1-10, 2017 | 89 | 2017 |
| Shotgun transcriptome and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions DJ Butler, C Mozsary, C Meydan, D Danko, J Foox, J Rosiene, A Shaiber, ... BioRxiv, 2020 | 86 | 2020 |
| Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 6: 3–6 AM Eren, E Kiefl, A Shaiber, I Veseli, SE Miller, MS Schechter, I Fink, ... | 83 | 2021 |
| Composite metagenome-assembled genomes reduce the quality of public genome repositories A Shaiber, AM Eren MBio 10 (3), 10.1128/mbio. 00725-19, 2019 | 81 | 2019 |
| Gut microbes contribute to variation in solid organ transplant outcomes in mice CM McIntosh, L Chen, A Shaiber, AM Eren, ML Alegre Microbiome 6, 1-12, 2018 | 66 | 2018 |
| The Wolbachia mobilome in Culex pipiens includes a putative plasmid J Reveillaud, SR Bordenstein, C Cruaud, A Shaiber, ÖC Esen, M Weill, ... Nature communications 10 (1), 1051, 2019 | 46 | 2019 |
| Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes. Nat Microbiol 3: 804–813 TO Delmont, C Quince, A Shaiber, ÖC Esen, ST Lee, MS Rappé, ... | 44 | 2018 |
| 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 |
| 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 | 31 | 2023 |
| System-wide transcriptome damage and tissue identity loss in COVID-19 patients J Park, J Foox, T Hether, DC Danko, S Warren, Y Kim, J Reeves, DJ Butler, ... Cell Reports Medicine 3 (2), 2022 | 30 | 2022 |
| Host, viral, and environmental transcriptome profiles of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) DJ Butler, C Mozsary, C Meydan, D Danko, J Foox, J Rosiene, A Shaiber, ... bioRxiv, 2020.04. 20.048066, 2020 | 24 | 2020 |
| 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 |
| Systemic tissue and cellular disruption from SARS-CoV-2 infection revealed in COVID-19 autopsies and spatial omics tissue maps J Park, J Foox, T Hether, D Danko, S Warren, Y Kim, J Reeves, DJ Butler, ... bioRxiv, 2021.03. 08.434433, 2021 | 13 | 2021 |
| Composite metagenome-assembled genomes reduce the quality of public genome repositories. mBio 10: e00725-19 A Shaiber, AM Eren, A Shaiber, AM Eren | 13 | 2019 |
