| Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach Y Wang, Y Yan, KN Thompson, S Bae, EK Accorsi, Y Zhang, J Shen, ... Microbiome 9 (1), 17, 2021 | 88 | 2021 |
| Improved PCR primers to amplify 16S rRNA genes from NC10 bacteria Z He, J Wang, J Hu, H Zhang, C Cai, J Shen, X Xu, P Zheng, B Hu Applied microbiology and biotechnology 100 (11), 5099-5108, 2016 | 54 | 2016 |
| RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities Y Wang, KN Thompson, Y Yan, MI Short, Y Zhang, EA Franzosa, J Shen, ... Microbiome 11 (1), 131, 2023 | 50 | 2023 |
| MaAsLin 3: Refining and extending generalized multivariable linear models for meta-omic association discovery WA Nickols, T Kuntz, J Shen, S Maharjan, H Mallick, EA Franzosa, ... Nature Methods, 1-11, 2026 | 43 | 2026 |
| From one species to another: A review on the interaction between chemistry and microbiology in relation to cleaning in the built environment S Velazquez, W Griffiths, L Dietz, P Horve, S Nunez, J Hu, J Shen, M Fretz, ... Indoor air 29 (6), 880-894, 2019 | 42 | 2019 |
| Toward accurate and robust environmental surveillance using metagenomics J Shen, AG McFarland, VB Young, MK Hayden, EM Hartmann Frontiers in Genetics 12, 151, 2021 | 38 | 2021 |
| An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics J Shen, AG McFarland, RA Blaustein, LJ Rose, KA Perry-Dow, ... Microbiome 10 (1), 206, 2022 | 29 | 2022 |
| Triclosan tolerance is driven by a conserved mechanism in diverse Pseudomonas species AG McFarland, HK Bertucci, E Littman, J Shen, C Huttenhower, ... Applied and Environmental Microbiology, 2021 | 19 | 2021 |
| Contrasting biomass, dynamics and diversity of microbial community following the air-drying and rewetting of an upland and a paddy soil of the same type Q Shen, K Zhang, J Song, J Shen, J Xu, K Inubushi, PC Brookes Biology and Fertility of Soils 54 (7), 871-875, 2018 | 18 | 2018 |
| Whole microbial community viability is not quantitatively reflected by propidium monoazide sequencing approach. Microbiome 9: 17 Y Wang, Y Yan, KN Thompson, S Bae, EK Accorsi, Y Zhang, J Shen, ... | 16 | 2021 |
| Potencial correlated environmental factors leading to the niche segregation of ammonia-oxidizing archaea and ammonia-oxidizing bacteria: A review S Liu, JJ Hu, JX Shen, S Chen, GM Tian, P Zheng, LP Lou, F Ma, BL Hu Applied Environmental Biotechnology 2 (2), 11-19, 2017 | 15 | 2017 |
| Multi-omic analysis reveals transkingdom gut dysbiosis in metabolic dysfunction-associated steatotic liver disease H Kim, P Nelson, E Nzabarushimana, J Shen, J Jensen, A Bhosle, C Li, ... Nature Metabolism, 1-17, 2025 | 6 | 2025 |
| Individual target pharmacokinetic/pharmacodynamic attainment rates among meropenem-treated patients admitted to the ICU with hospital-acquired pneumonia R Rohani, MH Scheetz, HK Donnelly, A Donayre, M Kang, E Diaz, ... Journal of Antimicrobial Chemotherapy, 2022 | 4 | 2022 |
| Transitions in lung microbiota landscape associate with distinct patterns of pneumonia progression JT Sumner, S Huttelmaier, CI Pickens, AA Moghadam, H Abdala-Valencia, ... Cell Host & Microbe 33 (12), 2148-2166. e8, 2025 | 3 | 2025 |
| Characterizing microbial community viability with RNA-based high-throughput sequencing Y Wang, KN Thompson, Y Yan, MI Short, Y Zhang, EA Franzosa, J Shen, ... | 3 | 2022 |
| Traditional serrated adenomas associated with risk of subsequent high-risk polyps and colorectal cancer Y Chen, G Polychronidis, Y Zhang, J Shen, Y Lu, M Du, M Song The American Journal of Gastroenterology, 10.14309, 2025 | 2 | 2025 |
| Composition and Function of the Gut Microbiome in Microscopic Colitis ASY Chen, H Kim, E Nzabarushimana, J Shen, K Williams, J Gurung, ... medRxiv, 2024 | 2 | 2024 |
| Collect, extract, pool, and cultivate surface swab samples from built environments J Shen, EM Hartmann | 2 | 2022 |
| Association of distinct microbial and metabolic signatures with microscopic colitis ASY Chen, H Kim, E Nzabarushimana, J Shen, K Williams, J Gurung, ... Nature Communications 16 (1), 4644, 2025 | 1 | 2025 |
| RefDeduR: A text-normalization and decision-tree aided R package enabling accurate and high-throughput reference deduplication for large datasets J Shen, F Ling, EM Hartmann bioRxiv, 2022.09. 29.510210, 2022 | 1 | 2022 |
Erica M. HartmannNorthwestern UniversityVerified email at northwestern.edu
