| Multivariable association discovery in population-scale meta-omics studies H Mallick, A Rahnavard, LJ McIver, S Ma, Y Zhang, LH Nguyen, TL Tickle, ... PLoS computational biology 17 (11), e1009442, 2021 | 2309 | 2021 |
| Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 A Blanco-Míguez, F Beghini, F Cumbo, LJ McIver, KN Thompson, M Zolfo, ... Nature biotechnology 41 (11), 1633-1644, 2023 | 1167 | 2023 |
| Metatranscriptomics for the human microbiome and microbial community functional profiling Y Zhang, KN Thompson, T Branck, Y Yan, LH Nguyen, EA Franzosa, ... Annual Review of Biomedical Data Science 4 (1), 279-311, 2021 | 123 | 2021 |
| Discovery of bioactive microbial gene products in inflammatory bowel disease Y Zhang, A Bhosle, S Bae, LJ McIver, G Pishchany, EK Accorsi, ... Nature 606 (7915), 754-760, 2022 | 100 | 2022 |
| 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 |
| Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4 A Blanco-Miguez, F Beghini, F Cumbo, LJ McIver, KN Thompson, M Zolfo, ... Biorxiv, 2022.08. 22.504593, 2022 | 79 | 2022 |
| Statistical approaches for differential expression analysis in metatranscriptomics Y Zhang, KN Thompson, C Huttenhower, EA Franzosa Bioinformatics 37 (Supplement_1), i34-i41, 2021 | 64 | 2021 |
| Homologous recombination repair signaling in chemical carcinogenesis: prolonged particulate hexavalent chromium exposure suppresses the Rad51 response in human lung cells Q Qin, H Xie, SS Wise, CL Browning, KN Thompson, AL Holmes, ... Toxicological Sciences 142 (1), 117-125, 2014 | 61 | 2014 |
| Coffee consumption is associated with intestinal Lawsonibacter asaccharolyticus abundance and prevalence across multiple cohorts P Manghi, A Bhosle, K Wang, R Marconi, M Selma-Royo, L Ricci, ... Nature Microbiology 9 (12), 3120-3134, 2024 | 53 | 2024 |
| Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes KN Thompson, KS Bonham, NE Ilott, GJ Britton, P Colmenero, SJ Bullers, ... Science translational medicine 15 (706), eabn4722, 2023 | 50 | 2023 |
| 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 |
| The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries C Young, HM Wood, RA Seshadri, P Van Nang, C Vaccaro, LC Melendez, ... Genome Medicine 13 (1), 27, 2021 | 44 | 2021 |
| 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 |
| Microbiome analysis of more than 2,000 NHS bowel cancer screening programme samples shows the potential to improve screening accuracy C Young, HM Wood, A Fuentes Balaguer, D Bottomley, N Gallop, ... Clinical Cancer Research 27 (8), 2246-2254, 2021 | 33 | 2021 |
| Effects of lifetime exposures to environmental contaminants on the adult gut microbiome KN Thompson, Y Oulhote, P Weihe, JE Wilkinson, S Ma, H Zhong, J Li, ... Environmental Science & Technology 56 (23), 16985-16995, 2022 | 31 | 2022 |
| Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer G Piccinno, KN Thompson, P Manghi, AR Ghazi, AM Thomas, ... Nature Medicine, 1-14, 2025 | 30 | 2025 |
| Metagenomic assessment of gut microbial communities and risk of severe COVID-19 LH Nguyen, D Okin, DA Drew, VM Battista, SJ Jesudasen, TM Kuntz, ... Genome Medicine 15 (1), 49, 2023 | 21 | 2023 |
| The sulfur microbial diet and risk of colorectal cancer by molecular subtypes and intratumoral microbial species in adult men DR Sikavi, LH Nguyen, K Haruki, T Ugai, W Ma, DD Wang, KN Thompson, ... Clinical and translational gastroenterology 12 (8), e00338, 2021 | 19 | 2021 |
| Use of nest bundles to monitor agrochemical exposure and effects among cavity nesting pollinators EM Peterson, KN Thompson, KR Shaw, C Tomlinson, SD Longing, ... Environmental Pollution 286, 117142, 2021 | 18 | 2021 |
| Trophic-Level Interactive Effects of Phosphorus Availability on the Toxicities of Cadmium, Arsenic, and Their Binary Mixture in Media-Exposed Scenedesmus acutus and … OM Awoyemi, S Subbiah, KN Thompson, A Velazquez, A Peace, ... Environmental Science & Technology 54 (9), 5651-5666, 2020 | 16 | 2020 |
