Kelsey N Thompson

Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes.

Thompson KN, Bonham KS, Ilott NE, Britton GJ, Colmenero P, Bullers SJ, McIver LJ, Ma S, Nguyen LH, Filer A, Brough I, Pearson C, Moussa C, Kumar V, Lam LH, Jackson MA, Pawluk A, Kiriakidis S, Taylor PC, Wedderburn LR, Marsden B, Young SP, Littman DR, Faith JJ, Pratt AG, Bowness P, Raza K, Powrie F, Huttenhower C.

Sci Transl Med. 2023 07 26. 15(706):eabn4722. PMID: 37494472

Metagenomic assessment of gut microbial communities and risk of severe COVID-19.

Nguyen LH, Okin D, Drew DA, Battista VM, Jesudasen SJ, Kuntz TM, Bhosle A, Thompson KN, Reinicke T, Lo CH, Woo JE, Caraballo A, Berra L, Vieira J, Huang CY, Das Adhikari U, Kim M, Sui HY, Magicheva-Gupta M, McIver L, Goldberg MB, Kwon DS, Huttenhower C, Chan AT, Lai PS.

Genome Med. 2023 07 12. 15(1):49. PMID: 37438797

RNA-based amplicon sequencing is ineffective in measuring metabolic activity in environmental microbial communities.

Wang Y, Thompson KN, Yan Y, Short MI, Zhang Y, Franzosa EA, Shen J, Hartmann EM, Huttenhower C.

Microbiome. 2023 06 13. 11(1):131. PMID: 37312147

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.

Blanco-Míguez A, Beghini F, Cumbo F, McIver LJ, Thompson KN, Zolfo M, Manghi P, Dubois L, Huang KD, Thomas AM, Nickols WA, Piccinno G, Piperni E, Puncochár M, Valles-Colomer M, Tett A, Giordano F, Davies R, Wolf J, Berry SE, Spector TD, Franzosa EA, Pasolli E, Asnicar F, Huttenhower C, Segata N.

Nat Biotechnol. 2023 Nov. 41(11):1633-1644. PMID: 36823356

Effects of Lifetime Exposures to Environmental Contaminants on the Adult Gut Microbiome.

Thompson KN, Oulhote Y, Weihe P, Wilkinson JE, Ma S, Zhong H, Li J, Kristiansen K, Huttenhower C, Grandjean P.

Environ Sci Technol. 2022 Dec 06. 56(23):16985-16995. PMID: 36394280

Discovery of bioactive microbial gene products in inflammatory bowel disease.

Zhang Y, Bhosle A, Bae S, McIver LJ, Pishchany G, Accorsi EK, Thompson KN, Arze C, Wang Y, Subramanian A, Kearney SM, Pawluk A, Plichta DR, Rahnavard A, Shafquat A, Xavier RJ, Vlamakis H, Garrett WS, Krueger A, Huttenhower C, Franzosa EA.

Nature. 2022 06. 606(7915):754-760. PMID: 35614211

Multivariable association discovery in population-scale meta-omics studies.

Mallick H, Rahnavard A, McIver LJ, Ma S, Zhang Y, Nguyen LH, Tickle TL, Weingart G, Ren B, Schwager EH, Chatterjee S, Thompson KN, Wilkinson JE, Subramanian A, Lu Y, Waldron L, Paulson JN, Franzosa EA, Bravo HC, Huttenhower C.

PLoS Comput Biol. 2021 11. 17(11):e1009442. PMID: 34784344

The Sulfur Microbial Diet and Risk of Colorectal Cancer by Molecular Subtypes and Intratumoral Microbial Species in Adult Men.

Sikavi DR, Nguyen LH, Haruki K, Ugai T, Ma W, Wang DD, Thompson KN, Yan Y, Branck T, Wilkinson JE, Akimoto N, Zhong R, Lau MC, Mima K, Kosumi K, Morikawa T, Rimm EB, Garrett WS, Izard J, Cao Y, Song M, Huttenhower C, Ogino S, Chan AT.

Clin Transl Gastroenterol. 2021 08 01. 12(8):e00338. PMID: 34333506

Statistical approaches for differential expression analysis in metatranscriptomics.

Zhang Y, Thompson KN, Huttenhower C, Franzosa EA.

Bioinformatics. 2021 07 12. 37(Suppl_1):i34-i41. PMID: 34252963

Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling.

Zhang Y, Thompson KN, Branck T, Nguyen LH, Franzosa EA, Huttenhower C.

Annu Rev Biomed Data Sci. 2021 07 20. 4:279-311. PMID: 34465175