Kelsey N Thompson

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 Feb 23. 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 12 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

Use of nest bundles to monitor agrochemical exposure and effects among cavity nesting pollinators.

Peterson EM, Thompson KN, Shaw KR, Tomlinson C, Longing SD, Smith PN.

Environ Pollut. 2021 Oct 01. 286:117142. PMID: 33965805

Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy.

Young C, Wood HM, Fuentes Balaguer A, Bottomley D, Gallop N, Wilkinson L, Benton SC, Brealey M, John C, Burtonwood C, Thompson KN, Yan Y, Barrett JH, Morris EJA, Huttenhower C, Quirke P.

Clin Cancer Res. 2021 04 15. 27(8):2246-2254. PMID: 33658300

The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries.

Young C, Wood HM, Seshadri RA, Van Nang P, Vaccaro C, Melendez LC, Bose M, Van Doi M, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P.

Genome Med. 2021 02 16. 13(1):27. PMID: 33593386