Kong L, Lloyd-Price J, Vatanen T, et al. Linking Strain Engraftment in Fecal Microbiota Transplantation With Maintenance of Remission in Crohn’s Disease. Gastroenterology. 2020;159(6):2193-2202.e5. doi:10.1053/j.gastro.2020.08.045
Stražar M, Mourits VP, Koeken VACM, et al. The influence of the gut microbiome on BCG-induced trained immunity. Genome Biol. 2021;22(1):275. doi:10.1186/s13059-021-02482-0
Emerson JB, Adams RI, Román CMB, et al. Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems. Microbiome. 2017;5(1):86. doi:10.1186/s40168-017-0285-3
Metsky HC, Siddle KJ, Gladden-Young A, et al. Capturing sequence diversity in metagenomes with comprehensive and scalable probe design. Nat Biotechnol. 2019;37(2):160-168. doi:10.1038/s41587-018-0006-x
Pasolli E, Schiffer L, Manghi P, et al. Accessible, curated metagenomic data through ExperimentHub. Nat Methods. 2017;14(11):1023-1024. doi:10.1038/nmeth.4468
Mallick H, Ma S, Franzosa EA, Vatanen T, Morgan XC, Huttenhower C. Experimental design and quantitative analysis of microbial community multiomics. Genome Biol. 2017;18(1):228. doi:10.1186/s13059-017-1359-z
McIver LJ, Abu-Ali G, Franzosa EA, et al. bioBakery: a meta’omic analysis environment. Bioinformatics. 2018;34(7):1235-1237. doi:10.1093/bioinformatics/btx754
Schirmer M, Franzosa EA, Lloyd-Price J, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018;3(3):337-346. doi:10.1038/s41564-017-0089-z
Abu-Ali GS, Mehta RS, Lloyd-Price J, et al. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat Microbiol. 2018;3(3):356-366. doi:10.1038/s41564-017-0084-4
Mehta RS, Abu-Ali GS, Drew DA, et al. Stability of the human faecal microbiome in a cohort of adult men. Nat Microbiol. 2018;3(3):347-355. doi:10.1038/s41564-017-0096-0