1.
Schaan AP, Vidal A, Zhang A-N, et al. Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia. mSystems. 2024:e0070723. doi:10.1128/msystems.00707-23.
1.
Schirmer M, Stražar M, Avila-Pacheco J, et al. Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course. Cell host & microbe. 2024. doi:10.1016/j.chom.2023.12.013.
1.
Hsu TY, Nzabarushimana E, Wong D, et al. Profiling novel lateral gene transfer events in the human microbiome. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.08.08.552500.
1.
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.
1.
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.
1.
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.
1.
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.
1.
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.
1.
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.
1.
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.