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Page 1
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. Mallick H, et al. Among authors: mciver lj. PLoS Comput Biol. 2021 Nov 16;17(11):e1009442. doi: 10.1371/journal.pcbi.1009442. eCollection 2021 Nov. PLoS Comput Biol. 2021. PMID: 34784344 Free PMC article.
Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ. Franzosa EA, et al. Among authors: mciver lj. Nat Microbiol. 2019 Feb;4(2):293-305. doi: 10.1038/s41564-018-0306-4. Epub 2018 Dec 10. Nat Microbiol. 2019. PMID: 30531976 Free PMC article.
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA 3rd; IBDMDB Investigators; Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C. Lloyd-Price J, et al. Nature. 2019 May;569(7758):655-662. doi: 10.1038/s41586-019-1237-9. Epub 2019 May 29. Nature. 2019. PMID: 31142855 Free PMC article. Review.
Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies.
Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Everett C, et al. Among authors: mciver lj. Nat Protoc. 2021 Jun;16(6):2724-2731. doi: 10.1038/s41596-021-00519-z. Epub 2021 Apr 21. Nat Protoc. 2021. PMID: 33883746 Free PMC article. Review.
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.
Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, Segata N. Beghini F, et al. Among authors: mciver lj. Elife. 2021 May 4;10:e65088. doi: 10.7554/eLife.65088. Elife. 2021. PMID: 33944776 Free PMC article.
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. Zhang Y, et al. Among authors: mciver lj. Nature. 2022 Jun;606(7915):754-760. doi: 10.1038/s41586-022-04648-7. Epub 2022 May 25. Nature. 2022. PMID: 35614211 Free PMC article.
High-sensitivity pattern discovery in large, paired multiomic datasets.
Ghazi AR, Sucipto K, Rahnavard A, Franzosa EA, McIver LJ, Lloyd-Price J, Schwager E, Weingart G, Moon YS, Morgan XC, Waldron L, Huttenhower C. Ghazi AR, et al. Among authors: mciver lj. Bioinformatics. 2022 Jun 24;38(Suppl 1):i378-i385. doi: 10.1093/bioinformatics/btac232. Bioinformatics. 2022. PMID: 35758795 Free PMC article.
bioBakery: a meta'omic analysis environment.
McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. McIver LJ, et al. Bioinformatics. 2018 Apr 1;34(7):1235-1237. doi: 10.1093/bioinformatics/btx754. Bioinformatics. 2018. PMID: 29194469 Free PMC article.
Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.
Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C. Schirmer M, et al. Among authors: mciver lj. Nat Microbiol. 2018 Mar;3(3):337-346. doi: 10.1038/s41564-017-0089-z. Epub 2018 Jan 8. Nat Microbiol. 2018. PMID: 29311644 Free PMC article.
Species-level functional profiling of metagenomes and metatranscriptomes.
Franzosa EA, McIver LJ, Rahnavard G, Thompson LR, Schirmer M, Weingart G, Lipson KS, Knight R, Caporaso JG, Segata N, Huttenhower C. Franzosa EA, et al. Among authors: mciver lj. Nat Methods. 2018 Nov;15(11):962-968. doi: 10.1038/s41592-018-0176-y. Epub 2018 Oct 30. Nat Methods. 2018. PMID: 30377376 Free PMC article.
52 results