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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; Inflammatory Arthritis Microbiome Consortium (IAMC) investigators group; Kiriakidis S, Taylor PC, Wedderburn LR, Marsden B, Young SP, Littman DR, Faith JJ, Pratt AG, Bowness P, Raza K, Powrie F, Huttenhower C; IAMC. Thompson KN, et al. Among authors: mciver lj. Sci Transl Med. 2023 Jul 26;15(706):eabn4722. doi: 10.1126/scitranslmed.abn4722. Epub 2023 Jul 26. Sci Transl Med. 2023. PMID: 37494472
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, Punčochář 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. Blanco-Míguez A, et al. Among authors: mciver lj. Nat Biotechnol. 2023 Nov;41(11):1633-1644. doi: 10.1038/s41587-023-01688-w. Epub 2023 Feb 23. Nat Biotechnol. 2023. PMID: 36823356 Free PMC article.
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. Nguyen LH, et al. Genome Med. 2023 Jul 12;15(1):49. doi: 10.1186/s13073-023-01202-6. Genome Med. 2023. PMID: 37438797 Free PMC article.
A two-cohort study on the association between the gut microbiota and bone density, microarchitecture, and strength.
Okoro PC, Orwoll ES, Huttenhower C, Morgan X, Kuntz TM, McIver LJ, Dufour AB, Bouxsein ML, Langsetmo L, Farsijani S, Kado DM, Pacifici R, Sahni S, Kiel DP. Okoro PC, et al. Among authors: mciver lj. Front Endocrinol (Lausanne). 2023 Sep 21;14:1237727. doi: 10.3389/fendo.2023.1237727. eCollection 2023. Front Endocrinol (Lausanne). 2023. PMID: 37810879 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.
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.
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.
Publisher Correction: 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 Sep;16(9):4538. doi: 10.1038/s41596-021-00570-w. Nat Protoc. 2021. PMID: 33986535 No abstract available.
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.
44 results