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Page 1
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Will… See abstract for full author list ➔ Bolyen E, et al. Among authors: bokulich na. Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. Nat Biotechnol. 2019. PMID: 31341288 Free PMC article. No abstract available.
Microbiomes in Neverland.
Slack E, Bokulich NA. Slack E, et al. Among authors: bokulich na. Cell Host Microbe. 2023 Apr 12;31(4):461-463. doi: 10.1016/j.chom.2023.03.011. Cell Host Microbe. 2023. PMID: 37054668 Free article.
Antibiotics, birth mode, and diet shape microbiome maturation during early life.
Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, D Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ. Bokulich NA, et al. Sci Transl Med. 2016 Jun 15;8(343):343ra82. doi: 10.1126/scitranslmed.aad7121. Sci Transl Med. 2016. PMID: 27306664 Free PMC article.
Oral Microbiome Profile of the US Population.
Chaturvedi AK, Vogtmann E, Shi J, Yano Y, Blaser MJ, Bokulich NA, Caporaso JG, Gillison ML, Graubard BI, Hua X, Hullings AG, Kahle L, Knight R, Li S, McLean J, Purandare V, Wan Y, Freedman ND, Abnet CC. Chaturvedi AK, et al. Among authors: bokulich na. JAMA Netw Open. 2025 May 1;8(5):e258283. doi: 10.1001/jamanetworkopen.2025.8283. JAMA Netw Open. 2025. PMID: 40323603 Free PMC article.
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet CC, Al-Ghalith GA, Alexander H, Alm EJ, Arumugam M, Asnicar F, Bai Y, Bisanz JE, Bittinger K, Brejnrod A, Brislawn CJ, Brown CT, Callahan BJ, Caraballo-Rodríguez AM, Chase J, Cope EK, Da Silva R, Diener C, Dorrestein PC, Douglas GM, Durall DM, Duvallet C, Edwardson CF, Ernst M, Estaki M, Fouquier J, Gauglitz JM, Gibbons SM, Gibson DL, Gonzalez A, Gorlick K, Guo J, Hillmann B, Holmes S, Holste H, Huttenhower C, Huttley GA, Janssen S, Jarmusch AK, Jiang L, Kaehler BD, Kang KB, Keefe CR, Keim P, Kelley ST, Knights D, Koester I, Kosciolek T, Kreps J, Langille MGI, Lee J, Ley R, Liu YX, Loftfield E, Lozupone C, Maher M, Marotz C, Martin BD, McDonald D, McIver LJ, Melnik AV, Metcalf JL, Morgan SC, Morton JT, Naimey AT, Navas-Molina JA, Nothias LF, Orchanian SB, Pearson T, Peoples SL, Petras D, Preuss ML, Pruesse E, Rasmussen LB, Rivers A, Robeson MS 2nd, Rosenthal P, Segata N, Shaffer M, Shiffer A, Sinha R, Song SJ, Spear JR, Swafford AD, Thompson LR, Torres PJ, Trinh P, Tripathi A, Turnbaugh PJ, Ul-Hasan S, van der Hooft JJJ, Vargas F, Vázquez-Baeza Y, Vogtmann E, von Hippel M, Walters W, Wan Y, Wang M, Warren J, Weber KC, Will… See abstract for full author list ➔ Bolyen E, et al. Among authors: bokulich na. Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6. Nat Biotechnol. 2019. PMID: 31399723
The Oral Microbiome and All-Cause Mortality in a US Population-Representative Prospective Cohort.
Vogtmann E, Yano Y, Shi J, Wan Y, Purandare V, McLean J, Li S, Knight R, Kahle L, Hullings AG, Hua X, Graubard BI, Gillison ML, Caporaso JG, Bokulich NA, Blaser MJ, Freedman ND, Chaturvedi AK, Abnet CC. Vogtmann E, et al. Among authors: bokulich na. J Infect Dis. 2025 Oct 15;232(4):790-795. doi: 10.1093/infdis/jiaf321. J Infect Dis. 2025. PMID: 40513117 Free PMC article.
Learning representations of microbe-metabolite interactions.
Morton JT, Aksenov AA, Nothias LF, Foulds JR, Quinn RA, Badri MH, Swenson TL, Van Goethem MW, Northen TR, Vazquez-Baeza Y, Wang M, Bokulich NA, Watters A, Song SJ, Bonneau R, Dorrestein PC, Knight R. Morton JT, et al. Among authors: bokulich na. Nat Methods. 2019 Dec;16(12):1306-1314. doi: 10.1038/s41592-019-0616-3. Epub 2019 Nov 4. Nat Methods. 2019. PMID: 31686038 Free PMC article.
The oral microbiome and all-cause mortality in the US population.
Vogtmann E, Yano Y, Shi J, Wan Y, Purandare V, McLean J, Li S, Knight R, Kahle L, Hullings AG, Hua X, Graubard BI, Gillison ML, Caporaso JG, Bokulich NA, Blaser MJ, Freedman ND, Chaturvedi AK, Abnet CC. Vogtmann E, et al. Among authors: bokulich na. medRxiv [Preprint]. 2024 Dec 5:2024.12.03.24318413. doi: 10.1101/2024.12.03.24318413. medRxiv. 2024. PMID: 39677439 Free PMC article. Preprint.
78 results