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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: hillmann b. 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.
Captivity humanizes the primate microbiome.
Clayton JB, Vangay P, Huang H, Ward T, Hillmann BM, Al-Ghalith GA, Travis DA, Long HT, Tuan BV, Minh VV, Cabana F, Nadler T, Toddes B, Murphy T, Glander KE, Johnson TJ, Knights D. Clayton JB, et al. Among authors: hillmann bm. Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10376-81. doi: 10.1073/pnas.1521835113. Epub 2016 Aug 29. Proc Natl Acad Sci U S A. 2016. PMID: 27573830 Free PMC article.
Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.
Maldonado-Gómez MX, Martínez I, Bottacini F, O'Callaghan A, Ventura M, van Sinderen D, Hillmann B, Vangay P, Knights D, Hutkins RW, Walter J. Maldonado-Gómez MX, et al. Among authors: hillmann b. Cell Host Microbe. 2016 Oct 12;20(4):515-526. doi: 10.1016/j.chom.2016.09.001. Epub 2016 Sep 29. Cell Host Microbe. 2016. PMID: 27693307 Free article.
Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity.
Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. Zhang XS, et al. Among authors: hillmann b. Elife. 2018 Jul 25;7:e37816. doi: 10.7554/eLife.37816. Elife. 2018. PMID: 30039798 Free PMC article.
CLOUD: a non-parametric detection test for microbiome outliers.
Montassier E, Al-Ghalith GA, Hillmann B, Viskocil K, Kabage AJ, McKinlay CE, Sadowsky MJ, Khoruts A, Knights D. Montassier E, et al. Among authors: hillmann b. Microbiome. 2018 Aug 6;6(1):137. doi: 10.1186/s40168-018-0514-4. Microbiome. 2018. PMID: 30081949 Free PMC article.
An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study.
Muñiz Pedrogo DA, Chen J, Hillmann B, Jeraldo P, Al-Ghalith G, Taneja V, Davis JM, Knights D, Nelson H, Faubion WA, Raffals L, Kashyap PC. Muñiz Pedrogo DA, et al. Among authors: hillmann b. Inflamm Bowel Dis. 2019 Apr 11;25(5):902-913. doi: 10.1093/ibd/izy318. Inflamm Bowel Dis. 2019. PMID: 30321331 Free PMC article.
US Immigration Westernizes the Human Gut Microbiome.
Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R, Paw B, Pergament SL, Saenyakul P, Xiong M, Kim AD, Kim G, Masopust D, Martens EC, Angkurawaranon C, McGready R, Kashyap PC, Culhane-Pera KA, Knights D. Vangay P, et al. Among authors: hillmann bm. Cell. 2018 Nov 1;175(4):962-972.e10. doi: 10.1016/j.cell.2018.10.029. Cell. 2018. PMID: 30388453 Free PMC article.
Evaluating the Information Content of Shallow Shotgun Metagenomics.
Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, Knight R, Knights D. Hillmann B, et al. mSystems. 2018 Nov 13;3(6):e00069-18. doi: 10.1128/mSystems.00069-18. eCollection 2018 Nov-Dec. mSystems. 2018. PMID: 30443602 Free PMC article.
33 results