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Items: 11

1.

Framework for rational donor selection in fecal microbiota transplant clinical trials.

Duvallet C, Zellmer C, Panchal P, Budree S, Osman M, Alm EJ.

PLoS One. 2019 Oct 10;14(10):e0222881. doi: 10.1371/journal.pone.0222881. eCollection 2019.

2.

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, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Sep;37(9):1091. doi: 10.1038/s41587-019-0252-6.

PMID:
31399723
3.

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, Williamson CHD, Willis AD, Xu ZZ, Zaneveld JR, Zhang Y, Zhu Q, Knight R, Caporaso JG.

Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9. No abstract available. Erratum in: Nat Biotechnol. 2019 Sep;37(9):1091.

PMID:
31341288
4.

A practical guide to methods controlling false discoveries in computational biology.

Korthauer K, Kimes PK, Duvallet C, Reyes A, Subramanian A, Teng M, Shukla C, Alm EJ, Hicks SC.

Genome Biol. 2019 Jun 4;20(1):118. doi: 10.1186/s13059-019-1716-1.

5.

Aerodigestive sampling reveals altered microbial exchange between lung, oropharyngeal, and gastric microbiomes in children with impaired swallow function.

Duvallet C, Larson K, Snapper S, Iosim S, Lee A, Freer K, May K, Alm E, Rosen R.

PLoS One. 2019 May 20;14(5):e0216453. doi: 10.1371/journal.pone.0216453. eCollection 2019.

6.

Predictability and persistence of prebiotic dietary supplementation in a healthy human cohort.

Gurry T; HST Microbiome Consortium*, Gibbons SM, Nguyen LTT, Kearney SM, Ananthakrishnan A, Jiang X, Duvallet C, Kassam Z, Alm EJ.

Sci Rep. 2018 Aug 23;8(1):12699. doi: 10.1038/s41598-018-30783-1.

7.

Correcting for batch effects in case-control microbiome studies.

Gibbons SM, Duvallet C, Alm EJ.

PLoS Comput Biol. 2018 Apr 23;14(4):e1006102. doi: 10.1371/journal.pcbi.1006102. eCollection 2018 Apr.

8.

Meta-analysis generates and prioritizes hypotheses for translational microbiome research.

Duvallet C.

Microb Biotechnol. 2018 Mar;11(2):273-276. doi: 10.1111/1751-7915.13047. Epub 2018 Jan 19. No abstract available.

9.

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.

Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ.

Nat Commun. 2017 Dec 5;8(1):1784. doi: 10.1038/s41467-017-01973-8.

10.

dbOTU3: A new implementation of distribution-based OTU calling.

Olesen SW, Duvallet C, Alm EJ.

PLoS One. 2017 May 4;12(5):e0176335. doi: 10.1371/journal.pone.0176335. eCollection 2017.

11.

[Improvement of the reproducibility of the Elisa test for detecting anti-Trypanosoma congolese antibodies in cattle].

Bocquentin R, Duvallet C.

Rev Elev Med Vet Pays Trop. 1990;43(2):179-86. French.

PMID:
2092352

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