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Items: 25

1.

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
2.

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
3.

Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans.

Johnson AJ, Vangay P, Al-Ghalith GA, Hillmann BM, Ward TL, Shields-Cutler RR, Kim AD, Shmagel AK, Syed AN; Personalized Microbiome Class Students, Walter J, Menon R, Koecher K, Knights D.

Cell Host Microbe. 2019 Jun 12;25(6):789-802.e5. doi: 10.1016/j.chom.2019.05.005.

PMID:
31194939
4.

Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus).

Clayton JB, Shields-Cutler RR, Hoops SL, Al-Ghalith GA, Sha JCM, Johnson TJ, Knights D.

Am J Primatol. 2019 Apr 18:e22977. doi: 10.1002/ajp.22977. [Epub ahead of print]

PMID:
30997937
5.

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.

mSystems. 2018 Nov 13;3(6). pii: e00069-18. doi: 10.1128/mSystems.00069-18. eCollection 2018 Nov-Dec.

6.

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.

Cell. 2018 Nov 1;175(4):962-972.e10. doi: 10.1016/j.cell.2018.10.029.

7.

Urinary microbiome associated with chronic allograft dysfunction in kidney transplant recipients.

Wu JF, Muthusamy A, Al-Ghalith GA, Knights D, Guo B, Wu B, Remmel RP, Schladt DP, Alegre ML, Oetting WS, Jacobson PA, Israni AK.

Clin Transplant. 2018 Dec;32(12):e13436. doi: 10.1111/ctr.13436. Epub 2018 Nov 18.

PMID:
30372560
8.

High-Throughput flaA Short Variable Region Sequencing to Assess Campylobacter Diversity in Fecal Samples From Birds.

Zhang Q, Al-Ghalith GA, Kobayashi M, Segawa T, Maeda M, Okabe S, Knights D, Ishii S.

Front Microbiol. 2018 Sep 25;9:2201. doi: 10.3389/fmicb.2018.02201. eCollection 2018.

9.

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.

Microbiome. 2018 Aug 6;6(1):137. doi: 10.1186/s40168-018-0514-4.

10.

Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model.

Clayton JB, Al-Ghalith GA, Long HT, Tuan BV, Cabana F, Huang H, Vangay P, Ward T, Minh VV, Tam NA, Dat NT, Travis DA, Murtaugh MP, Covert H, Glander KE, Nadler T, Toddes B, Sha JCM, Singer R, Knights D, Johnson TJ.

Sci Rep. 2018 Jul 24;8(1):11159. doi: 10.1038/s41598-018-29277-x.

11.

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.

Elife. 2018 Jul 25;7. pii: e37816. doi: 10.7554/eLife.37816.

12.

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies.

Shields-Cutler RR, Al-Ghalith GA, Yassour M, Knights D.

Front Microbiol. 2018 Apr 23;9:785. doi: 10.3389/fmicb.2018.00785. eCollection 2018.

13.

SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control.

Al-Ghalith GA, Hillmann B, Ang K, Shields-Cutler R, Knights D.

mSystems. 2018 Apr 24;3(3). pii: e00202-17. doi: 10.1128/mSystems.00202-17. eCollection 2018 May-Jun.

14.

Pretransplant Gut Colonization with Intrinsically Vancomycin-Resistant Enterococci (E. gallinarum and E. casseliflavus) and Outcomes of Allogeneic Hematopoietic Cell Transplantation.

Rashidi A, Ebadi M, Shields-Cutler RR, DeFor TE, Al-Ghalith GA, Ferrieri P, Young JH, Dunny GM, Knights D, Weisdorf DJ.

Biol Blood Marrow Transplant. 2018 Jun;24(6):1260-1263. doi: 10.1016/j.bbmt.2018.01.025. Epub 2018 Jan 31.

15.

Systematic review: human gut dysbiosis induced by non-antibiotic prescription medications.

Le Bastard Q, Al-Ghalith GA, Grégoire M, Chapelet G, Javaudin F, Dailly E, Batard E, Knights D, Montassier E.

Aliment Pharmacol Ther. 2018 Feb;47(3):332-345. doi: 10.1111/apt.14451. Epub 2017 Dec 5.

16.

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux's sifakas (Propithecus verreauxi).

Springer A, Fichtel C, Al-Ghalith GA, Koch F, Amato KR, Clayton JB, Knights D, Kappeler PM.

Ecol Evol. 2017 Jun 15;7(15):5732-5745. doi: 10.1002/ece3.3148. eCollection 2017 Aug.

17.

Moving beyond de novo clustering in fungal community ecology.

Cline LC, Song Z, Al-Ghalith GA, Knights D, Kennedy PG.

New Phytol. 2017 Nov;216(3):629-634. doi: 10.1111/nph.14752. Epub 2017 Aug 7. No abstract available.

18.

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.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10376-81. doi: 10.1073/pnas.1521835113. Epub 2016 Aug 29.

19.

Erratum to: Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection.

Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, De La Cochetiere MF, Batard E, Knights D.

Genome Med. 2016 May 26;8(1):61. No abstract available.

20.

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection.

Montassier E, Al-Ghalith GA, Ward T, Corvec S, Gastinne T, Potel G, Moreau P, de la Cochetiere MF, Batard E, Knights D.

Genome Med. 2016 Apr 28;8(1):49. doi: 10.1186/s13073-016-0301-4. Erratum in: Genome Med. 2016;8(1):61.

21.

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.

Al-Ghalith GA, Montassier E, Ward HN, Knights D.

PLoS Comput Biol. 2016 Jan 28;12(1):e1004658. doi: 10.1371/journal.pcbi.1004658. eCollection 2016 Jan.

22.

Bygiene: The New Paradigm of Bidirectional Hygiene.

Al-Ghalith GA, Knights D.

Yale J Biol Med. 2015 Nov 24;88(4):359-65. eCollection 2015 Dec. Review.

23.

Chemotherapy-driven dysbiosis in the intestinal microbiome.

Montassier E, Gastinne T, Vangay P, Al-Ghalith GA, Bruley des Varannes S, Massart S, Moreau P, Potel G, de La Cochetière MF, Batard E, Knights D.

Aliment Pharmacol Ther. 2015 Sep;42(5):515-28. doi: 10.1111/apt.13302. Epub 2015 Jul 6.

24.

The guts of obesity: progress and challenges in linking gut microbes to obesity.

Al-Ghalith GA, Vangay P, Knights D.

Discov Med. 2015 Feb;19(103):81-8. Review.

25.

Complex host genetics influence the microbiome in inflammatory bowel disease.

Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ.

Genome Med. 2014 Dec 2;6(12):107. doi: 10.1186/s13073-014-0107-1. eCollection 2014.

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