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Items: 1 to 20 of 48

1.

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.

2.

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment.

Danzeisen JL, Clayton JB, Huang H, Knights D, McComb B, Hayer SS, Johnson TJ.

Front Vet Sci. 2015 Nov 20;2:56. doi: 10.3389/fvets.2015.00056. eCollection 2015.

3.

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.

4.

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.

Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng AC, Doench JG, Root DE, Clish CB, Xavier RJ.

Nat Commun. 2015 Jul 21;6:7838. doi: 10.1038/ncomms8838.

5.

Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment.

Burns MB, Lynch J, Starr TK, Knights D, Blekhman R.

Genome Med. 2015 Jun 24;7(1):55. doi: 10.1186/s13073-015-0177-8. eCollection 2015.

6.

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.

PMID:
26147207
7.

Antibiotics, pediatric dysbiosis, and disease.

Vangay P, Ward T, Gerber JS, Knights D.

Cell Host Microbe. 2015 May 13;17(5):553-64. doi: 10.1016/j.chom.2015.04.006. Review.

PMID:
25974298
8.

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection.

Weingarden A, González A, Vázquez-Baeza Y, Weiss S, Humphry G, Berg-Lyons D, Knights D, Unno T, Bobr A, Kang J, Khoruts A, Knight R, Sadowsky MJ.

Microbiome. 2015 Mar 30;3:10. doi: 10.1186/s40168-015-0070-0. eCollection 2015.

9.

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.

10.

Complementary amplicon-based genomic approaches for the study of fungal communities in humans.

Heisel T, Podgorski H, Staley CM, Knights D, Sadowsky MJ, Gale CA.

PLoS One. 2015 Feb 23;10(2):e0116705. doi: 10.1371/journal.pone.0116705. eCollection 2015.

11.

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.

12.

Advancing the microbiome research community.

Huttenhower C, Knight R, Brown CT, Caporaso JG, Clemente JC, Gevers D, Franzosa EA, Kelley ST, Knights D, Ley RE, Mahurkar A, Ravel J; Scientists for Advancement of Microbiome Research, White O.

Cell. 2014 Oct 9;159(2):227-30. doi: 10.1016/j.cell.2014.09.022.

13.

Rethinking "enterotypes".

Knights D, Ward TL, McKinlay CE, Miller H, Gonzalez A, McDonald D, Knight R.

Cell Host Microbe. 2014 Oct 8;16(4):433-7. doi: 10.1016/j.chom.2014.09.013.

14.

Multi-omics analysis of inflammatory bowel disease.

Huang H, Vangay P, McKinlay CE, Knights D.

Immunol Lett. 2014 Dec;162(2 Pt A):62-8. doi: 10.1016/j.imlet.2014.07.014. Epub 2014 Aug 15. Review.

PMID:
25131220
15.

The treatment-naive microbiome in new-onset Crohn's disease.

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ.

Cell Host Microbe. 2014 Mar 12;15(3):382-92. doi: 10.1016/j.chom.2014.02.005.

16.

The Liverpool Care Pathway for the dying: what went wrong?

Knights D, Wood D, Barclay S.

Br J Gen Pract. 2013 Oct;63(615):509-10. doi: 10.3399/bjgp13X673559. No abstract available.

17.

A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system.

Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R.

Elife. 2013 Oct 15;2:e01104. doi: 10.7554/eLife.01104.

18.

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.

Knights D, Lassen KG, Xavier RJ.

Gut. 2013 Oct;62(10):1505-10. doi: 10.1136/gutjnl-2012-303954. Review.

19.

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences.

Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C.

Nat Biotechnol. 2013 Sep;31(9):814-21. doi: 10.1038/nbt.2676. Epub 2013 Aug 25.

20.

Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet.

Manichanh C, Eck A, Varela E, Roca J, Clemente JC, González A, Knights D, Knight R, Estrella S, Hernandez C, Guyonnet D, Accarino A, Santos J, Malagelada JR, Guarner F, Azpiroz F.

Gut. 2014 Mar;63(3):401-8. doi: 10.1136/gutjnl-2012-303013. Epub 2013 Jun 13.

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